diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf index 7b5369d8..58e8eda7 100644 Binary files a/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf and b/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf index aaaf90e0..a6c0d151 100644 Binary files a/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf and b/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/pysces_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/pysces_autogen_plot_for_task1.pdf index 2586f58d..ab72f0e4 100644 Binary files a/BioModels/BIOMD0000000001/tests/d1_plots_local/pysces_autogen_plot_for_task1.pdf and b/BioModels/BIOMD0000000001/tests/d1_plots_local/pysces_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/tellurium_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/tellurium_autogen_plot_for_task1.pdf index 7c32c1c5..26e29013 100644 Binary files a/BioModels/BIOMD0000000001/tests/d1_plots_local/tellurium_autogen_plot_for_task1.pdf and b/BioModels/BIOMD0000000001/tests/d1_plots_local/tellurium_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/vcell_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/vcell_autogen_plot_for_task1.pdf index e3a7974b..c31075b1 100644 Binary files a/BioModels/BIOMD0000000001/tests/d1_plots_local/vcell_autogen_plot_for_task1.pdf and b/BioModels/BIOMD0000000001/tests/d1_plots_local/vcell_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_remote/amici_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_remote/amici_autogen_plot_for_task1.pdf index 6853f052..5dbadff8 100644 Binary files a/BioModels/BIOMD0000000001/tests/d1_plots_remote/amici_autogen_plot_for_task1.pdf and b/BioModels/BIOMD0000000001/tests/d1_plots_remote/amici_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_remote/copasi_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_remote/copasi_autogen_plot_for_task1.pdf index de08229f..969aa979 100644 Binary files a/BioModels/BIOMD0000000001/tests/d1_plots_remote/copasi_autogen_plot_for_task1.pdf and b/BioModels/BIOMD0000000001/tests/d1_plots_remote/copasi_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_remote/masspy_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_remote/masspy_autogen_plot_for_task1.pdf index 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b/BioModels/BIOMD0000000001/tests/d1_plots_remote/tellurium_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_remote/vcell_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_remote/vcell_autogen_plot_for_task1.pdf index 2a526468..84b28b1b 100644 Binary files a/BioModels/BIOMD0000000001/tests/d1_plots_remote/vcell_autogen_plot_for_task1.pdf and b/BioModels/BIOMD0000000001/tests/d1_plots_remote/vcell_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md b/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md index 9b9f7574..bd58a772 100644 --- a/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md +++ b/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:-----------------------------------------------------------------------| -|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Could not load MassModel 'BIOMD0000000001'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | -|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
VCellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:-----------------------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with AMICI.

SED-ML and SBML are compatible with AMICI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

Only BNGL, SED-ML are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with CBMPy.

SED-ML and SBML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with COBRApy.

SED-ML and SBML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with COPASI.

SED-ML and SBML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with GillesPy2.

SED-ML and SBML are compatible with GillesPy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with LibSBMLSim.

SED-ML and SBML are compatible with LibSBMLSim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with MASSpy.

SED-ML and SBML are compatible with MASSpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Could not load MassModel 'BIOMD0000000001'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

Only CellML, SED-ML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with PySCeS.

SED-ML and SBML are compatible with PySCeS.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

Only RBApy, SED-ML are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

Only Smoldyn, SED-ML are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with Tellurium.

SED-ML and SBML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with VCell.

BNGL, SED-ML and SBML are compatible with VCell.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

Only XPP, SED-ML are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/BioModels/BIOMD0000000001/tests/results_local.json b/BioModels/BIOMD0000000001/tests/results_local.json index 607166d7..497dc6e0 100644 --- a/BioModels/BIOMD0000000001/tests/results_local.json +++ b/BioModels/BIOMD0000000001/tests/results_local.json @@ -2,12 +2,12 @@ "amici": { "exception_message": "", "log_yml": { - "duration": 345.061273, + "duration": 19.08304, "exception": null, "output": "", "sedDocuments": [ { - "duration": 344.712319, + "duration": 18.56752, "exception": null, "location": "BIOMD0000000001_url.sedml", "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", @@ -279,7 +279,7 @@ "status": "SUCCEEDED" } ], - "duration": 25.52741, + "duration": 0.274286, "exception": null, "id": "autogen_report_for_task1", "output": "", @@ -337,7 +337,7 @@ "status": "SUCCEEDED" } ], - "duration": 10.885187, + "duration": 0.521209, "exception": null, "id": "autogen_plot_for_task1", "output": "", @@ -350,10 +350,10 @@ "tasks": [ { "algorithm": "KISAO_0000496", - "duration": 308.129996, + "duration": 17.605662, "exception": null, "id": "task1", - "output": "2024-11-19 09:58:49.944 - amici.swig_wrappers - DEBUG - [CVODES:CVode:TOO_MUCH_WORK] AMICI ERROR: in module CVODES in function CVode : At t = 455.172, mxstep steps taken before reaching tout. \r\n2024-11-19 09:58:49.944 - amici.swig_wrappers - ERROR - [FORWARD_FAILURE] AMICI forward simulation failed at t = 455.172: AMICI failed to integrate the forward problem\r\n", + "output": "", "simulatorDetails": [ { "key": "solver", @@ -380,14 +380,14 @@ "detailed_error_log": {} }, "brian2": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", "log_yml": { - "duration": 0.070201, + "duration": 0.072886, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" }, - "output": "WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpjiz9loaw/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n [py.warnings]\r\npyNeuroML >>> WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpjiz9loaw/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n\r\n", + "output": "WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpa3e54sxx/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n [py.warnings]\r\npyNeuroML >>> WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpa3e54sxx/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -395,14 +395,14 @@ "detailed_error_log": {} }, "bionetgen": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", "log_yml": { - "duration": 0.299193, + "duration": 0.185835, "exception": { "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpk1vrgtil/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpkjoig1rs/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -410,14 +410,14 @@ "detailed_error_log": {} }, "boolnet": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", "log_yml": { - "duration": 0.244705, + "duration": 0.216644, "exception": { "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpgwq63r9x/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpc9mkmrb6/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -425,14 +425,14 @@ "detailed_error_log": {} }, "cbmpy": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", "log_yml": { - "duration": 0.295067, + "duration": 0.301019, "exception": { "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" }, - "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpea9v4i1l/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpwxih3v5i/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -440,14 +440,14 @@ "detailed_error_log": {} }, "cobrapy": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", "log_yml": { - "duration": 0.188426, + "duration": 0.216432, "exception": { "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp4ikj0x1c/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp3ppvomy9/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -457,12 +457,12 @@ "copasi": { "exception_message": "", "log_yml": { - "duration": 44.757602, + "duration": 2.000256, "exception": null, - "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpdbztmaty/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpdbztmaty/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpa48fmj5t/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpa48fmj5t/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [ { - "duration": 44.321433, + "duration": 1.526767, "exception": null, "location": "BIOMD0000000001_url.sedml", "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", @@ -734,7 +734,7 @@ "status": "SUCCEEDED" } ], - "duration": 26.531954, + "duration": 0.295481, "exception": null, "id": "autogen_report_for_task1", "output": "", @@ -792,7 +792,7 @@ "status": "SUCCEEDED" } ], - "duration": 13.399035, + "duration": 0.765147, "exception": null, "id": "autogen_plot_for_task1", "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", @@ -805,10 +805,10 @@ "tasks": [ { "algorithm": "KISAO_0000560", - "duration": 4.085217, + "duration": 0.220913, "exception": null, "id": "task1", - "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `BIOMD0000000001_url` may be invalid.\r\n - The model file `/tmp/tmpdbztmaty/./BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `BIOMD0000000001_url` may be invalid.\r\n - The model file `/tmp/tmpa48fmj5t/./BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", "simulatorDetails": [ { "key": "methodName", @@ -831,14 +831,14 @@ "detailed_error_log": {} }, "gillespy2": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", "log_yml": { - "duration": 0.269059, + "duration": 0.188466, "exception": { "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpk996qbgr/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp34r8pwto/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -846,14 +846,14 @@ "detailed_error_log": {} }, "ginsim": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", "log_yml": { - "duration": 0.215349, + "duration": 0.176294, "exception": { "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp7ujh4tae/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpbwmx5fn0/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -861,14 +861,14 @@ "detailed_error_log": {} }, "libsbmlsim": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", "log_yml": { - "duration": 0.181664, + "duration": 0.175115, "exception": { "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpvf8mjq9l/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpq3f7kad5/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -876,14 +876,14 @@ "detailed_error_log": {} }, "masspy": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", "log_yml": { - "duration": 0.194957, + "duration": 0.17209, "exception": { "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mSedmlFeatureNotSupportedWarning\u001b[0m: \u001b[33m`/tmp/tmplpf58_yz/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mSedmlFeatureNotSupportedWarning\u001b[0m: \u001b[33m`/tmp/tmp76c1ld8t/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -891,9 +891,9 @@ "detailed_error_log": {} }, "netpyne": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", "log_yml": { - "duration": 0.045945, + "duration": 0.051213, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -906,14 +906,14 @@ "detailed_error_log": {} }, "neuron": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", "log_yml": { - "duration": 0.075117, + "duration": 0.069633, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpr20_52il/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp2skidr9o/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -921,14 +921,14 @@ "detailed_error_log": {} }, "opencor": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", "log_yml": { - "duration": 0.079007, + "duration": 0.083552, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" }, - "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpo64fo3wz/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpi752n5v7/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -936,14 +936,14 @@ "detailed_error_log": {} }, "pyneuroml": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", "log_yml": { - "duration": 0.051567, + "duration": 0.057976, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpht6_guy4/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpheu2qy5l/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -953,15 +953,15 @@ "pysces": { "exception_message": "", "log_yml": { - "duration": 50.11715, + "duration": 1.8624, "exception": null, - "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpn0re_la7/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpn0re_la7/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp1bvdpoj_/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp1bvdpoj_/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [ { - "duration": 49.733133, + "duration": 1.291807, "exception": null, "location": "BIOMD0000000001_url.sedml", - "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nINFO: Rescaling compartment with size 1e-16 to 1.0\r\ncsymbol time defined as \"time\" in event \r\nInfo: single compartment model: locating \"React0\" in default compartment\r\nInfo: single compartment model: locating \"React1\" in default compartment\r\nInfo: single compartment model: locating \"React2\" in default compartment\r\nInfo: single compartment model: locating \"React3\" in default compartment\r\nInfo: single compartment model: locating \"React4\" in default compartment\r\nInfo: single compartment model: locating \"React5\" in default compartment\r\nInfo: single compartment model: locating \"React6\" in default compartment\r\nInfo: single compartment model: locating \"React7\" in default compartment\r\nInfo: single compartment model: locating \"React8\" in default compartment\r\nInfo: single compartment model: locating \"React9\" in default compartment\r\nInfo: single compartment model: locating \"React10\" in default compartment\r\nInfo: single compartment model: locating \"React11\" in default compartment\r\nInfo: single compartment model: locating \"React12\" in default compartment\r\nInfo: single compartment model: locating \"React13\" in default compartment\r\nInfo: single compartment model: locating \"React14\" in default compartment\r\nInfo: single compartment model: locating \"React15\" in default compartment\r\nInfo: single compartment model: locating \"React16\" in default compartment\r\nWriting file: /tmp/tmpq6ma9hof.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpj_50x55w.xml\r\nout: /tmp/tmpq6ma9hof.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmpq6ma9hof.psc loading ..... \r\nParsing file: /tmp/tmpq6ma9hof.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"t2\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . done.\r\n \r\nEvent(s) detected.\r\n\r\nINFO: events detected and we have Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nevent RemovalACh is evaluating at 20.000998\r\nevent RemovalACh is assigning at 20.000998 (delay=0.0)\r\nexecuting RemovalACh\r\nCVODE time for 100001 points: 7.120683193206787\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nINFO: Rescaling compartment with size 1e-16 to 1.0\r\ncsymbol time defined as \"time\" in event \r\nInfo: single compartment model: locating \"React0\" in default compartment\r\nInfo: single compartment model: locating \"React1\" in default compartment\r\nInfo: single compartment model: locating \"React2\" in default compartment\r\nInfo: single compartment model: locating \"React3\" in default compartment\r\nInfo: single compartment model: locating \"React4\" in default compartment\r\nInfo: single compartment model: locating \"React5\" in default compartment\r\nInfo: single compartment model: locating \"React6\" in default compartment\r\nInfo: single compartment model: locating \"React7\" in default compartment\r\nInfo: single compartment model: locating \"React8\" in default compartment\r\nInfo: single compartment model: locating \"React9\" in default compartment\r\nInfo: single compartment model: locating \"React10\" in default compartment\r\nInfo: single compartment model: locating \"React11\" in default compartment\r\nInfo: single compartment model: locating \"React12\" in default compartment\r\nInfo: single compartment model: locating \"React13\" in default compartment\r\nInfo: single compartment model: locating \"React14\" in default compartment\r\nInfo: single compartment model: locating \"React15\" in default compartment\r\nInfo: single compartment model: locating \"React16\" in default compartment\r\nWriting file: /tmp/tmp0of36sck.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmp1rlz78qy.xml\r\nout: /tmp/tmp0of36sck.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmp0of36sck.psc loading ..... \r\nParsing file: /tmp/tmp0of36sck.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"t2\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . done.\r\n \r\nEvent(s) detected.\r\n\r\nINFO: events detected and we have Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\nCVODE time for 1001 points: 0.06111741065979004\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", "outputs": [ { "dataSets": [ @@ -1230,7 +1230,7 @@ "status": "SUCCEEDED" } ], - "duration": 28.192101, + "duration": 0.343783, "exception": null, "id": "autogen_report_for_task1", "output": "", @@ -1288,7 +1288,7 @@ "status": "SUCCEEDED" } ], - "duration": 13.982287, + "duration": 0.481102, "exception": null, "id": "autogen_plot_for_task1", "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", @@ -1301,10 +1301,10 @@ "tasks": [ { "algorithm": "KISAO_0000019", - "duration": 7.299818, + "duration": 0.246468, "exception": null, "id": "task1", - "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", "simulatorDetails": [ { "key": "method", @@ -1339,14 +1339,14 @@ "detailed_error_log": {} }, "rbapy": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", "log_yml": { - "duration": 0.211235, + "duration": 0.224329, "exception": { "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpye2xsxa5/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp97k3fqra/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -1354,19 +1354,19 @@ "detailed_error_log": {} }, "smoldyn": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", "log_yml": {}, "detailed_error_log": {} }, "tellurium": { "exception_message": "", "log_yml": { - "duration": 40.289412, + "duration": 1.856703, "exception": null, - "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpx3ltypf9/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpx3ltypf9/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpfgwihkqx/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpfgwihkqx/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n", "sedDocuments": [ { - "duration": 39.849291, + "duration": 1.296451, "exception": null, "location": "BIOMD0000000001_url.sedml", "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", @@ -1638,7 +1638,7 @@ "status": "SUCCEEDED" } ], - "duration": 25.996882, + "duration": 0.312898, "exception": null, "id": "autogen_report_for_task1", "output": "", @@ -1696,7 +1696,7 @@ "status": "SUCCEEDED" } ], - "duration": 12.508398, + "duration": 0.545357, "exception": null, "id": "autogen_plot_for_task1", "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning:\r\n\r\n\u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n\r\n", @@ -1709,10 +1709,10 @@ "tasks": [ { "algorithm": "KISAO_0000019", - "duration": 1.183695, + "duration": 0.218948, "exception": null, "id": "task1", - "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mModel `BIOMD0000000001_url` may be invalid.\r\n - The model file `/tmp/tmpx3ltypf9/./BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning:\r\n\r\n\u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n\r\n", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mModel `BIOMD0000000001_url` may be invalid.\r\n - The model file `/tmp/tmpfgwihkqx/./BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning:\r\n\r\n\u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n\r\n", "simulatorDetails": [ { "key": "method", @@ -1785,7 +1785,7 @@ "vcell": { "exception_message": "", "log_yml": { - "duration": 103, + "duration": 16, "exception": null, "output": "Processing BIOMD0000000001_url.sedml. Done", "sedDocuments": [ @@ -2133,7 +2133,7 @@ "tasks": [ { "algorithm": "KISAO_0000019", - "duration": 33, + "duration": 1, "exception": null, "id": "task1", "output": "Initializing simulation job 0 ... done. Starting simulation... done.", @@ -2150,14 +2150,14 @@ "detailed_error_log": {} }, "xpp": { - "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000001_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1", "log_yml": { - "duration": 0.09879, + "duration": 0.07199, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpjba2rckk/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpw1eoj_aw/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" diff --git a/BioModels/BIOMD0000000001/tests/results_remote.json b/BioModels/BIOMD0000000001/tests/results_remote.json index 63eca8a7..3f24f903 100644 --- a/BioModels/BIOMD0000000001/tests/results_remote.json +++ b/BioModels/BIOMD0000000001/tests/results_remote.json @@ -1,16 +1,16 @@ { "amici": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5d8c0d09353e8f124846", - "download": "https://api.biosimulations.org/results/673c5d8c0d09353e8f124846/download", - "logs": "https://api.biosimulations.org/logs/673c5d8c0d09353e8f124846?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc49e10bb4455d6187451", + "download": "https://api.biosimulations.org/results/674dc49e10bb4455d6187451/download", + "logs": "https://api.biosimulations.org/logs/674dc49e10bb4455d6187451?includeOutput=true", "log_yml": { - "duration": 399.401152, + "duration": 34.42093, "exception": null, "output": "", "sedDocuments": [ { - "duration": 398.906364, + "duration": 33.900116, "exception": null, "location": "BIOMD0000000001_url.sedml", "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", @@ -282,7 +282,7 @@ "status": "SUCCEEDED" } ], - "duration": 27.057213, + "duration": 0.432449, "exception": null, "id": "autogen_report_for_task1", "output": "", @@ -340,7 +340,7 @@ "status": "SUCCEEDED" } ], - "duration": 11.680141, + "duration": 0.581878, "exception": null, "id": "autogen_plot_for_task1", "output": "", @@ -353,10 +353,10 @@ "tasks": [ { "algorithm": "KISAO_0000496", - "duration": 360.010204, + "duration": 32.711017, "exception": null, "id": "task1", - "output": "2024-11-19 04:48:43.644 - amici.swig_wrappers - DEBUG - [CVODES:CVode:TOO_MUCH_WORK] AMICI ERROR: in module CVODES in function CVode : At t = 455.172, mxstep steps taken before reaching tout. \r\n2024-11-19 04:48:43.646 - amici.swig_wrappers - ERROR - [FORWARD_FAILURE] AMICI forward simulation failed at t = 455.172: AMICI failed to integrate the forward problem\r\n", + "output": "", "simulatorDetails": [ { "key": "solver", @@ -383,11 +383,11 @@ }, "brian2": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5d8e0d09353e8f124849", - "download": "https://api.biosimulations.org/results/673c5d8e0d09353e8f124849/download", - "logs": "https://api.biosimulations.org/logs/673c5d8e0d09353e8f124849?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4a0261553b9bc253ca0", + "download": "https://api.biosimulations.org/results/674dc4a0261553b9bc253ca0/download", + "logs": "https://api.biosimulations.org/logs/674dc4a0261553b9bc253ca0?includeOutput=true", "log_yml": { - "duration": 0.076678, + "duration": 0.078477, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -400,11 +400,11 @@ }, "bionetgen": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5d90b678b3883bb8a008", - "download": "https://api.biosimulations.org/results/673c5d90b678b3883bb8a008/download", - "logs": "https://api.biosimulations.org/logs/673c5d90b678b3883bb8a008?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4a2261553b9bc253ca3", + "download": "https://api.biosimulations.org/results/674dc4a2261553b9bc253ca3/download", + "logs": "https://api.biosimulations.org/logs/674dc4a2261553b9bc253ca3?includeOutput=true", "log_yml": { - "duration": 0.240846, + "duration": 0.198329, "exception": { "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" @@ -417,11 +417,11 @@ }, "boolnet": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5d920d09353e8f124850", - "download": "https://api.biosimulations.org/results/673c5d920d09353e8f124850/download", - "logs": "https://api.biosimulations.org/logs/673c5d920d09353e8f124850?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4a4261553b9bc253ca6", + "download": "https://api.biosimulations.org/results/674dc4a4261553b9bc253ca6/download", + "logs": "https://api.biosimulations.org/logs/674dc4a4261553b9bc253ca6?includeOutput=true", "log_yml": { - "duration": 0.24272, + "duration": 0.192251, "exception": { "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" @@ -434,11 +434,11 @@ }, "cbmpy": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5d950d09353e8f124853", - "download": "https://api.biosimulations.org/results/673c5d950d09353e8f124853/download", - "logs": "https://api.biosimulations.org/logs/673c5d950d09353e8f124853?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4a610bb4455d6187455", + "download": "https://api.biosimulations.org/results/674dc4a610bb4455d6187455/download", + "logs": "https://api.biosimulations.org/logs/674dc4a610bb4455d6187455?includeOutput=true", "log_yml": { - "duration": 0.307212, + "duration": 0.292882, "exception": { "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" @@ -451,11 +451,11 @@ }, "cobrapy": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5d970d09353e8f124858", - "download": "https://api.biosimulations.org/results/673c5d970d09353e8f124858/download", - "logs": "https://api.biosimulations.org/logs/673c5d970d09353e8f124858?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4a810bb4455d6187458", + "download": "https://api.biosimulations.org/results/674dc4a810bb4455d6187458/download", + "logs": "https://api.biosimulations.org/logs/674dc4a810bb4455d6187458?includeOutput=true", "log_yml": { - "duration": 0.220452, + "duration": 0.22812, "exception": { "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" @@ -468,16 +468,16 @@ }, "copasi": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5d9ab678b3883bb8a00e", - "download": "https://api.biosimulations.org/results/673c5d9ab678b3883bb8a00e/download", - "logs": "https://api.biosimulations.org/logs/673c5d9ab678b3883bb8a00e?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4aa261553b9bc253cad", + "download": "https://api.biosimulations.org/results/674dc4aa261553b9bc253cad/download", + "logs": "https://api.biosimulations.org/logs/674dc4aa261553b9bc253cad?includeOutput=true", "log_yml": { - "duration": 54.716714, + "duration": 2.005031, "exception": null, "output": "", "sedDocuments": [ { - "duration": 54.325968, + "duration": 1.627087, "exception": null, "location": "BIOMD0000000001_url.sedml", "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...woohoo!\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", @@ -749,7 +749,7 @@ "status": "SUCCEEDED" } ], - "duration": 34.002966, + "duration": 0.617875, "exception": null, "id": "autogen_report_for_task1", "output": "", @@ -807,7 +807,7 @@ "status": "SUCCEEDED" } ], - "duration": 15.430493, + "duration": 0.591273, "exception": null, "id": "autogen_plot_for_task1", "output": "", @@ -820,7 +820,7 @@ "tasks": [ { "algorithm": "KISAO_0000560", - "duration": 4.739973, + "duration": 0.239033, "exception": null, "id": "task1", "output": "", @@ -846,11 +846,11 @@ }, "gillespy2": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5d9cb678b3883bb8a015", - "download": "https://api.biosimulations.org/results/673c5d9cb678b3883bb8a015/download", - "logs": "https://api.biosimulations.org/logs/673c5d9cb678b3883bb8a015?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4ac10bb4455d618745d", + "download": "https://api.biosimulations.org/results/674dc4ac10bb4455d618745d/download", + "logs": "https://api.biosimulations.org/logs/674dc4ac10bb4455d618745d?includeOutput=true", "log_yml": { - "duration": 0.228324, + "duration": 0.21099, "exception": { "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" @@ -863,11 +863,11 @@ }, "ginsim": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5d9eb678b3883bb8a019", - "download": "https://api.biosimulations.org/results/673c5d9eb678b3883bb8a019/download", - "logs": "https://api.biosimulations.org/logs/673c5d9eb678b3883bb8a019?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4ae261553b9bc253cb2", + "download": "https://api.biosimulations.org/results/674dc4ae261553b9bc253cb2/download", + "logs": "https://api.biosimulations.org/logs/674dc4ae261553b9bc253cb2?includeOutput=true", "log_yml": { - "duration": 0.216675, + "duration": 0.183826, "exception": { "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" @@ -880,11 +880,11 @@ }, "libsbmlsim": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5da00d09353e8f124870", - "download": "https://api.biosimulations.org/results/673c5da00d09353e8f124870/download", - "logs": "https://api.biosimulations.org/logs/673c5da00d09353e8f124870?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4b0ef911d5d452598d2", + "download": "https://api.biosimulations.org/results/674dc4b0ef911d5d452598d2/download", + "logs": "https://api.biosimulations.org/logs/674dc4b0ef911d5d452598d2?includeOutput=true", "log_yml": { - "duration": 0.225096, + "duration": 0.238018, "exception": { "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" @@ -897,11 +897,11 @@ }, "masspy": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5da35a60072d20f74291", - "download": "https://api.biosimulations.org/results/673c5da35a60072d20f74291/download", - "logs": "https://api.biosimulations.org/logs/673c5da35a60072d20f74291?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4b210bb4455d6187463", + "download": "https://api.biosimulations.org/results/674dc4b210bb4455d6187463/download", + "logs": "https://api.biosimulations.org/logs/674dc4b210bb4455d6187463?includeOutput=true", "log_yml": { - "duration": 1.503824, + "duration": 1.69877, "exception": { "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Could not load MassModel 'BIOMD0000000001'", "type": "CombineArchiveExecutionError" @@ -909,7 +909,7 @@ "output": "", "sedDocuments": [ { - "duration": 0.956937, + "duration": 1.072114, "exception": { "message": "The SED document did not execute successfully:\n\n Could not load MassModel 'BIOMD0000000001'", "type": "SedmlExecutionError" @@ -1184,7 +1184,7 @@ "status": "SKIPPED" } ], - "duration": 0.061037, + "duration": 0.074924, "exception": null, "id": "autogen_report_for_task1", "output": "", @@ -1242,7 +1242,7 @@ "status": "SKIPPED" } ], - "duration": 0.344134, + "duration": 0.376117, "exception": null, "id": "autogen_plot_for_task1", "output": "", @@ -1255,7 +1255,7 @@ "tasks": [ { "algorithm": null, - "duration": 0.341199, + "duration": 0.395851, "exception": { "message": "Could not load MassModel 'BIOMD0000000001'", "type": "MassSimulationError" @@ -1275,11 +1275,11 @@ }, "netpyne": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5da40d09353e8f12487b", - "download": "https://api.biosimulations.org/results/673c5da40d09353e8f12487b/download", - "logs": "https://api.biosimulations.org/logs/673c5da40d09353e8f12487b?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4b410bb4455d6187470", + "download": "https://api.biosimulations.org/results/674dc4b410bb4455d6187470/download", + "logs": "https://api.biosimulations.org/logs/674dc4b410bb4455d6187470?includeOutput=true", "log_yml": { - "duration": 0.057357, + "duration": 0.068815, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -1292,11 +1292,11 @@ }, "neuron": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5da65a60072d20f7429d", - "download": "https://api.biosimulations.org/results/673c5da65a60072d20f7429d/download", - "logs": "https://api.biosimulations.org/logs/673c5da65a60072d20f7429d?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4b5261553b9bc253cc5", + "download": "https://api.biosimulations.org/results/674dc4b5261553b9bc253cc5/download", + "logs": "https://api.biosimulations.org/logs/674dc4b5261553b9bc253cc5?includeOutput=true", "log_yml": { - "duration": 0.053578, + "duration": 0.072554, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -1309,16 +1309,16 @@ }, "opencor": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5da80d09353e8f124892", - "download": "https://api.biosimulations.org/results/673c5da80d09353e8f124892/download", - "logs": "https://api.biosimulations.org/logs/673c5da80d09353e8f124892?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4b710bb4455d6187475", + "download": "https://api.biosimulations.org/results/674dc4b710bb4455d6187475/download", + "logs": "https://api.biosimulations.org/logs/674dc4b710bb4455d6187475?includeOutput=true", "log_yml": { - "duration": 0.041006, + "duration": 0.064603, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" }, - "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpuzt6zjfi/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp8qdnji7v/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -1326,11 +1326,11 @@ }, "pyneuroml": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5daa5a60072d20f742af", - "download": "https://api.biosimulations.org/results/673c5daa5a60072d20f742af/download", - "logs": "https://api.biosimulations.org/logs/673c5daa5a60072d20f742af?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4b910bb4455d618747c", + "download": "https://api.biosimulations.org/results/674dc4b910bb4455d618747c/download", + "logs": "https://api.biosimulations.org/logs/674dc4b910bb4455d618747c?includeOutput=true", "log_yml": { - "duration": 0.053685, + "duration": 0.091066, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -1343,19 +1343,19 @@ }, "pysces": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5dac0d09353e8f124896", - "download": "https://api.biosimulations.org/results/673c5dac0d09353e8f124896/download", - "logs": "https://api.biosimulations.org/logs/673c5dac0d09353e8f124896?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4bbef911d5d452598e2", + "download": "https://api.biosimulations.org/results/674dc4bbef911d5d452598e2/download", + "logs": "https://api.biosimulations.org/logs/674dc4bbef911d5d452598e2?includeOutput=true", "log_yml": { - "duration": 51.927413, + "duration": 1.614328, "exception": null, "output": "libtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified in the user configuration file, set \"matplotlib_backend = \" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems *\r\n* http://pysces.sourceforge.net *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", "sedDocuments": [ { - "duration": 51.566999, + "duration": 1.296853, "exception": null, "location": "BIOMD0000000001_url.sedml", - "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nINFO: Rescaling compartment with size 1e-16 to 1.0\r\ncsymbol time defined as \"time\" in event \r\nInfo: single compartment model: locating \"React0\" in default compartment\r\nInfo: single compartment model: locating \"React1\" in default compartment\r\nInfo: single compartment model: locating \"React2\" in default compartment\r\nInfo: single compartment model: locating \"React3\" in default compartment\r\nInfo: single compartment model: locating \"React4\" in default compartment\r\nInfo: single compartment model: locating \"React5\" in default compartment\r\nInfo: single compartment model: locating \"React6\" in default compartment\r\nInfo: single compartment model: locating \"React7\" in default compartment\r\nInfo: single compartment model: locating \"React8\" in default compartment\r\nInfo: single compartment model: locating \"React9\" in default compartment\r\nInfo: single compartment model: locating \"React10\" in default compartment\r\nInfo: single compartment model: locating \"React11\" in default compartment\r\nInfo: single compartment model: locating \"React12\" in default compartment\r\nInfo: single compartment model: locating \"React13\" in default compartment\r\nInfo: single compartment model: locating \"React14\" in default compartment\r\nInfo: single compartment model: locating \"React15\" in default compartment\r\nInfo: single compartment model: locating \"React16\" in default compartment\r\nWriting file: /tmp/tmpkv0bdkg1.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpa8hro1wx.xml\r\nout: /tmp/tmpkv0bdkg1.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpkv0bdkg1.psc loading ..... \r\nParsing file: /tmp/tmpkv0bdkg1.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"t2\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . done.\r\n \r\nEvent(s) detected.\r\n\r\nINFO: events detected and we have Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nevent RemovalACh is evaluating at 20.000998\r\nevent RemovalACh is assigning at 20.000998 (delay=0.0)\r\nexecuting RemovalACh\r\nCVODE time for 100001 points: 7.514819145202637\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nINFO: Rescaling compartment with size 1e-16 to 1.0\r\ncsymbol time defined as \"time\" in event \r\nInfo: single compartment model: locating \"React0\" in default compartment\r\nInfo: single compartment model: locating \"React1\" in default compartment\r\nInfo: single compartment model: locating \"React2\" in default compartment\r\nInfo: single compartment model: locating \"React3\" in default compartment\r\nInfo: single compartment model: locating \"React4\" in default compartment\r\nInfo: single compartment model: locating \"React5\" in default compartment\r\nInfo: single compartment model: locating \"React6\" in default compartment\r\nInfo: single compartment model: locating \"React7\" in default compartment\r\nInfo: single compartment model: locating \"React8\" in default compartment\r\nInfo: single compartment model: locating \"React9\" in default compartment\r\nInfo: single compartment model: locating \"React10\" in default compartment\r\nInfo: single compartment model: locating \"React11\" in default compartment\r\nInfo: single compartment model: locating \"React12\" in default compartment\r\nInfo: single compartment model: locating \"React13\" in default compartment\r\nInfo: single compartment model: locating \"React14\" in default compartment\r\nInfo: single compartment model: locating \"React15\" in default compartment\r\nInfo: single compartment model: locating \"React16\" in default compartment\r\nWriting file: /tmp/tmpnk0gukmy.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpef1rqg3q.xml\r\nout: /tmp/tmpnk0gukmy.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpnk0gukmy.psc loading ..... \r\nParsing file: /tmp/tmpnk0gukmy.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"t2\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . done.\r\n \r\nEvent(s) detected.\r\n\r\nINFO: events detected and we have Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\nCVODE time for 1001 points: 0.07132816314697266\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", "outputs": [ { "dataSets": [ @@ -1624,7 +1624,7 @@ "status": "SUCCEEDED" } ], - "duration": 29.840529, + "duration": 0.354192, "exception": null, "id": "autogen_report_for_task1", "output": "", @@ -1682,7 +1682,7 @@ "status": "SUCCEEDED" } ], - "duration": 13.873922, + "duration": 0.457523, "exception": null, "id": "autogen_plot_for_task1", "output": "", @@ -1695,7 +1695,7 @@ "tasks": [ { "algorithm": "KISAO_0000019", - "duration": 7.696954, + "duration": 0.31707, "exception": null, "id": "task1", "output": "", @@ -1733,11 +1733,11 @@ }, "rbapy": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5daeb678b3883bb8a041", - "download": "https://api.biosimulations.org/results/673c5daeb678b3883bb8a041/download", - "logs": "https://api.biosimulations.org/logs/673c5daeb678b3883bb8a041?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4bcef911d5d452598e9", + "download": "https://api.biosimulations.org/results/674dc4bcef911d5d452598e9/download", + "logs": "https://api.biosimulations.org/logs/674dc4bcef911d5d452598e9?includeOutput=true", "log_yml": { - "duration": 0.245626, + "duration": 0.177701, "exception": { "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", "type": "ValueError" @@ -1750,11 +1750,11 @@ }, "smoldyn": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5db05a60072d20f742c7", - "download": "https://api.biosimulations.org/results/673c5db05a60072d20f742c7/download", - "logs": "https://api.biosimulations.org/logs/673c5db05a60072d20f742c7?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4be10bb4455d6187487", + "download": "https://api.biosimulations.org/results/674dc4be10bb4455d6187487/download", + "logs": "https://api.biosimulations.org/logs/674dc4be10bb4455d6187487?includeOutput=true", "log_yml": { - "duration": 0.068369, + "duration": 0.051893, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -1767,16 +1767,16 @@ }, "tellurium": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5db25a60072d20f742d6", - "download": "https://api.biosimulations.org/results/673c5db25a60072d20f742d6/download", - "logs": "https://api.biosimulations.org/logs/673c5db25a60072d20f742d6?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4c010bb4455d618748a", + "download": "https://api.biosimulations.org/results/674dc4c010bb4455d618748a/download", + "logs": "https://api.biosimulations.org/logs/674dc4c010bb4455d618748a?includeOutput=true", "log_yml": { - "duration": 60.797345, + "duration": 2.16265, "exception": null, "output": "", "sedDocuments": [ { - "duration": 60.294564, + "duration": 1.573024, "exception": null, "location": "BIOMD0000000001_url.sedml", "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", @@ -2048,7 +2048,7 @@ "status": "SUCCEEDED" } ], - "duration": 41.163941, + "duration": 0.430861, "exception": null, "id": "autogen_report_for_task1", "output": "", @@ -2106,7 +2106,7 @@ "status": "SUCCEEDED" } ], - "duration": 17.532498, + "duration": 0.633544, "exception": null, "id": "autogen_plot_for_task1", "output": "", @@ -2119,7 +2119,7 @@ "tasks": [ { "algorithm": "KISAO_0000019", - "duration": 1.422447, + "duration": 0.30838, "exception": null, "id": "task1", "output": "", @@ -2193,11 +2193,11 @@ }, "vcell": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5db7b678b3883bb8a067", - "download": "https://api.biosimulations.org/results/673c5db7b678b3883bb8a067/download", - "logs": "https://api.biosimulations.org/logs/673c5db7b678b3883bb8a067?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4c510bb4455d61874b6", + "download": "https://api.biosimulations.org/results/674dc4c510bb4455d61874b6/download", + "logs": "https://api.biosimulations.org/logs/674dc4c510bb4455d61874b6?includeOutput=true", "log_yml": { - "duration": 37, + "duration": 14, "exception": null, "output": "Processing BIOMD0000000001_url.sedml. Done", "sedDocuments": [ @@ -2545,7 +2545,7 @@ "tasks": [ { "algorithm": "KISAO_0000019", - "duration": 4, + "duration": 1, "exception": null, "id": "task1", "output": "Initializing simulation job 0 ... done. Starting simulation... done.", @@ -2562,11 +2562,11 @@ }, "xpp": { "response": 201, - "view": "https://api.biosimulations.org/runs/673c5db95a60072d20f742ed", - "download": "https://api.biosimulations.org/results/673c5db95a60072d20f742ed/download", - "logs": "https://api.biosimulations.org/logs/673c5db95a60072d20f742ed?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc4c7ef911d5d45259935", + "download": "https://api.biosimulations.org/results/674dc4c7ef911d5d45259935/download", + "logs": "https://api.biosimulations.org/logs/674dc4c7ef911d5d45259935?includeOutput=true", "log_yml": { - "duration": 0.070283, + "duration": 0.077165, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" diff --git a/BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md b/BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md index 7d6c70ea..04d2a983 100644 --- a/BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md +++ b/BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:-----------------------------------------------------------------------| -|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/

|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
| plot | plot | -|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
| plot | plot | -|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | -|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
| plot | plot | -|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
| plot | plot | -|
VCellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | plot | -|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with AMICI.

SED-ML and SBML are compatible with AMICI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| plot | plot | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

Only BNGL, SED-ML are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| | | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| | | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with CBMPy.

SED-ML and SBML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| | | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with COBRApy.

SED-ML and SBML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with COPASI.

SED-ML and SBML are compatible with COPASI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with GillesPy2.

SED-ML and SBML are compatible with GillesPy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| | | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with LibSBMLSim.

SED-ML and SBML are compatible with LibSBMLSim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with MASSpy.

SED-ML and SBML are compatible with MASSpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| plot | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

Only CellML, SED-ML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with PySCeS.

SED-ML and SBML are compatible with PySCeS.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

Only RBApy, SED-ML are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| | | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

Only Smoldyn, SED-ML are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with Tellurium.

SED-ML and SBML are compatible with Tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Output `autogen_plot3` is invalid.
- Plot must have at least one curve.

ERROR TYPE:
ValueError
| plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with VCell.

BNGL, SED-ML and SBML are compatible with VCell.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | plot | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

Only XPP, SED-ML are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/BioModels/BIOMD0000000138/tests/results_local.json b/BioModels/BIOMD0000000138/tests/results_local.json index 6d361657..5ea3813a 100644 --- a/BioModels/BIOMD0000000138/tests/results_local.json +++ b/BioModels/BIOMD0000000138/tests/results_local.json @@ -1,1024 +1,253 @@ { "amici": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/amici' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/amici' returned non-zero exit status 1", "log_yml": { - "duration": 1.327694, + "duration": 0.232865, "exception": { - "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\n TokenError: Starred arguments in lambda not supported.", - "type": "CombineArchiveExecutionError" - }, - "output": "", - "sedDocuments": [ - { - "duration": 0.919753, - "exception": { - "message": "The SED document did not execute successfully:\n\n rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\n TokenError: Starred arguments in lambda not supported.", - "type": "SedmlExecutionError" - }, - "location": "BIOMD0000000138_url.sedml", - "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", - "outputs": [ - { - "dataSets": [ - { - "id": "autogen_time_for_task1", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_c", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vca", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_Cm", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gcal", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gsk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ga", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vn", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_va", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vm", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vh", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sn", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sa", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sm", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sh", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_taun", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_tauh", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_lambda", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_kc", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ks", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ff", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_alpha", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phik", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phia", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phih", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phif", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phical", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_cinf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ica", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_isk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ibk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ikdr", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ia", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ik", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_n", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_h", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_V", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_cell", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_reaction_0000004", - "status": "SKIPPED" - } - ], - "duration": 0.050763, - "exception": null, - "id": "autogen_report_for_task1", - "output": "", - "skipReason": null, - "status": "SKIPPED" - }, - { - "curves": [ - { - "id": "autogen_curve_task1_c", - "status": "SKIPPED" - } - ], - "duration": 0.264934, - "exception": null, - "id": "autogen_plot1", - "output": "", - "skipReason": null, - "status": "SKIPPED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_V", - "status": "SKIPPED" - } - ], - "duration": 0.182554, - "exception": null, - "id": "autogen_plot2", - "output": "", - "skipReason": null, - "status": "SKIPPED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_vk", - "status": "SKIPPED" - } - ], - "duration": 0.170817, - "exception": null, - "id": "autogen_plot3", - "output": "", - "skipReason": null, - "status": "SKIPPED" - } - ], - "skipReason": null, - "status": "FAILED", - "tasks": [ - { - "algorithm": null, - "duration": 0.090092, - "exception": { - "message": "rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\nTokenError: Starred arguments in lambda not supported.", - "type": "SBMLException" - }, - "id": "task1", - "output": "", - "simulatorDetails": null, - "skipReason": null, - "status": "FAILED" - } - ] - } - ], - "skipReason": null, - "status": "FAILED" - }, - "detailed_error_log": {} - }, - "brian2": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", - "log_yml": { - "duration": 0.078752, - "exception": { - "message": "No module named 'libsbml'", - "type": "ModuleNotFoundError" - }, - "output": "WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpnbtryz96/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n [py.warnings]\r\npyNeuroML >>> WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpnbtryz96/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n\r\n", - "sedDocuments": [], - "skipReason": null, - "status": "FAILED" - }, - "detailed_error_log": {} - }, - "bionetgen": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", - "log_yml": { - "duration": 0.137257, - "exception": { - "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp1hfxb1k_/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", - "sedDocuments": [], - "skipReason": null, - "status": "FAILED" - }, - "detailed_error_log": {} - }, - "boolnet": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", - "log_yml": { - "duration": 0.163477, - "exception": { - "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", - "type": "ValueError" - }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpx4ed22ha/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", - "sedDocuments": [], - "skipReason": null, - "status": "FAILED" - }, - "detailed_error_log": {} - }, - "cbmpy": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", - "log_yml": { - "duration": 0.265387, - "exception": { - "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", - "type": "ValueError" - }, - "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpn2t50ntg/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", - "sedDocuments": [], - "skipReason": null, - "status": "FAILED" - }, - "detailed_error_log": {} - }, - "cobrapy": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", - "log_yml": { - "duration": 0.18121, - "exception": { - "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", - "type": "ValueError" - }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpggckd_22/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "", "sedDocuments": [], "skipReason": null, "status": "FAILED" }, "detailed_error_log": {} }, - "copasi": { - "exception_message": "", - "log_yml": { - "duration": 21.274612, - "exception": null, - "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpyne0jvhm/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpyne0jvhm/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", - "sedDocuments": [ - { - "duration": 20.833371, - "exception": null, - "location": "BIOMD0000000138_url.sedml", - "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", - "outputs": [ - { - "dataSets": [ - { - "id": "autogen_time_for_task1", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_c", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vca", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_Cm", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_gk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_gcal", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_gsk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ga", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_gf", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vn", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_va", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vm", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vh", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vf", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sn", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sa", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sm", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sh", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sf", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_taun", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_tauh", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_lambda", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_kc", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ks", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ff", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_alpha", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phik", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phia", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phih", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phif", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phical", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_cinf", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ica", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_isk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ibk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ikdr", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ia", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ik", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_n", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_h", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_V", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_cell", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_reaction_0000004", - "status": "SUCCEEDED" - } - ], - "duration": 13.560127, - "exception": null, - "id": "autogen_report_for_task1", - "output": "", - "skipReason": null, - "status": "SUCCEEDED" - }, - { - "curves": [ - { - "id": "autogen_curve_task1_c", - "status": "SUCCEEDED" - } - ], - "duration": 1.601553, - "exception": null, - "id": "autogen_plot1", - "output": "", - "skipReason": null, - "status": "SUCCEEDED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_V", - "status": "SUCCEEDED" - } - ], - "duration": 1.51774, - "exception": null, - "id": "autogen_plot2", - "output": "", - "skipReason": null, - "status": "SUCCEEDED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_vk", - "status": "SUCCEEDED" - } - ], - "duration": 1.464575, - "exception": null, - "id": "autogen_plot3", - "output": "", - "skipReason": null, - "status": "SUCCEEDED" - } - ], - "skipReason": null, - "status": "SUCCEEDED", - "tasks": [ - { - "algorithm": "KISAO_0000560", - "duration": 2.479855, - "exception": null, - "id": "task1", - "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_ks__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_c__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phif__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_Cm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_h__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_tauh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ibk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ga__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_taun__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_n__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_isk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_reaction_0000004__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gsk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gcal__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ica__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ikdr__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_alpha__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_lambda__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_va__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_V__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ff__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cinf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phih__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vca__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phical__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `BIOMD0000000138_url` may be invalid.\r\n - The model file `/tmp/tmpyne0jvhm/./BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", - "simulatorDetails": [ - { - "key": "methodName", - "value": "lsoda" - }, - { - "key": "parameters", - "value": null - } - ], - "skipReason": null, - "status": "SUCCEEDED" - } - ] - } - ], + "brian2": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.047684, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpx0vgohlx/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n [py.warnings]\r\npyNeuroML >>> WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpx0vgohlx/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n\r\n", + "sedDocuments": [], "skipReason": null, - "status": "SUCCEEDED" + "status": "FAILED" }, "detailed_error_log": {} }, - "gillespy2": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", + "bionetgen": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", "log_yml": { - "duration": 0.14013, + "duration": 0.119514, "exception": { - "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpw3c__qs2/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpq4pve922/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" }, "detailed_error_log": {} }, - "ginsim": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "boolnet": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", "log_yml": { - "duration": 0.239827, + "duration": 0.149829, "exception": { - "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpxz_0cvez/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpdn6t5rna/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" }, "detailed_error_log": {} }, - "libsbmlsim": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", + "cbmpy": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", "log_yml": { - "duration": 0.136508, + "duration": 0.243411, "exception": { - "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp_ti9exkh/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpnagbpqkf/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" }, "detailed_error_log": {} }, - "masspy": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "cobrapy": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", "log_yml": { - "duration": 0.195684, + "duration": 0.153885, "exception": { - "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mSedmlFeatureNotSupportedWarning\u001b[0m: \u001b[33m`/tmp/tmp0541o_1y/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpw7m6sol2/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" }, "detailed_error_log": {} }, - "netpyne": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "copasi": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1", "log_yml": { - "duration": 0.054786, + "duration": 0.229305, "exception": { - "message": "No module named 'libsbml'", - "type": "ModuleNotFoundError" + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", + "type": "ValueError" }, - "output": "", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpgd_wnzus/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" }, "detailed_error_log": {} }, - "neuron": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "gillespy2": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", "log_yml": { - "duration": 0.089654, + "duration": 0.189886, "exception": { - "message": "No module named 'libsbml'", - "type": "ModuleNotFoundError" + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", + "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp6zvd7eaf/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp3eepjbrx/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" }, "detailed_error_log": {} }, - "opencor": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "ginsim": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.218339, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpzgpopmtt/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "libsbmlsim": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.149336, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpeu75f1jg/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "masspy": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.15721, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mSedmlFeatureNotSupportedWarning\u001b[0m: \u001b[33m`/tmp/tmpp2zmjef3/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "netpyne": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", "log_yml": { - "duration": 0.082571, + "duration": 0.071159, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" }, - "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp8lfs4oo0/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "output": "", "sedDocuments": [], "skipReason": null, "status": "FAILED" }, "detailed_error_log": {} }, - "pyneuroml": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "neuron": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", "log_yml": { - "duration": 0.050177, + "duration": 0.060616, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmphj27fwjc/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp6scw4iqz/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" }, "detailed_error_log": {} }, - "pysces": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1", + "opencor": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", "log_yml": { - "duration": 6.349912, + "duration": 0.064517, "exception": { - "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :'PysMod' object has no attribute 'lambda'", - "type": "CombineArchiveExecutionError" - }, - "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpue2cy78w/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpue2cy78w/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", - "sedDocuments": [ - { - "duration": 6.037383, - "exception": { - "message": "The SED document did not execute successfully:\n\n :'PysMod' object has no attribute 'lambda'", - "type": "SedmlExecutionError" - }, - "location": "BIOMD0000000138_url.sedml", - "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V1\r\nlambda is a reserved symbol, replacing with Lambda\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpub1jsm9k.xml\r\n*******************************************************************\r\n\r\nReserved symbol lambda replaced with Lambda \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"reaction_0000004\" in default compartment\r\nWriting file: /tmp/tmpvmsv1kvp.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpub1jsm9k.xml\r\nout: /tmp/tmpvmsv1kvp.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmpvmsv1kvp.psc loading ..... \r\nParsing file: /tmp/tmpvmsv1kvp.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"vca\" has been initialised but does not occur in a rate equation\r\nInfo: \"vk\" has been initialised but does not occur in a rate equation\r\nInfo: \"Cm\" has been initialised but does not occur in a rate equation\r\nInfo: \"gk\" has been initialised but does not occur in a rate equation\r\nInfo: \"gcal\" has been initialised but does not occur in a rate equation\r\nInfo: \"gsk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ga\" has been initialised but does not occur in a rate equation\r\nInfo: \"gf\" has been initialised but does not occur in a rate equation\r\nInfo: \"vn\" has been initialised but does not occur in a rate equation\r\nInfo: \"va\" has been initialised but does not occur in a rate equation\r\nInfo: \"vm\" has been initialised but does not occur in a rate equation\r\nInfo: \"vh\" has been initialised but does not occur in a rate equation\r\nInfo: \"vf\" has been initialised but does not occur in a rate equation\r\nInfo: \"sn\" has been initialised but does not occur in a rate equation\r\nInfo: \"sa\" has been initialised but does not occur in a rate equation\r\nInfo: \"sm\" has been initialised but does not occur in a rate equation\r\nInfo: \"sh\" has been initialised but does not occur in a rate equation\r\nInfo: \"sf\" has been initialised but does not occur in a rate equation\r\nInfo: \"taun\" has been initialised but does not occur in a rate equation\r\nInfo: \"tauh\" has been initialised but does not occur in a rate equation\r\nInfo: \"Lambda\" has been initialised but does not occur in a rate equation\r\nInfo: \"ks\" has been initialised but does not occur in a rate equation\r\nInfo: \"phik\" has been initialised but does not occur in a rate equation\r\nInfo: \"phia\" has been initialised but does not occur in a rate equation\r\nInfo: \"phih\" has been initialised but does not occur in a rate equation\r\nInfo: \"phif\" has been initialised but does not occur in a rate equation\r\nInfo: \"phical\" has been initialised but does not occur in a rate equation\r\nInfo: \"cinf\" has been initialised but does not occur in a rate equation\r\nInfo: \"isk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ibk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ikdr\" has been initialised but does not occur in a rate equation\r\nInfo: \"ia\" has been initialised but does not occur in a rate equation\r\nInfo: \"ik\" has been initialised but does not occur in a rate equation\r\nInfo: \"n\" has been initialised but does not occur in a rate equation\r\nInfo: \"h\" has been initialised but does not occur in a rate equation\r\nInfo: \"V\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . no flux conservation\r\n done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nRate rule(s) detected.\r\nINFO: RateRules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 100001 points: 3.946280002593994\r\nRateRules evaluated and added to mod.data_sim.\r\n \u001b[31mfailed - 'PysMod' object has no attribute 'lambda'\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", - "outputs": [ - { - "dataSets": [ - { - "id": "autogen_time_for_task1", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_c", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vca", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_Cm", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gcal", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gsk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ga", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vn", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_va", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vm", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vh", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sn", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sa", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sm", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sh", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_taun", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_tauh", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_lambda", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_kc", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ks", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ff", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_alpha", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phik", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phia", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phih", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phif", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phical", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_cinf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ica", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_isk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ibk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ikdr", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ia", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ik", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_n", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_h", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_V", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_cell", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_reaction_0000004", - "status": "SKIPPED" - } - ], - "duration": 0.079275, - "exception": null, - "id": "autogen_report_for_task1", - "output": "", - "skipReason": null, - "status": "SKIPPED" - }, - { - "curves": [ - { - "id": "autogen_curve_task1_c", - "status": "SKIPPED" - } - ], - "duration": 0.415905, - "exception": null, - "id": "autogen_plot1", - "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", - "skipReason": null, - "status": "SKIPPED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_V", - "status": "SKIPPED" - } - ], - "duration": 0.100176, - "exception": null, - "id": "autogen_plot2", - "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", - "skipReason": null, - "status": "SKIPPED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_vk", - "status": "SKIPPED" - } - ], - "duration": 0.109016, - "exception": null, - "id": "autogen_plot3", - "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", - "skipReason": null, - "status": "SKIPPED" - } - ], - "skipReason": null, - "status": "FAILED", - "tasks": [ - { - "algorithm": null, - "duration": 5.14013, - "exception": { - "message": "'PysMod' object has no attribute 'lambda'", - "type": "AttributeError" - }, - "id": "task1", - "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_kc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ks__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_va__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_lambda__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ga__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_taun__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gcal__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_h__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vca__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ica__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_alpha__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phical__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_V__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gsk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phif__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_Cm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_c__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_n__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_isk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ibk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_reaction_0000004__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_tauh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ff__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cinf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phih__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ikdr__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sm__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", - "simulatorDetails": null, - "skipReason": null, - "status": "FAILED" - } - ] - } - ], + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp51cbr68v/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pyneuroml": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "log_yml": { + "duration": 0.055285, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpibqx6tao/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pysces": { + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1", + "log_yml": { + "duration": 0.165074, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpvzoxtq7p/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], "skipReason": null, "status": "FAILED" }, "detailed_error_log": {} }, "rbapy": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", "log_yml": { - "duration": 0.136502, + "duration": 0.186807, "exception": { - "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpcsezzj2y/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpifk6hn52/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" @@ -1026,348 +255,46 @@ "detailed_error_log": {} }, "smoldyn": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", "log_yml": {}, "detailed_error_log": {} }, "tellurium": { - "exception_message": "", + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/tellurium' returned non-zero exit status 1", "log_yml": { - "duration": 19.62254, - "exception": null, - "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpxvgd3ay6/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpxvgd3ay6/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n", - "sedDocuments": [ - { - "duration": 19.212037, - "exception": null, - "location": "BIOMD0000000138_url.sedml", - "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", - "outputs": [ - { - "dataSets": [ - { - "id": "autogen_time_for_task1", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_c", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vca", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_Cm", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_gk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_gcal", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_gsk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ga", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_gf", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vn", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_va", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vm", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vh", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vf", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sn", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sa", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sm", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sh", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sf", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_taun", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_tauh", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_lambda", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_kc", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ks", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ff", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_alpha", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phik", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phia", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phih", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phif", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phical", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_cinf", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ica", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_isk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ibk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ikdr", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ia", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ik", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_n", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_h", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_V", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_cell", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_reaction_0000004", - "status": "SUCCEEDED" - } - ], - "duration": 13.677893, - "exception": null, - "id": "autogen_report_for_task1", - "output": "", - "skipReason": null, - "status": "SUCCEEDED" - }, - { - "curves": [ - { - "id": "autogen_curve_task1_c", - "status": "SUCCEEDED" - } - ], - "duration": 1.595941, - "exception": null, - "id": "autogen_plot1", - "output": "", - "skipReason": null, - "status": "SUCCEEDED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_V", - "status": "SUCCEEDED" - } - ], - "duration": 1.504026, - "exception": null, - "id": "autogen_plot2", - "output": "", - "skipReason": null, - "status": "SUCCEEDED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_vk", - "status": "SUCCEEDED" - } - ], - "duration": 1.504957, - "exception": null, - "id": "autogen_plot3", - "output": "", - "skipReason": null, - "status": "SUCCEEDED" - } - ], - "skipReason": null, - "status": "SUCCEEDED", - "tasks": [ - { - "algorithm": "KISAO_0000019", - "duration": 0.756946, - "exception": null, - "id": "task1", - "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `auto_dg_for_task1_va__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gsk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ff__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_taun__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ks__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_V__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ga__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phih__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_n__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_alpha__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_Cm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ibk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_tauh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ikdr__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phical__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phif__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cinf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_c__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vca__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ica__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_isk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_lambda__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_h__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_reaction_0000004__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gcal__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sf__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mModel `BIOMD0000000138_url` may be invalid.\r\n - The model file `/tmp/tmpxvgd3ay6/./BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning:\r\n\r\n\u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n\r\n", - "simulatorDetails": [ - { - "key": "method", - "value": "simulate" - }, - { - "key": "solver", - "value": "cvode" - }, - { - "key": "relative_tolerance", - "value": 1e-06 - }, - { - "key": "absolute_tolerance", - "value": 1e-12 - }, - { - "key": "stiff", - "value": true - }, - { - "key": "maximum_bdf_order", - "value": 5 - }, - { - "key": "maximum_adams_order", - "value": 12 - }, - { - "key": "maximum_num_steps", - "value": 20000 - }, - { - "key": "maximum_time_step", - "value": 0.0 - }, - { - "key": "minimum_time_step", - "value": 0.0 - }, - { - "key": "initial_time_step", - "value": 0.0 - }, - { - "key": "multiple_steps", - "value": false - }, - { - "key": "variable_step_size", - "value": false - }, - { - "key": "max_output_rows", - "value": 100000 - } - ], - "skipReason": null, - "status": "SUCCEEDED" - } - ] - } - ], + "duration": 0.353767, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmp4vvnu6xd/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n", + "sedDocuments": [], "skipReason": null, - "status": "SUCCEEDED" + "status": "FAILED" }, "detailed_error_log": {} }, "vcell": { - "exception_message": "", + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1", "log_yml": { - "duration": 51, + "duration": 3, "exception": null, "output": "Processing BIOMD0000000138_url.sedml. Done", "sedDocuments": [ { "duration": null, - "exception": null, + "exception": { + "message": "Cannot invoke 'org.jlibsedml.SedML.getPathForURI()' because 'this.sedml' is nullCannot invoke 'org.jlibsedml.SedML.getPathForURI()' because 'sedml' is nullFailure executing the sed document.", + "type": "RuntimeException" + }, "location": "BIOMD0000000138_url.sedml", - "output": "Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating CSV file... Done. Generating HDF5 file...", + "output": "Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating HDF5 file...", "outputs": [ { "curves": [ { "id": "autogen_curve_task1_c", - "status": "SUCCEEDED" + "status": "QUEUED" } ], "duration": null, @@ -1375,13 +302,13 @@ "id": "autogen_plot1", "output": null, "skipReason": null, - "status": "SUCCEEDED" + "status": "QUEUED" }, { "curves": [ { "id": "autogen_curve_for_task1_V", - "status": "SUCCEEDED" + "status": "QUEUED" } ], "duration": null, @@ -1389,199 +316,194 @@ "id": "autogen_plot2", "output": null, "skipReason": null, - "status": "SUCCEEDED" + "status": "QUEUED" }, { - "curves": [ - { - "id": "autogen_curve_for_task1_vk", - "status": "SUCCEEDED" - } - ], + "curves": [], "duration": null, "exception": null, "id": "autogen_plot3", "output": null, "skipReason": null, - "status": "SUCCEEDED" + "status": "QUEUED" }, { "dataSets": [ { "id": "autogen_time_for_task1", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_c", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_vca", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_vk", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_Cm", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_gk", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_gcal", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_gsk", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_ga", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_gf", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_vn", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_va", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_vm", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_vh", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_vf", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_sn", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_sa", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_sm", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_sh", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_sf", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_taun", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_tauh", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_lambda", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_kc", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_ks", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_ff", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_alpha", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_phik", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_phia", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_phih", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_phif", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_phical", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_cinf", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_ica", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_isk", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_ibk", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_ikdr", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_ia", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_ik", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_n", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_h", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_V", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_cell", - "status": "SUCCEEDED" + "status": "QUEUED" }, { "id": "autogen_task1_reaction_0000004", - "status": "SUCCEEDED" + "status": "QUEUED" } ], "duration": null, @@ -1589,21 +511,21 @@ "id": "autogen_report_for_task1", "output": null, "skipReason": null, - "status": "SUCCEEDED" + "status": "QUEUED" } ], "skipReason": null, - "status": "SUCCEEDED", + "status": "FAILED", "tasks": [ { - "algorithm": "KISAO_0000019", - "duration": 19, + "algorithm": null, + "duration": null, "exception": null, "id": "task1", - "output": "Initializing simulation job 0 ... done. Starting simulation... done.", + "output": null, "simulatorDetails": null, "skipReason": null, - "status": "SUCCEEDED" + "status": "QUEUED" } ] } @@ -1611,17 +533,20 @@ "skipReason": null, "status": "SUCCEEDED" }, - "detailed_error_log": {} + "detailed_error_log": { + "status": "FAIL", + "error_message": "Runtime Exception" + } }, "xpp": { - "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1", + "exception_message": "Command '-i '/root/in/BIOMD0000000138_url.omex' -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1", "log_yml": { - "duration": 0.055421, + "duration": 0.045898, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" }, - "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp_xh0paiw/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp6b2m0qxt/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", "sedDocuments": [], "skipReason": null, "status": "FAILED" diff --git a/BioModels/BIOMD0000000138/tests/results_remote.json b/BioModels/BIOMD0000000138/tests/results_remote.json index 0a6b8b92..87b12930 100644 --- a/BioModels/BIOMD0000000138/tests/results_remote.json +++ b/BioModels/BIOMD0000000138/tests/results_remote.json @@ -1,23 +1,47 @@ { - "amici": [ - "FAIL", - "Failed to download amici results.", - "HTTPError" - ], - "brian2": [ - "FAIL", - "Failed to download brian2 results.", - "HTTPError" - ], + "amici": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc5a4ef911d5d452599d0", + "download": "https://api.biosimulations.org/results/674dc5a4ef911d5d452599d0/download", + "logs": "https://api.biosimulations.org/logs/674dc5a4ef911d5d452599d0?includeOutput=true", + "log_yml": { + "duration": 0.367675, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "brian2": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc5a6261553b9bc253da5", + "download": "https://api.biosimulations.org/results/674dc5a6261553b9bc253da5/download", + "logs": "https://api.biosimulations.org/logs/674dc5a6261553b9bc253da5?includeOutput=true", + "log_yml": { + "duration": 0.060828, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, "bionetgen": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fca45a60072d20f5cf7e", - "download": "https://api.biosimulations.org/results/6735fca45a60072d20f5cf7e/download", - "logs": "https://api.biosimulations.org/logs/6735fca45a60072d20f5cf7e?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5a8ef911d5d452599d3", + "download": "https://api.biosimulations.org/results/674dc5a8ef911d5d452599d3/download", + "logs": "https://api.biosimulations.org/logs/674dc5a8ef911d5d452599d3?includeOutput=true", "log_yml": { - "duration": 12.710861, + "duration": 0.225267, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, "output": "", @@ -28,13 +52,13 @@ }, "boolnet": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fca6b678b3883bb72747", - "download": "https://api.biosimulations.org/results/6735fca6b678b3883bb72747/download", - "logs": "https://api.biosimulations.org/logs/6735fca6b678b3883bb72747?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5aaef911d5d452599d6", + "download": "https://api.biosimulations.org/results/674dc5aaef911d5d452599d6/download", + "logs": "https://api.biosimulations.org/logs/674dc5aaef911d5d452599d6?includeOutput=true", "log_yml": { - "duration": 0.183129, + "duration": 0.221115, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, "output": "", @@ -45,13 +69,13 @@ }, "cbmpy": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fca85a60072d20f5cf81", - "download": "https://api.biosimulations.org/results/6735fca85a60072d20f5cf81/download", - "logs": "https://api.biosimulations.org/logs/6735fca85a60072d20f5cf81?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5abef911d5d452599d9", + "download": "https://api.biosimulations.org/results/674dc5abef911d5d452599d9/download", + "logs": "https://api.biosimulations.org/logs/674dc5abef911d5d452599d9?includeOutput=true", "log_yml": { - "duration": 0.266413, + "duration": 0.391473, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n", @@ -62,13 +86,13 @@ }, "cobrapy": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcaa0d09353e8f10cf46", - "download": "https://api.biosimulations.org/results/6735fcaa0d09353e8f10cf46/download", - "logs": "https://api.biosimulations.org/logs/6735fcaa0d09353e8f10cf46?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5ae10bb4455d618755b", + "download": "https://api.biosimulations.org/results/674dc5ae10bb4455d618755b/download", + "logs": "https://api.biosimulations.org/logs/674dc5ae10bb4455d618755b?includeOutput=true", "log_yml": { - "duration": 0.173905, + "duration": 0.205544, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, "output": "", @@ -79,287 +103,30 @@ }, "copasi": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcad0d09353e8f10cf4c", - "download": "https://api.biosimulations.org/results/6735fcad0d09353e8f10cf4c/download", - "logs": "https://api.biosimulations.org/logs/6735fcad0d09353e8f10cf4c?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5b010bb4455d6187562", + "download": "https://api.biosimulations.org/results/674dc5b010bb4455d6187562/download", + "logs": "https://api.biosimulations.org/logs/674dc5b010bb4455d6187562?includeOutput=true", "log_yml": { - "duration": 31.82576, - "exception": null, + "duration": 0.241913, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", + "type": "ValueError" + }, "output": "", - "sedDocuments": [ - { - "duration": 31.502274, - "exception": null, - "location": "BIOMD0000000138_url.sedml", - "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", - "outputs": [ - { - "dataSets": [ - { - "id": "autogen_time_for_task1", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_c", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vca", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_Cm", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_gk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_gcal", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_gsk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ga", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_gf", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vn", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_va", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vm", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vh", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_vf", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sn", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sa", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sm", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sh", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_sf", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_taun", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_tauh", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_lambda", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_kc", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ks", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ff", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_alpha", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phik", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phia", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phih", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phif", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_phical", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_cinf", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ica", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_isk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ibk", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ikdr", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ia", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_ik", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_n", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_h", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_V", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_cell", - "status": "SUCCEEDED" - }, - { - "id": "autogen_task1_reaction_0000004", - "status": "SUCCEEDED" - } - ], - "duration": 21.243813, - "exception": null, - "id": "autogen_report_for_task1", - "output": "", - "skipReason": null, - "status": "SUCCEEDED" - }, - { - "curves": [ - { - "id": "autogen_curve_task1_c", - "status": "SUCCEEDED" - } - ], - "duration": 2.297007, - "exception": null, - "id": "autogen_plot1", - "output": "", - "skipReason": null, - "status": "SUCCEEDED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_V", - "status": "SUCCEEDED" - } - ], - "duration": 1.976225, - "exception": null, - "id": "autogen_plot2", - "output": "", - "skipReason": null, - "status": "SUCCEEDED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_vk", - "status": "SUCCEEDED" - } - ], - "duration": 1.959338, - "exception": null, - "id": "autogen_plot3", - "output": "", - "skipReason": null, - "status": "SUCCEEDED" - } - ], - "skipReason": null, - "status": "SUCCEEDED", - "tasks": [ - { - "algorithm": "KISAO_0000560", - "duration": 3.857735, - "exception": null, - "id": "task1", - "output": "", - "simulatorDetails": [ - { - "key": "methodName", - "value": "lsoda" - }, - { - "key": "parameters", - "value": null - } - ], - "skipReason": null, - "status": "SUCCEEDED" - } - ] - } - ], + "sedDocuments": [], "skipReason": null, - "status": "SUCCEEDED" + "status": "FAILED" } }, "gillespy2": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcafb678b3883bb72756", - "download": "https://api.biosimulations.org/results/6735fcafb678b3883bb72756/download", - "logs": "https://api.biosimulations.org/logs/6735fcafb678b3883bb72756?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5b2ef911d5d452599de", + "download": "https://api.biosimulations.org/results/674dc5b2ef911d5d452599de/download", + "logs": "https://api.biosimulations.org/logs/674dc5b2ef911d5d452599de?includeOutput=true", "log_yml": { - "duration": 0.185009, + "duration": 0.219933, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, "output": "", @@ -370,13 +137,13 @@ }, "ginsim": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcb15a60072d20f5cf8f", - "download": "https://api.biosimulations.org/results/6735fcb15a60072d20f5cf8f/download", - "logs": "https://api.biosimulations.org/logs/6735fcb15a60072d20f5cf8f?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5b4ef911d5d452599e3", + "download": "https://api.biosimulations.org/results/674dc5b4ef911d5d452599e3/download", + "logs": "https://api.biosimulations.org/logs/674dc5b4ef911d5d452599e3?includeOutput=true", "log_yml": { - "duration": 0.177393, + "duration": 0.2174, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, "output": "", @@ -387,13 +154,13 @@ }, "libsbmlsim": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcb30d09353e8f10cf55", - "download": "https://api.biosimulations.org/results/6735fcb30d09353e8f10cf55/download", - "logs": "https://api.biosimulations.org/logs/6735fcb30d09353e8f10cf55?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5b6ef911d5d452599e6", + "download": "https://api.biosimulations.org/results/674dc5b6ef911d5d452599e6/download", + "logs": "https://api.biosimulations.org/logs/674dc5b6ef911d5d452599e6?includeOutput=true", "log_yml": { - "duration": 0.183238, + "duration": 0.214185, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, "output": "", @@ -404,285 +171,28 @@ }, "masspy": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcb5b678b3883bb7275f", - "download": "https://api.biosimulations.org/results/6735fcb5b678b3883bb7275f/download", - "logs": "https://api.biosimulations.org/logs/6735fcb5b678b3883bb7275f?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5b9261553b9bc253db3", + "download": "https://api.biosimulations.org/results/674dc5b9261553b9bc253db3/download", + "logs": "https://api.biosimulations.org/logs/674dc5b9261553b9bc253db3?includeOutput=true", "log_yml": { - "duration": 1.461313, + "duration": 0.434822, "exception": { - "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n \t`(model, errors) = validate_sbml_model(filename)`\n If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", - "type": "CombineArchiveExecutionError" + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", + "type": "ValueError" }, "output": "", - "sedDocuments": [ - { - "duration": 0.955101, - "exception": { - "message": "The SED document did not execute successfully:\n\n Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n \t`(model, errors) = validate_sbml_model(filename)`\n If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", - "type": "SedmlExecutionError" - }, - "location": "BIOMD0000000138_url.sedml", - "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", - "outputs": [ - { - "dataSets": [ - { - "id": "autogen_time_for_task1", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_c", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vca", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_Cm", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gcal", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gsk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ga", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vn", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_va", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vm", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vh", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sn", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sa", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sm", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sh", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_taun", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_tauh", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_lambda", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_kc", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ks", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ff", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_alpha", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phik", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phia", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phih", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phif", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phical", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_cinf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ica", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_isk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ibk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ikdr", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ia", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ik", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_n", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_h", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_V", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_cell", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_reaction_0000004", - "status": "SKIPPED" - } - ], - "duration": 0.066305, - "exception": null, - "id": "autogen_report_for_task1", - "output": "", - "skipReason": null, - "status": "SKIPPED" - }, - { - "curves": [ - { - "id": "autogen_curve_task1_c", - "status": "SKIPPED" - } - ], - "duration": 0.319888, - "exception": null, - "id": "autogen_plot1", - "output": "", - "skipReason": null, - "status": "SKIPPED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_V", - "status": "SKIPPED" - } - ], - "duration": 0.123432, - "exception": null, - "id": "autogen_plot2", - "output": "", - "skipReason": null, - "status": "SKIPPED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_vk", - "status": "SKIPPED" - } - ], - "duration": 0.138534, - "exception": null, - "id": "autogen_plot3", - "output": "", - "skipReason": null, - "status": "SKIPPED" - } - ], - "skipReason": null, - "status": "FAILED", - "tasks": [ - { - "algorithm": null, - "duration": 0.083005, - "exception": { - "message": "Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n\t`(model, errors) = validate_sbml_model(filename)`\nIf the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", - "type": "MassSBMLError" - }, - "id": "task1", - "output": "\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML fbc package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML groups package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'model_0000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'model_0000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n", - "simulatorDetails": null, - "skipReason": null, - "status": "FAILED" - } - ] - } - ], + "sedDocuments": [], "skipReason": null, "status": "FAILED" } }, "netpyne": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcb7b678b3883bb72762", - "download": "https://api.biosimulations.org/results/6735fcb7b678b3883bb72762/download", - "logs": "https://api.biosimulations.org/logs/6735fcb7b678b3883bb72762?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5bb261553b9bc253db8", + "download": "https://api.biosimulations.org/results/674dc5bb261553b9bc253db8/download", + "logs": "https://api.biosimulations.org/logs/674dc5bb261553b9bc253db8?includeOutput=true", "log_yml": { - "duration": 0.051625, + "duration": 0.057637, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -695,11 +205,11 @@ }, "neuron": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcb9b678b3883bb72767", - "download": "https://api.biosimulations.org/results/6735fcb9b678b3883bb72767/download", - "logs": "https://api.biosimulations.org/logs/6735fcb9b678b3883bb72767?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5bcef911d5d452599f3", + "download": "https://api.biosimulations.org/results/674dc5bcef911d5d452599f3/download", + "logs": "https://api.biosimulations.org/logs/674dc5bcef911d5d452599f3?includeOutput=true", "log_yml": { - "duration": 0.06773, + "duration": 0.053141, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -712,321 +222,64 @@ }, "opencor": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcbab678b3883bb7276f", - "download": "https://api.biosimulations.org/results/6735fcbab678b3883bb7276f/download", - "logs": "https://api.biosimulations.org/logs/6735fcbab678b3883bb7276f?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5beef911d5d452599f6", + "download": "https://api.biosimulations.org/results/674dc5beef911d5d452599f6/download", + "logs": "https://api.biosimulations.org/logs/674dc5beef911d5d452599f6?includeOutput=true", "log_yml": { - "duration": 0.031996, + "duration": 0.036307, "exception": { "message": "No module named 'libsbml'", - "type": "ModuleNotFoundError" - }, - "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmptvny277r/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", - "sedDocuments": [], - "skipReason": null, - "status": "FAILED" - } - }, - "pyneuroml": { - "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcbdb678b3883bb72777", - "download": "https://api.biosimulations.org/results/6735fcbdb678b3883bb72777/download", - "logs": "https://api.biosimulations.org/logs/6735fcbdb678b3883bb72777?includeOutput=true", - "log_yml": { - "duration": 0.052296, - "exception": { - "message": "No module named 'libsbml'", - "type": "ModuleNotFoundError" - }, - "output": "", - "sedDocuments": [], - "skipReason": null, - "status": "FAILED" - } - }, - "pysces": { - "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcbf0d09353e8f10cf76", - "download": "https://api.biosimulations.org/results/6735fcbf0d09353e8f10cf76/download", - "logs": "https://api.biosimulations.org/logs/6735fcbf0d09353e8f10cf76?includeOutput=true", - "log_yml": { - "duration": 8.88908, - "exception": { - "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :'PysMod' object has no attribute 'lambda'", - "type": "CombineArchiveExecutionError" - }, - "output": "libtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified in the user configuration file, set \"matplotlib_backend = \" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems *\r\n* http://pysces.sourceforge.net *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", - "sedDocuments": [ - { - "duration": 8.562459, - "exception": { - "message": "The SED document did not execute successfully:\n\n :'PysMod' object has no attribute 'lambda'", - "type": "SedmlExecutionError" - }, - "location": "BIOMD0000000138_url.sedml", - "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V1\r\nlambda is a reserved symbol, replacing with Lambda\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpku3lpobu.xml\r\n*******************************************************************\r\n\r\nReserved symbol lambda replaced with Lambda \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"reaction_0000004\" in default compartment\r\nWriting file: /tmp/tmp2s4xbeay.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpku3lpobu.xml\r\nout: /tmp/tmp2s4xbeay.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmp2s4xbeay.psc loading ..... \r\nParsing file: /tmp/tmp2s4xbeay.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"vca\" has been initialised but does not occur in a rate equation\r\nInfo: \"vk\" has been initialised but does not occur in a rate equation\r\nInfo: \"Cm\" has been initialised but does not occur in a rate equation\r\nInfo: \"gk\" has been initialised but does not occur in a rate equation\r\nInfo: \"gcal\" has been initialised but does not occur in a rate equation\r\nInfo: \"gsk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ga\" has been initialised but does not occur in a rate equation\r\nInfo: \"gf\" has been initialised but does not occur in a rate equation\r\nInfo: \"vn\" has been initialised but does not occur in a rate equation\r\nInfo: \"va\" has been initialised but does not occur in a rate equation\r\nInfo: \"vm\" has been initialised but does not occur in a rate equation\r\nInfo: \"vh\" has been initialised but does not occur in a rate equation\r\nInfo: \"vf\" has been initialised but does not occur in a rate equation\r\nInfo: \"sn\" has been initialised but does not occur in a rate equation\r\nInfo: \"sa\" has been initialised but does not occur in a rate equation\r\nInfo: \"sm\" has been initialised but does not occur in a rate equation\r\nInfo: \"sh\" has been initialised but does not occur in a rate equation\r\nInfo: \"sf\" has been initialised but does not occur in a rate equation\r\nInfo: \"taun\" has been initialised but does not occur in a rate equation\r\nInfo: \"tauh\" has been initialised but does not occur in a rate equation\r\nInfo: \"Lambda\" has been initialised but does not occur in a rate equation\r\nInfo: \"ks\" has been initialised but does not occur in a rate equation\r\nInfo: \"phik\" has been initialised but does not occur in a rate equation\r\nInfo: \"phia\" has been initialised but does not occur in a rate equation\r\nInfo: \"phih\" has been initialised but does not occur in a rate equation\r\nInfo: \"phif\" has been initialised but does not occur in a rate equation\r\nInfo: \"phical\" has been initialised but does not occur in a rate equation\r\nInfo: \"cinf\" has been initialised but does not occur in a rate equation\r\nInfo: \"isk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ibk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ikdr\" has been initialised but does not occur in a rate equation\r\nInfo: \"ia\" has been initialised but does not occur in a rate equation\r\nInfo: \"ik\" has been initialised but does not occur in a rate equation\r\nInfo: \"n\" has been initialised but does not occur in a rate equation\r\nInfo: \"h\" has been initialised but does not occur in a rate equation\r\nInfo: \"V\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . no flux conservation\r\n done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nRate rule(s) detected.\r\nINFO: RateRules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 100001 points: 6.472142934799194\r\nRateRules evaluated and added to mod.data_sim.\r\n \u001b[31mfailed - 'PysMod' object has no attribute 'lambda'\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", - "outputs": [ - { - "dataSets": [ - { - "id": "autogen_time_for_task1", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_c", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vca", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_Cm", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gcal", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gsk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ga", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_gf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vn", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_va", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vm", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vh", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_vf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sn", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sa", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sm", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sh", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_sf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_taun", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_tauh", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_lambda", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_kc", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ks", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ff", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_alpha", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phik", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phia", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phih", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phif", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_phical", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_cinf", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ica", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_isk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ibk", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ikdr", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ia", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_ik", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_n", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_h", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_V", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_cell", - "status": "SKIPPED" - }, - { - "id": "autogen_task1_reaction_0000004", - "status": "SKIPPED" - } - ], - "duration": 0.074844, - "exception": null, - "id": "autogen_report_for_task1", - "output": "", - "skipReason": null, - "status": "SKIPPED" - }, - { - "curves": [ - { - "id": "autogen_curve_task1_c", - "status": "SKIPPED" - } - ], - "duration": 0.279991, - "exception": null, - "id": "autogen_plot1", - "output": "", - "skipReason": null, - "status": "SKIPPED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_V", - "status": "SKIPPED" - } - ], - "duration": 0.109229, - "exception": null, - "id": "autogen_plot2", - "output": "", - "skipReason": null, - "status": "SKIPPED" - }, - { - "curves": [ - { - "id": "autogen_curve_for_task1_vk", - "status": "SKIPPED" - } - ], - "duration": 0.108525, - "exception": null, - "id": "autogen_plot3", - "output": "", - "skipReason": null, - "status": "SKIPPED" - } - ], - "skipReason": null, - "status": "FAILED", - "tasks": [ - { - "algorithm": null, - "duration": 7.802336, - "exception": { - "message": "'PysMod' object has no attribute 'lambda'", - "type": "AttributeError" - }, - "id": "task1", - "output": "", - "simulatorDetails": null, - "skipReason": null, - "status": "FAILED" - } - ] - } - ], + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpsxy4ki5b/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pyneuroml": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc5c0ef911d5d452599fd", + "download": "https://api.biosimulations.org/results/674dc5c0ef911d5d452599fd/download", + "logs": "https://api.biosimulations.org/logs/674dc5c0ef911d5d452599fd?includeOutput=true", + "log_yml": { + "duration": 0.050251, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pysces": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc5c1261553b9bc253dcc", + "download": "https://api.biosimulations.org/results/674dc5c1261553b9bc253dcc/download", + "logs": "https://api.biosimulations.org/logs/674dc5c1261553b9bc253dcc?includeOutput=true", + "log_yml": { + "duration": 0.202896, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", + "type": "ValueError" + }, + "output": "libtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified in the user configuration file, set \"matplotlib_backend = \" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems *\r\n* http://pysces.sourceforge.net *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", + "sedDocuments": [], "skipReason": null, "status": "FAILED" } }, "rbapy": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcc00d09353e8f10cf7d", - "download": "https://api.biosimulations.org/results/6735fcc00d09353e8f10cf7d/download", - "logs": "https://api.biosimulations.org/logs/6735fcc00d09353e8f10cf7d?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5c3ef911d5d45259a11", + "download": "https://api.biosimulations.org/results/674dc5c3ef911d5d45259a11/download", + "logs": "https://api.biosimulations.org/logs/674dc5c3ef911d5d45259a11?includeOutput=true", "log_yml": { - "duration": 0.171239, + "duration": 0.188687, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", "type": "ValueError" }, "output": "", @@ -1037,11 +290,11 @@ }, "smoldyn": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcc25a60072d20f5cfc8", - "download": "https://api.biosimulations.org/results/6735fcc25a60072d20f5cfc8/download", - "logs": "https://api.biosimulations.org/logs/6735fcc25a60072d20f5cfc8?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5c5ef911d5d45259a27", + "download": "https://api.biosimulations.org/results/674dc5c5ef911d5d45259a27/download", + "logs": "https://api.biosimulations.org/logs/674dc5c5ef911d5d45259a27?includeOutput=true", "log_yml": { - "duration": 0.052537, + "duration": 0.047552, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -1054,341 +307,39 @@ }, "tellurium": { "response": 201, - "view": "https://api.biosimulations.org/runs/6735fcc40d09353e8f10cf8b", - "download": "https://api.biosimulations.org/results/6735fcc40d09353e8f10cf8b/download", - "logs": "https://api.biosimulations.org/logs/6735fcc40d09353e8f10cf8b?includeOutput=true", + "view": "https://api.biosimulations.org/runs/674dc5c710bb4455d6187595", + "download": "https://api.biosimulations.org/results/674dc5c710bb4455d6187595/download", + "logs": "https://api.biosimulations.org/logs/674dc5c710bb4455d6187595?includeOutput=true", "log_yml": { - "duration": 27.86198, - "exception": null, + "duration": 0.304898, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Output `autogen_plot3` is invalid.\n - Plot must have at least one curve.", + "type": "ValueError" + }, "output": "", - "sedDocuments": [ - { - "duration": 27.339058, - "exception": null, - "location": "BIOMD0000000138_url.sedml", - "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", - 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+Its a Deterministic ODE model showcasing mechanism of PDL1 induced TCR and CD38 signalling inhibition. The model also contains the LCK activation and inactivation phenomenon dependent on the particular phosphorylation site. This model is relevant in immunotherapy.
+ + + + + + + + + + Sheriff + Rahuman + + sheriff@ebi.ac.uk + + EMBL-EBI + + + + + Tiwari + Krishna + + tiwarik@babraham.ac.uk + + Babraham Institute + + + + + + 2018-11-20T11:21:29Z + + + 2018-11-20T11:21:29Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PDL-1 medaited inhibition of TCR and costimulatory signals. + + + + + + 2018-11-20T11:21:29Z + + + + + tiwarik@babraham.ac.uk + + + Tiwari + Krishna + + + + + Babraham Institute + + + + + + + sheriff@ebi.ac.uk + + + Sheriff + Rahuman + + + + + EMBL-EBI + + + + + + + + + + + + + + + + + + 2018-11-20T15:31:17Z + + + + + + + + + + kcat + + + Enzyme + + + Substrate + + + Km + + + + + + kcat + Enzyme + Substrate + + + + Km + Substrate + + + + + + + + + + + + + 2018-11-20T13:40:01Z + + + + + + + + + + kcat + + + Enzyme + + + Substrate + + + Km + + + X1 + + + X2 + + + Y1 + + + k + + + + + + + + kcat + Enzyme + Substrate + + + + Km + Substrate + + + + + 1 + + + + + X1 + X2 + + + + Y1 + k + + + + + + + + + + + + + + + 2018-11-20T14:22:12Z + + + + + + + + + + ka + + + Enzyme + + + Substrate + + + + ka + Enzyme + Substrate + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2018-11-20T11:29:03Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2018-11-20T11:47:32Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2018-11-20T13:04:42Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2018-11-20T13:04:41Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2018-11-20T11:47:26Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2018-11-20T11:47:33Z + + + + + + + + + + + + 
{[LCKt]}-({[LCKyiya]}+{[LCKyi]}+{[LCKya]}+{[LCKpi]})
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{[CD28t]}-({[CD28a]}+{[PI3Kb]})
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-0,0 +1,23 @@ +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------|:-------------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with AMICI.

SED-ML and SBML are compatible with AMICI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Cannot turn parameter ModelValue_0 into a constant/fixed parameter since it either has an initial assignment or is the target of an assignment or rate rule.

target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='LCK_switch'] is not a valid XPath to an attribute of a model element

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Cannot turn parameter ModelValue_0 into a constant/fixed parameter since it either has an initial assignment or is the target of an assignment or rate rule.

target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='LCK_switch'] is not a valid XPath to an attribute of a model element

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

Only BNGL, SED-ML are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with CBMPy.

SED-ML and SBML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with COBRApy.

SED-ML and SBML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with COPASI.

SED-ML and SBML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with GillesPy2.

SED-ML and SBML are compatible with GillesPy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with LibSBMLSim.

SED-ML and SBML are compatible with LibSBMLSim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with MASSpy.

SED-ML and SBML are compatible with MASSpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Could not load MassModel '_30356330_Theinmozhi_PDL1_TCR_regulation'

target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='LCK_switch'] cannot be changed by XML manipulation, as the target is not an attribute of a model element

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

Only CellML, SED-ML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with PySCeS.

SED-ML and SBML are compatible with PySCeS.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

Only RBApy, SED-ML are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

Only Smoldyn, SED-ML are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with Tellurium.

SED-ML and SBML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with VCell.

BNGL, SED-ML and SBML are compatible with VCell.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| plot | | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

Only XPP, SED-ML are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/BioModels/BIOMD0000000724/tests/results_local.json b/BioModels/BIOMD0000000724/tests/results_local.json new file mode 100644 index 00000000..7f894940 --- /dev/null +++ b/BioModels/BIOMD0000000724/tests/results_local.json @@ -0,0 +1,3265 @@ +{ + "amici": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/amici' returned non-zero exit status 1", + "log_yml": { + "duration": 3.6184, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Cannot turn parameter ModelValue_0 into a constant/fixed parameter since it either has an initial assignment or is the target of an assignment or rate rule.\n \n target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='LCK_switch'] is not a valid XPath to an attribute of a model element", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 3.100733, + "exception": { + "message": "The SED document did not execute successfully:\n\n Cannot turn parameter ModelValue_0 into a constant/fixed parameter since it either has an initial assignment or is the target of an assignment or rate rule.\n\n target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='LCK_switch'] is not a valid XPath to an attribute of a model element", + "type": "SedmlExecutionError" + }, + "location": "Theinmozhi_2018.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 5 plots:\r\n Theinmozhi_2018.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 120 data sets\r\n Plots (5):\r\n plot_10_task2: 1 curves\r\n plot_6_task2: 1 curves\r\n plot_7_task2: 1 curves\r\n plot_8_task2: 2 curves\r\n plot_9_task2: 1 curves\r\n\r\nExecuting SED-ML file 1: Theinmozhi_2018.sedml ...\r\n Found 2 tasks and 6 outputs:\r\n Tasks:\r\n `task1`\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_10_task2`\r\n `plot_6_task2`\r\n `plot_7_task2`\r\n `plot_8_task2`\r\n `plot_9_task2`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 6 outputs ...\r\n Generating output 1: `plot_6_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `plot_7_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `plot_8_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `plot_9_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 5: `plot_10_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 6: `autogen_report_for_task2` ... \u001b[36mqueued\u001b[0m\r\n Executing task 2: `task2`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 6 outputs ...\r\n Generating output 1: `plot_6_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `plot_7_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `plot_8_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `plot_9_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 5: `plot_10_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 6: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SKIPPED" + } + ], + "duration": 0.210577, + "exception": null, + "id": "plot_6_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "p2_curve_1_task2", + "status": "SKIPPED" + } + ], + "duration": 0.229413, + "exception": null, + "id": "plot_7_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "p3_curve_1_task2", + "status": "SKIPPED" + }, + { + "id": "p3_curve_2_task2", + "status": "SKIPPED" + } + ], + "duration": 0.205022, + "exception": null, + "id": "plot_8_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "p4_curve_1_task2", + "status": "SKIPPED" + } + ], + "duration": 0.31253, + "exception": null, + "id": "plot_9_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "p5_curve_1_task2", + "status": "SKIPPED" + } + ], + "duration": 0.205306, + "exception": null, + "id": "plot_10_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_perc_PI3K_free", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_perc_ZAP70_free", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_perc_LCK_active", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_perc_LCK_inactive", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SLP76a", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ZAP70a2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKi", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKyi", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKya", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKyiya", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKpi", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKt", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKactive", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_PD1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_PD1p1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_PD1p2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CP1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SHP2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CP2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CPactive", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD28a", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD28i", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_PI3K", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_PI3Kb", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD28t", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD3a", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD3i", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ZAP70a1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ZAP70i", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ZAP70", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_PI3Kt", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ZAP70t", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LATa", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LATi", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LATt", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_GADS", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SLP76", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SLP76i", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_GADSt", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SLP76t", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD3t", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_GADSa", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKinactive", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kdpa_yiya", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kdpi_yi", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kdpi_yiya", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kdpa_ya", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kdpa_pi", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kpi_i", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kpi_ya", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kpa_i", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kpa_yi", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_k", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kp_pd1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_KMp_pd1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Ka_shp", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kd1_shp", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kd2_shp", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kdp_cp2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kp_cd28", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_KMp_cd28", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kdp_cd28", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_KMdp_cd28", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Ka_pi3k", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kd_pi3k", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kp_cd3", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_KMp_cd3", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kdp_cd3", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_KMdp_cd3", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Ka_zap", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kd_zap", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kp1_zap", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kp2_zap", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kp_lat", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Ka_gads", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kd_gads", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Ka_slp", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kd_slp", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kp_slp", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_perc_SHP2_bound", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD3z_phosphorylated", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD28_phosphorylated", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_perc_SHP2_free", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ZAP70_phos_Y315", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ZAP70_phos_Y93", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCK_phos_Y505", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCK_phos_Y394", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LAT_phosphorylated", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCK_switch", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ModelValue_0", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCK_P_LCKyi_inh", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCK_P_LCKya_act", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKya_P_LCKyiya_act", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKyi_P_LCKpi_inh", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKyiya_DP_LCKyi", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKya_DP_LCKi", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKyi_DP_LCKi", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKyiya_DP_LCKya", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LCKpi_DP_LCKyi", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_PD1_P_PD1p1_act", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_PD1p1_P_PD1p2_act", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_PD1p1_Bd_SHP2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_PD1p2_Bd_SHP2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CP2_Diss_SHP2_PD1p1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CP2_DP_CP1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CP1_Diss_PD1_SHP2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD28i_P_CD28a", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD28a_DP_CD28i", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD28a_Bd_PI3K", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD3i_P_CD3a", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD3a_DP_CD3i", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD3a_Bd_ZAP70", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ZAP70i_P_ZAP70a1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ZAP70a1_P_ZAP70a2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LATi_P_LATa", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LATa_Bd_GADS", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_GADSa_Bd_SLP76", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SLP76i_P_SLC76a", + "status": "SKIPPED" + } + ], + "duration": 0.070285, + "exception": null, + "id": "autogen_report_for_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.13237, + "exception": { + "message": "Cannot turn parameter ModelValue_0 into a constant/fixed parameter since it either has an initial assignment or is the target of an assignment or rate rule.", + "type": "SBMLException" + }, + "id": "task1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + }, + { + "algorithm": null, + "duration": 0.041637, + "exception": { + "message": "target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='LCK_switch'] is not a valid XPath to an attribute of a model element", + "type": "ValueError" + }, + "id": "task2", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "brian2": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.065134, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpjvi4hy8h/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n [py.warnings]\r\npyNeuroML >>> WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpjvi4hy8h/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "bionetgen": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", + "log_yml": { + "duration": 0.191136, + "exception": { + "message": "`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpc4csjd_w/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` has warnings.\r\n - Variable `p1_perc_PI3K_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` has warnings.\r\n - Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` has warnings.\r\n - Variable `p3_perc_LCK_active_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` has warnings.\r\n - Variable `p3_perc_LCK_inactive_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` has warnings.\r\n - Variable `p4_SLP76a_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` has warnings.\r\n - Variable `p5_ZAP70a2_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` has warnings.\r\n - Variable `auto_dg_for_task2_LCKt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` has warnings.\r\n - Variable `auto_dg_for_task2_CPactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` has warnings.\r\n - Variable `auto_dg_for_task2_CD28t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` has warnings.\r\n - Variable `auto_dg_for_task2_LATi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` has warnings.\r\n - Variable `auto_dg_for_task2_LATt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` has warnings.\r\n - Variable `auto_dg_for_task2_GADSt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` has warnings.\r\n - Variable `auto_dg_for_task2_CD3t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` has warnings.\r\n - Variable `auto_dg_for_task2_k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` has warnings.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` has warnings.\r\n - Variable `auto_dg_for_task2_Cell__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Theinmozhi_2018.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` has warnings.\r\n - Variable `p1_perc_PI3K_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` has warnings.\r\n - Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` has warnings.\r\n - Variable `p3_perc_LCK_active_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` has warnings.\r\n - Variable `p3_perc_LCK_inactive_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` has warnings.\r\n - Variable `p4_SLP76a_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` has warnings.\r\n - Variable `p5_ZAP70a2_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` has warnings.\r\n - Variable `auto_dg_for_task2_LCKt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` has warnings.\r\n - Variable `auto_dg_for_task2_CPactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` has warnings.\r\n - Variable `auto_dg_for_task2_CD28t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` has warnings.\r\n - Variable `auto_dg_for_task2_LATi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` has warnings.\r\n - Variable `auto_dg_for_task2_LATt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` has warnings.\r\n - Variable `auto_dg_for_task2_GADSt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` has warnings.\r\n - Variable `auto_dg_for_task2_CD3t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` has warnings.\r\n - Variable `auto_dg_for_task2_k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` has warnings.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` has warnings.\r\n - Variable `auto_dg_for_task2_Cell__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "boolnet": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", + "log_yml": { + "duration": 0.200382, + "exception": { + "message": "`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpt_td9jjh/./Theinmozhi_2018.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` may be invalid.\r\n - The model file `Theinmozhi_2018.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-7 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKinactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ZAP70 / (ZAP70 + ZAP70i + ZAP70a1 + ZAP70a2) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'PI3K / (PI3Kb + PI3K) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '6e-6 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'SHP2 / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'CPactive / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Cell * Equation_for_PD1_activation(Kp_pd1, LCKactive, PD1, KMp_pd1, PD1p1, PD1p2, LCKt, k)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD3z_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD28_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_SHP2_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_PI3K_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_ZAP70_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y315' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y93' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y505' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y394' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LAT_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_active' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_inactive' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_switch' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ModelValue_0' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` may be invalid.\r\n - Variable `p1_perc_PI3K_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` may be invalid.\r\n - Variable `p2_perc_ZAP70_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` may be invalid.\r\n - Variable `p3_perc_LCK_active_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` may be invalid.\r\n - Variable `p3_perc_LCK_inactive_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` may be invalid.\r\n - Variable `p4_SLP76a_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` may be invalid.\r\n - Variable `p5_ZAP70a2_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` may be invalid.\r\n - Variable `auto_dg_for_task2_CPactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` may be invalid.\r\n - Variable `auto_dg_for_task2_LATt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` may be invalid.\r\n - Variable `auto_dg_for_task2_k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` may be invalid.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` may be invalid.\r\n - Variable `auto_dg_for_task2_Cell__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_7_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_8_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_9_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_10_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Theinmozhi_2018.sedml` may be invalid.\r\n - Model `model` may be invalid.\r\n - The model file `Theinmozhi_2018.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-7 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKinactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ZAP70 / (ZAP70 + ZAP70i + ZAP70a1 + ZAP70a2) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'PI3K / (PI3Kb + PI3K) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '6e-6 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'SHP2 / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'CPactive / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Cell * Equation_for_PD1_activation(Kp_pd1, LCKactive, PD1, KMp_pd1, PD1p1, PD1p2, LCKt, k)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD3z_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD28_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_SHP2_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_PI3K_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_ZAP70_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y315' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y93' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y505' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y394' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LAT_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_active' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_inactive' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_switch' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ModelValue_0' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` may be invalid.\r\n - Variable `p1_perc_PI3K_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` may be invalid.\r\n - Variable `p2_perc_ZAP70_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` may be invalid.\r\n - Variable `p3_perc_LCK_active_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` may be invalid.\r\n - Variable `p3_perc_LCK_inactive_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` may be invalid.\r\n - Variable `p4_SLP76a_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` may be invalid.\r\n - Variable `p5_ZAP70a2_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` may be invalid.\r\n - Variable `auto_dg_for_task2_CPactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` may be invalid.\r\n - Variable `auto_dg_for_task2_LATt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` may be invalid.\r\n - Variable `auto_dg_for_task2_k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` may be invalid.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` may be invalid.\r\n - Variable `auto_dg_for_task2_Cell__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_7_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_8_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_9_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_10_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cbmpy": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.299514, + "exception": { + "message": "`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpugzxtcse/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` has warnings.\r\n - Variable `p1_perc_PI3K_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` has warnings.\r\n - Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` has warnings.\r\n - Variable `p3_perc_LCK_active_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` has warnings.\r\n - Variable `p3_perc_LCK_inactive_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` has warnings.\r\n - Variable `p4_SLP76a_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` has warnings.\r\n - Variable `p5_ZAP70a2_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` has warnings.\r\n - Variable `auto_dg_for_task2_LCKt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` has warnings.\r\n - Variable `auto_dg_for_task2_CPactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` has warnings.\r\n - Variable `auto_dg_for_task2_CD28t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` has warnings.\r\n - Variable `auto_dg_for_task2_LATi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` has warnings.\r\n - Variable `auto_dg_for_task2_LATt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` has warnings.\r\n - Variable `auto_dg_for_task2_GADSt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` has warnings.\r\n - Variable `auto_dg_for_task2_CD3t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` has warnings.\r\n - Variable `auto_dg_for_task2_k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` has warnings.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` has warnings.\r\n - Variable `auto_dg_for_task2_Cell__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Theinmozhi_2018.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` has warnings.\r\n - Variable `p1_perc_PI3K_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` has warnings.\r\n - Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` has warnings.\r\n - Variable `p3_perc_LCK_active_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` has warnings.\r\n - Variable `p3_perc_LCK_inactive_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` has warnings.\r\n - Variable `p4_SLP76a_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` has warnings.\r\n - Variable `p5_ZAP70a2_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` has warnings.\r\n - Variable `auto_dg_for_task2_LCKt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` has warnings.\r\n - Variable `auto_dg_for_task2_CPactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` has warnings.\r\n - Variable `auto_dg_for_task2_CD28t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` has warnings.\r\n - Variable `auto_dg_for_task2_LATi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` has warnings.\r\n - Variable `auto_dg_for_task2_LATt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` has warnings.\r\n - Variable `auto_dg_for_task2_GADSt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` has warnings.\r\n - Variable `auto_dg_for_task2_CD3t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` has warnings.\r\n - Variable `auto_dg_for_task2_k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` has warnings.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` has warnings.\r\n - Variable `auto_dg_for_task2_Cell__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cobrapy": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.209949, + "exception": { + "message": "`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp8nq63fqb/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` has warnings.\r\n - Variable `p1_perc_PI3K_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` has warnings.\r\n - Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` has warnings.\r\n - Variable `p3_perc_LCK_active_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` has warnings.\r\n - Variable `p3_perc_LCK_inactive_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` has warnings.\r\n - Variable `p4_SLP76a_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` has warnings.\r\n - Variable `p5_ZAP70a2_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` has warnings.\r\n - Variable `auto_dg_for_task2_LCKt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` has warnings.\r\n - Variable `auto_dg_for_task2_CPactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` has warnings.\r\n - Variable `auto_dg_for_task2_CD28t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` has warnings.\r\n - Variable `auto_dg_for_task2_LATi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` has warnings.\r\n - Variable `auto_dg_for_task2_LATt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` has warnings.\r\n - Variable `auto_dg_for_task2_GADSt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` has warnings.\r\n - Variable `auto_dg_for_task2_CD3t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` has warnings.\r\n - Variable `auto_dg_for_task2_k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` has warnings.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` has warnings.\r\n - Variable `auto_dg_for_task2_Cell__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Theinmozhi_2018.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` has warnings.\r\n - Variable `p1_perc_PI3K_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` has warnings.\r\n - Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` has warnings.\r\n - Variable `p3_perc_LCK_active_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` has warnings.\r\n - Variable `p3_perc_LCK_inactive_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` has warnings.\r\n - Variable `p4_SLP76a_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` has warnings.\r\n - Variable `p5_ZAP70a2_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` has warnings.\r\n - Variable `auto_dg_for_task2_LCKt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` has warnings.\r\n - Variable `auto_dg_for_task2_CPactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` has warnings.\r\n - Variable `auto_dg_for_task2_CD28t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` has warnings.\r\n - Variable `auto_dg_for_task2_LATi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` has warnings.\r\n - Variable `auto_dg_for_task2_LATt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` has warnings.\r\n - Variable `auto_dg_for_task2_GADSt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` has warnings.\r\n - Variable `auto_dg_for_task2_CD3t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` has warnings.\r\n - Variable `auto_dg_for_task2_k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` has warnings.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` has warnings.\r\n - Variable `auto_dg_for_task2_Cell__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "copasi": { + "exception_message": "", + "log_yml": { + "duration": 3.112999, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmps3zyvh7q/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Theinmozhi_2018.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmps3zyvh7q/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 2.540741, + "exception": null, + "location": "Theinmozhi_2018.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 5 plots:\r\n Theinmozhi_2018.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 120 data sets\r\n Plots (5):\r\n plot_10_task2: 1 curves\r\n plot_6_task2: 1 curves\r\n plot_7_task2: 1 curves\r\n plot_8_task2: 2 curves\r\n plot_9_task2: 1 curves\r\n\r\nExecuting SED-ML file 1: Theinmozhi_2018.sedml ...\r\n Found 1 tasks and 6 outputs:\r\n Tasks:\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_10_task2`\r\n `plot_6_task2`\r\n `plot_7_task2`\r\n `plot_8_task2`\r\n `plot_9_task2`\r\n Executing task 1: `task2`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 6 outputs ...\r\n Generating output 1: `plot_6_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `plot_7_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `plot_8_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `plot_9_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 5: `plot_10_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 6: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.352941, + "exception": null, + "id": "plot_6_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p2_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.252996, + "exception": null, + "id": "plot_7_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p3_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p3_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.24955, + "exception": null, + "id": "plot_8_task2", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p4_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.216039, + "exception": null, + "id": "plot_9_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p5_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.208084, + "exception": null, + "id": "plot_10_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_PI3K_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_ZAP70_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_LCK_active", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_LCK_inactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKpi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CPactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3K", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3Kb", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3Kt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKinactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_yiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpi_yi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpi_yiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_ya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_pi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpi_i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpi_ya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpa_i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpa_yi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_pd1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_pd1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd1_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd2_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cp2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMdp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_pi3k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_pi3k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMdp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp1_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp2_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_lat", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_gads", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_gads", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_SHP2_bound", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3z_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_SHP2_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70_phos_Y315", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70_phos_Y93", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_phos_Y505", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_phos_Y394", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LAT_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_switch", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ModelValue_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_P_LCKyi_inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_P_LCKya_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya_P_LCKyiya_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi_P_LCKpi_inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya_DP_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya_DP_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi_DP_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya_DP_LCKya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKpi_DP_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1_P_PD1p1_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1_P_PD1p2_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1_Bd_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p2_Bd_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2_Diss_SHP2_PD1p1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2_DP_CP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP1_Diss_PD1_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28i_P_CD28a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a_DP_CD28i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a_Bd_PI3K", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3i_P_CD3a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a_DP_CD3i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a_Bd_ZAP70", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70i_P_ZAP70a1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a1_P_ZAP70a2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATi_P_LATa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATa_Bd_GADS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSa_Bd_SLP76", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76i_P_SLC76a", + "status": "SUCCEEDED" + } + ], + "duration": 0.221001, + "exception": null, + "id": "autogen_report_for_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": null, + "duration": 0.524146, + "exception": null, + "id": "task2", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task2_Ka_gads__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd_slp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_perc_SHP2_free__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdpa_ya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCK_phos_Y505__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LAT_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCK_phos_Y394__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kpi_ya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCK_switch__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kpi_i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdpa_pi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd2_shp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_GADSa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28i_P_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_GADSt__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_perc_SHP2_bound__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_KMp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LATi_P_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SLP76i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LATi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd1_shp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_KMdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_KMp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28t__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kpa_i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Ka_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Ka_slp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKactive__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LATt__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKt__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p3_perc_LCK_active_1_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKpi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_KMp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p3_perc_LCK_inactive_2_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3t__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Ka_zap__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p4_SLP76a_1_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp_slp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_KMdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdpi_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyiya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd_zap__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p5_ZAP70a2_1_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3z_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p1_perc_PI3K_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp1_zap__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CP2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CP2_DP_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LATa_Bd_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CPactive__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Ka_shp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kpa_yi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKinactive__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdpa_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PI3Kb__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3i_P_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdpi_yi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SLP76t__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp_lat__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_k__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PI3Kt__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `model` may be invalid.\r\n - The model file `/tmp/tmps3zyvh7q/tmph_tsi_o4.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `model` may be invalid.\r\n - The model file `/tmp/tmps3zyvh7q/tmpknf5u8wc.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "gillespy2": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.223186, + "exception": { + "message": "`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmph_hayu60/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` has warnings.\r\n - Variable `p1_perc_PI3K_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` has warnings.\r\n - Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` has warnings.\r\n - Variable `p3_perc_LCK_active_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` has warnings.\r\n - Variable `p3_perc_LCK_inactive_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` has warnings.\r\n - Variable `p4_SLP76a_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` has warnings.\r\n - Variable `p5_ZAP70a2_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` has warnings.\r\n - Variable `auto_dg_for_task2_LCKt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` has warnings.\r\n - Variable `auto_dg_for_task2_CPactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` has warnings.\r\n - Variable `auto_dg_for_task2_CD28t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` has warnings.\r\n - Variable `auto_dg_for_task2_LATi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` has warnings.\r\n - Variable `auto_dg_for_task2_LATt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` has warnings.\r\n - Variable `auto_dg_for_task2_GADSt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` has warnings.\r\n - Variable `auto_dg_for_task2_CD3t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` has warnings.\r\n - Variable `auto_dg_for_task2_k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` has warnings.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` has warnings.\r\n - Variable `auto_dg_for_task2_Cell__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Theinmozhi_2018.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` has warnings.\r\n - Variable `p1_perc_PI3K_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` has warnings.\r\n - Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` has warnings.\r\n - Variable `p3_perc_LCK_active_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` has warnings.\r\n - Variable `p3_perc_LCK_inactive_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` has warnings.\r\n - Variable `p4_SLP76a_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` has warnings.\r\n - Variable `p5_ZAP70a2_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` has warnings.\r\n - Variable `auto_dg_for_task2_LCKt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` has warnings.\r\n - Variable `auto_dg_for_task2_CPactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` has warnings.\r\n - Variable `auto_dg_for_task2_CD28t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` has warnings.\r\n - Variable `auto_dg_for_task2_LATi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` has warnings.\r\n - Variable `auto_dg_for_task2_LATt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` has warnings.\r\n - Variable `auto_dg_for_task2_GADSt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` has warnings.\r\n - Variable `auto_dg_for_task2_CD3t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` has warnings.\r\n - Variable `auto_dg_for_task2_k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` has warnings.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` has warnings.\r\n - Variable `auto_dg_for_task2_Cell__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "ginsim": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.194907, + "exception": { + "message": "`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpvzuea892/./Theinmozhi_2018.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` may be invalid.\r\n - The model file `Theinmozhi_2018.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-7 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKinactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ZAP70 / (ZAP70 + ZAP70i + ZAP70a1 + ZAP70a2) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'PI3K / (PI3Kb + PI3K) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '6e-6 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'SHP2 / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'CPactive / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Cell * Equation_for_PD1_activation(Kp_pd1, LCKactive, PD1, KMp_pd1, PD1p1, PD1p2, LCKt, k)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD3z_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD28_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_SHP2_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_PI3K_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_ZAP70_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y315' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y93' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y505' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y394' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LAT_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_active' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_inactive' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_switch' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ModelValue_0' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` may be invalid.\r\n - Variable `p1_perc_PI3K_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` may be invalid.\r\n - Variable `p2_perc_ZAP70_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` may be invalid.\r\n - Variable `p3_perc_LCK_active_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` may be invalid.\r\n - Variable `p3_perc_LCK_inactive_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` may be invalid.\r\n - Variable `p4_SLP76a_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` may be invalid.\r\n - Variable `p5_ZAP70a2_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` may be invalid.\r\n - Variable `auto_dg_for_task2_CPactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` may be invalid.\r\n - Variable `auto_dg_for_task2_LATt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` may be invalid.\r\n - Variable `auto_dg_for_task2_k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` may be invalid.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` may be invalid.\r\n - Variable `auto_dg_for_task2_Cell__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_7_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_8_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_9_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_10_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Theinmozhi_2018.sedml` may be invalid.\r\n - Model `model` may be invalid.\r\n - The model file `Theinmozhi_2018.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-7 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKinactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ZAP70 / (ZAP70 + ZAP70i + ZAP70a1 + ZAP70a2) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'PI3K / (PI3Kb + PI3K) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '6e-6 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'SHP2 / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'CPactive / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Cell * Equation_for_PD1_activation(Kp_pd1, LCKactive, PD1, KMp_pd1, PD1p1, PD1p2, LCKt, k)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD3z_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD28_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_SHP2_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_PI3K_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_ZAP70_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y315' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y93' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y505' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y394' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LAT_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_active' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_inactive' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_switch' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ModelValue_0' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` may be invalid.\r\n - Variable `p1_perc_PI3K_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` may be invalid.\r\n - Variable `p2_perc_ZAP70_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` may be invalid.\r\n - Variable `p3_perc_LCK_active_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` may be invalid.\r\n - Variable `p3_perc_LCK_inactive_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` may be invalid.\r\n - Variable `p4_SLP76a_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` may be invalid.\r\n - Variable `p5_ZAP70a2_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` may be invalid.\r\n - Variable `auto_dg_for_task2_CPactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` may be invalid.\r\n - Variable `auto_dg_for_task2_LATt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` may be invalid.\r\n - Variable `auto_dg_for_task2_k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` may be invalid.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` may be invalid.\r\n - Variable `auto_dg_for_task2_Cell__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_7_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_8_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_9_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_10_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "libsbmlsim": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.214332, + "exception": { + "message": "`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpv0kzovyl/./Theinmozhi_2018.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` may be invalid.\r\n - The model file `Theinmozhi_2018.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-7 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKinactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ZAP70 / (ZAP70 + ZAP70i + ZAP70a1 + ZAP70a2) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'PI3K / (PI3Kb + PI3K) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '6e-6 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'SHP2 / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'CPactive / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Cell * Equation_for_PD1_activation(Kp_pd1, LCKactive, PD1, KMp_pd1, PD1p1, PD1p2, LCKt, k)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD3z_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD28_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_SHP2_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_PI3K_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_ZAP70_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y315' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y93' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y505' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y394' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LAT_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_active' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_inactive' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_switch' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ModelValue_0' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` may be invalid.\r\n - Variable `p1_perc_PI3K_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` may be invalid.\r\n - Variable `p2_perc_ZAP70_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` may be invalid.\r\n - Variable `p3_perc_LCK_active_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` may be invalid.\r\n - Variable `p3_perc_LCK_inactive_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` may be invalid.\r\n - Variable `p4_SLP76a_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` may be invalid.\r\n - Variable `p5_ZAP70a2_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` may be invalid.\r\n - Variable `auto_dg_for_task2_CPactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` may be invalid.\r\n - Variable `auto_dg_for_task2_LATt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` may be invalid.\r\n - Variable `auto_dg_for_task2_k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` may be invalid.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` may be invalid.\r\n - Variable `auto_dg_for_task2_Cell__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_7_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_8_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_9_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_10_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Theinmozhi_2018.sedml` may be invalid.\r\n - Model `model` may be invalid.\r\n - The model file `Theinmozhi_2018.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-7 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKinactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ZAP70 / (ZAP70 + ZAP70i + ZAP70a1 + ZAP70a2) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'PI3K / (PI3Kb + PI3K) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '6e-6 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'SHP2 / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'CPactive / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Cell * Equation_for_PD1_activation(Kp_pd1, LCKactive, PD1, KMp_pd1, PD1p1, PD1p2, LCKt, k)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD3z_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD28_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_SHP2_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_PI3K_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_ZAP70_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y315' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y93' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y505' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y394' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LAT_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_active' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_inactive' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_switch' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ModelValue_0' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` may be invalid.\r\n - Variable `p1_perc_PI3K_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` may be invalid.\r\n - Variable `p2_perc_ZAP70_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` may be invalid.\r\n - Variable `p3_perc_LCK_active_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` may be invalid.\r\n - Variable `p3_perc_LCK_inactive_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` may be invalid.\r\n - Variable `p4_SLP76a_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` may be invalid.\r\n - Variable `p5_ZAP70a2_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` may be invalid.\r\n - Variable `auto_dg_for_task2_CPactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` may be invalid.\r\n - Variable `auto_dg_for_task2_LATt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` may be invalid.\r\n - Variable `auto_dg_for_task2_k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` may be invalid.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` may be invalid.\r\n - Variable `auto_dg_for_task2_Cell__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_7_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_8_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_9_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_10_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "masspy": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.192383, + "exception": { + "message": "`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mSedmlFeatureNotSupportedWarning\u001b[0m: \u001b[33m`/tmp/tmpsjq8q5mt/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` has warnings.\r\n - Variable `p1_perc_PI3K_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` has warnings.\r\n - Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` has warnings.\r\n - Variable `p3_perc_LCK_active_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` has warnings.\r\n - Variable `p3_perc_LCK_inactive_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` has warnings.\r\n - Variable `p4_SLP76a_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` has warnings.\r\n - Variable `p5_ZAP70a2_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` has warnings.\r\n - Variable `auto_dg_for_task2_LCKt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` has warnings.\r\n - Variable `auto_dg_for_task2_CPactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` has warnings.\r\n - Variable `auto_dg_for_task2_CD28t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` has warnings.\r\n - Variable `auto_dg_for_task2_LATi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` has warnings.\r\n - Variable `auto_dg_for_task2_LATt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` has warnings.\r\n - Variable `auto_dg_for_task2_GADSt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` has warnings.\r\n - Variable `auto_dg_for_task2_CD3t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` has warnings.\r\n - Variable `auto_dg_for_task2_k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` has warnings.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` has warnings.\r\n - Variable `auto_dg_for_task2_Cell__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Theinmozhi_2018.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` has warnings.\r\n - Variable `p1_perc_PI3K_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` has warnings.\r\n - Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` has warnings.\r\n - Variable `p3_perc_LCK_active_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` has warnings.\r\n - Variable `p3_perc_LCK_inactive_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` has warnings.\r\n - Variable `p4_SLP76a_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` has warnings.\r\n - Variable `p5_ZAP70a2_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` has warnings.\r\n - Variable `auto_dg_for_task2_LCKt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` has warnings.\r\n - Variable `auto_dg_for_task2_CPactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` has warnings.\r\n - Variable `auto_dg_for_task2_CD28t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` has warnings.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` has warnings.\r\n - Variable `auto_dg_for_task2_LATi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` has warnings.\r\n - Variable `auto_dg_for_task2_LATt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` has warnings.\r\n - Variable `auto_dg_for_task2_GADSt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` has warnings.\r\n - Variable `auto_dg_for_task2_CD3t__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` has warnings.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` has warnings.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` has warnings.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` has warnings.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` has warnings.\r\n - Variable `auto_dg_for_task2_k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` has warnings.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` has warnings.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` has warnings.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` has warnings.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` has warnings.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` has warnings.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` has warnings.\r\n - Variable `auto_dg_for_task2_Cell__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` has warnings.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` has warnings.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` has warnings.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` has warnings.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` has warnings.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` has warnings.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` has warnings.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` has warnings.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` has warnings.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` has warnings.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` has warnings.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` has warnings.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` has warnings.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "netpyne": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "log_yml": { + "duration": 0.050738, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "neuron": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "log_yml": { + "duration": 0.067088, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpb8dynd_6/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "opencor": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "log_yml": { + "duration": 0.081607, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpwe1w_br6/./Theinmozhi_2018.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pyneuroml": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "log_yml": { + "duration": 0.057649, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpyztwzgfb/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pysces": { + "exception_message": "", + "log_yml": { + "duration": 5.233583, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp21yngzy2/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Theinmozhi_2018.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp21yngzy2/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 4.715052, + "exception": null, + "location": "Theinmozhi_2018.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 5 plots:\r\n Theinmozhi_2018.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 120 data sets\r\n Plots (5):\r\n plot_10_task2: 1 curves\r\n plot_6_task2: 1 curves\r\n plot_7_task2: 1 curves\r\n plot_8_task2: 2 curves\r\n plot_9_task2: 1 curves\r\n\r\nExecuting SED-ML file 1: Theinmozhi_2018.sedml ...\r\n Found 1 tasks and 6 outputs:\r\n Tasks:\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_10_task2`\r\n `plot_6_task2`\r\n `plot_7_task2`\r\n `plot_8_task2`\r\n `plot_9_task2`\r\n Executing task 1: `task2`\r\n Executing simulation ...Info: single compartment model: locating \"CP2_DP_CP1\" in default compartment\r\nInfo: single compartment model: locating \"CP1_Diss_PD1_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"CD28i_P_CD28a\" in default compartment\r\nInfo: single compartment model: locating \"CD28a_DP_CD28i\" in default compartment\r\nInfo: single compartment model: locating \"CD28a_Bd_PI3K\" in default compartment\r\nInfo: single compartment model: locating \"CD3i_P_CD3a\" in default compartment\r\nInfo: single compartment model: locating \"CD3a_DP_CD3i\" in default compartment\r\nInfo: single compartment model: locating \"CD3a_Bd_ZAP70\" in default compartment\r\nInfo: single compartment model: locating \"ZAP70i_P_ZAP70a1\" in default compartment\r\nInfo: single compartment model: locating \"ZAP70a1_P_ZAP70a2\" in default compartment\r\nInfo: single compartment model: locating \"LATi_P_LATa\" in default compartment\r\nInfo: single compartment model: locating \"LATa_Bd_GADS\" in default compartment\r\nInfo: single compartment model: locating \"GADSa_Bd_SLP76\" in default compartment\r\nInfo: single compartment model: locating \"SLP76i_P_SLC76a\" in default compartment\r\nWriting file: /tmp/tmplbpihl9w.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpm2swa43p.xml\r\nout: /tmp/tmplbpihl9w.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmplbpihl9w.psc loading ..... \r\nParsing file: /tmp/tmplbpihl9w.psc\r\nWarning: species \"LCKinactive\" (fixed) does not occur in any reaction\r\nWarning: species \"CD3t\" (fixed) does not occur in any reaction\r\nWarning: species \"SLP76t\" (fixed) does not occur in any reaction\r\nWarning: species \"GADSt\" (fixed) does not occur in any reaction\r\nWarning: species \"LATt\" (fixed) does not occur in any reaction\r\nWarning: species \"ZAP70t\" (fixed) does not occur in any reaction\r\nWarning: species \"PI3Kt\" (fixed) does not occur in any reaction\r\nWarning: species \"CD28t\" (fixed) does not occur in any reaction\r\nWarning: species \"CPactive\" (fixed) does not occur in any reaction\r\nWarning: species \"LCKactive\" (fixed) does not occur in any reaction\r\nWarning: species \"LCKt\" (fixed) does not occur in any reaction\r\nInfo: \"CD28t\" has been initialised but does not occur in a rate equation\r\nInfo: \"PI3Kt\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70t\" has been initialised but does not occur in a rate equation\r\nInfo: \"LATt\" has been initialised but does not occur in a rate equation\r\nInfo: \"GADSt\" has been initialised but does not occur in a rate equation\r\nInfo: \"SLP76t\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD3t\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCKinactive\" has been initialised but does not occur in a rate equation\r\nInfo: \"Kdpa_yiya\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_SHP2_bound\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD3z_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD28_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_SHP2_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_PI3K_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_ZAP70_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70_phos_Y315\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70_phos_Y93\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_phos_Y505\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_phos_Y394\" has been initialised but does not occur in a rate equation\r\nInfo: \"LAT_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_LCK_active\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_LCK_inactive\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_switch\" has been initialised but does not occur in a rate equation\r\nInfo: \"ModelValue_0\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . . . done.\r\nCalculating K matrix . . . . . . . . . . . done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 101 points: 0.10462474822998047\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 6 outputs ...\r\n Generating output 1: `plot_6_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `plot_7_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `plot_8_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `plot_9_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 5: `plot_10_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 6: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.324473, + "exception": null, + "id": "plot_6_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p2_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.139231, + "exception": null, + "id": "plot_7_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p3_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p3_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.171815, + "exception": null, + "id": "plot_8_task2", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p4_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.138369, + "exception": null, + "id": "plot_9_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p5_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.160614, + "exception": null, + "id": "plot_10_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_PI3K_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_ZAP70_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_LCK_active", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_LCK_inactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKpi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CPactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3K", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3Kb", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3Kt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKinactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_yiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpi_yi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpi_yiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_ya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_pi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpi_i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpi_ya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpa_i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpa_yi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_pd1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_pd1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd1_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd2_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cp2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMdp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_pi3k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_pi3k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMdp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp1_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp2_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_lat", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_gads", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_gads", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_SHP2_bound", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3z_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_SHP2_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70_phos_Y315", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70_phos_Y93", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_phos_Y505", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_phos_Y394", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LAT_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_switch", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ModelValue_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_P_LCKyi_inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_P_LCKya_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya_P_LCKyiya_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi_P_LCKpi_inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya_DP_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya_DP_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi_DP_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya_DP_LCKya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKpi_DP_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1_P_PD1p1_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1_P_PD1p2_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1_Bd_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p2_Bd_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2_Diss_SHP2_PD1p1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2_DP_CP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP1_Diss_PD1_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28i_P_CD28a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a_DP_CD28i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a_Bd_PI3K", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3i_P_CD3a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a_DP_CD3i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a_Bd_ZAP70", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70i_P_ZAP70a1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a1_P_ZAP70a2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATi_P_LATa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATa_Bd_GADS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSa_Bd_SLP76", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76i_P_SLC76a", + "status": "SUCCEEDED" + } + ], + "duration": 0.361611, + "exception": null, + "id": "autogen_report_for_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": null, + "duration": 2.790847, + "exception": null, + "id": "task2", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CPactive__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PI3Kt__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_KMp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p3_perc_LCK_inactive_2_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kpi_i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Ka_slp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_KMp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_perc_SHP2_bound__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Ka_shp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd2_shp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdpa_ya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LATt__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd1_shp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdpa_pi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp_lat__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PI3Kb__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Ka_gads__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdpi_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kpa_i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd_slp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Ka_zap__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCK_switch__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKinactive__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Ka_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kpi_ya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdpa_yiya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3z_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_KMdp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_GADSa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LATi_P_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyiya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd_zap__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp_slp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p5_ZAP70a2_1_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LAT_phosphorylated__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LATa_Bd_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_KMp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p1_perc_PI3K_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p3_perc_LCK_active_1_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdpi_yi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKpi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_KMdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p4_SLP76a_1_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3i_P_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_GADSt__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCK_phos_Y505__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp1_zap__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SLP76__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd_pi3k__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SLP76i__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKya__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_GADS__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCK_phos_Y394__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3t__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CP2_DP_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CP2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LATi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SLP76t__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_perc_SHP2_free__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28i_P_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kpa_yi__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp_cd28__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKt__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_k__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKactive__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PI3K__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28t__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\nCheck SBML support is at action level 2\r\nSBML file is L2V4\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmp75era17h.xml\r\n*******************************************************************\r\n\r\nParameter units ignored for parameters:\r\n['Kdpa_yiya', 'Kdpi_yi', 'Kdpi_yiya', 'Kdpa_ya', 'Kdpa_pi', 'Kpi_i', 'Kpi_ya', 'Kpa_i', 'Kpa_yi', 'Kp_pd1', 'KMp_pd1', 'Ka_shp', 'Kd1_shp', 'Kd2_shp', 'Kdp_cp2', 'Kp_cd28', 'KMp_cd28', 'Kdp_cd28', 'KMdp_cd28', 'Ka_pi3k', 'Kd_pi3k', 'Kp_cd3', 'KMp_cd3', 'Kdp_cd3', 'KMdp_cd3', 'Ka_zap', 'Kd_zap', 'Kp1_zap', 'Kp2_zap', 'Kp_lat', 'Ka_gads', 'Kd_gads', 'Ka_slp', 'Kd_slp', 'Kp_slp', 'perc_SHP2_bound'] \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"LCK_P_LCKyi_inh\" in default compartment\r\nInfo: single compartment model: locating \"LCK_P_LCKya_act\" in default compartment\r\nInfo: single compartment model: locating \"LCKya_P_LCKyiya_act\" in default compartment\r\nInfo: single compartment model: locating \"LCKyi_P_LCKpi_inh\" in default compartment\r\nInfo: single compartment model: locating \"LCKyiya_DP_LCKyi\" in default compartment\r\nInfo: single compartment model: locating \"LCKya_DP_LCKi\" in default compartment\r\nInfo: single compartment model: locating \"LCKyi_DP_LCKi\" in default compartment\r\nInfo: single compartment model: locating \"LCKyiya_DP_LCKya\" in default compartment\r\nInfo: single compartment model: locating \"LCKpi_DP_LCKyi\" in default compartment\r\nInfo: single compartment model: locating \"PD1_P_PD1p1_act\" in default compartment\r\nInfo: single compartment model: locating \"PD1p1_P_PD1p2_act\" in default compartment\r\nInfo: single compartment model: locating \"PD1p1_Bd_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"PD1p2_Bd_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"CP2_Diss_SHP2_PD1p1\" in default compartment\r\nInfo: single compartment model: locating \"CP2_DP_CP1\" in default compartment\r\nInfo: single compartment model: locating \"CP1_Diss_PD1_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"CD28i_P_CD28a\" in default compartment\r\nInfo: single compartment model: locating \"CD28a_DP_CD28i\" in default compartment\r\nInfo: single compartment model: locating \"CD28a_Bd_PI3K\" in default compartment\r\nInfo: single compartment model: locating \"CD3i_P_CD3a\" in default compartment\r\nInfo: single compartment model: locating \"CD3a_DP_CD3i\" in default compartment\r\nInfo: single compartment model: locating \"CD3a_Bd_ZAP70\" in default compartment\r\nInfo: single compartment model: locating \"ZAP70i_P_ZAP70a1\" in default compartment\r\nInfo: single compartment model: locating \"ZAP70a1_P_ZAP70a2\" in default compartment\r\nInfo: single compartment model: locating \"LATi_P_LATa\" in default compartment\r\nInfo: single compartment model: locating \"LATa_Bd_GADS\" in default compartment\r\nInfo: single compartment model: locating \"GADSa_Bd_SLP76\" in default compartment\r\nInfo: single compartment model: locating \"SLP76i_P_SLC76a\" in default compartment\r\nWriting file: /tmp/tmptwr2y1mz.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmp75era17h.xml\r\nout: /tmp/tmptwr2y1mz.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmptwr2y1mz.psc loading ..... \r\nParsing file: /tmp/tmptwr2y1mz.psc\r\nWarning: species \"LCKinactive\" (fixed) does not occur in any reaction\r\nWarning: species \"CD3t\" (fixed) does not occur in any reaction\r\nWarning: species \"SLP76t\" (fixed) does not occur in any reaction\r\nWarning: species \"GADSt\" (fixed) does not occur in any reaction\r\nWarning: species \"LATt\" (fixed) does not occur in any reaction\r\nWarning: species \"ZAP70t\" (fixed) does not occur in any reaction\r\nWarning: species \"PI3Kt\" (fixed) does not occur in any reaction\r\nWarning: species \"CD28t\" (fixed) does not occur in any reaction\r\nWarning: species \"CPactive\" (fixed) does not occur in any reaction\r\nWarning: species \"LCKactive\" (fixed) does not occur in any reaction\r\nWarning: species \"LCKt\" (fixed) does not occur in any reaction\r\nInfo: \"CD28t\" has been initialised but does not occur in a rate equation\r\nInfo: \"PI3Kt\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70t\" has been initialised but does not occur in a rate equation\r\nInfo: \"LATt\" has been initialised but does not occur in a rate equation\r\nInfo: \"GADSt\" has been initialised but does not occur in a rate equation\r\nInfo: \"SLP76t\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD3t\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCKinactive\" has been initialised but does not occur in a rate equation\r\nInfo: \"Kdpa_yiya\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_SHP2_bound\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD3z_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD28_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_SHP2_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_PI3K_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_ZAP70_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70_phos_Y315\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70_phos_Y93\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_phos_Y505\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_phos_Y394\" has been initialised but does not occur in a rate equation\r\nInfo: \"LAT_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_LCK_active\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_LCK_inactive\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_switch\" has been initialised but does not occur in a rate equation\r\nInfo: \"ModelValue_0\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . . . done.\r\nCalculating K matrix . . . . . . . . . . . done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 101 points: 0.11254334449768066\r\nCheck SBML support is at action level 2\r\nSBML file is L2V4\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpm2swa43p.xml\r\n*******************************************************************\r\n\r\nParameter units ignored for parameters:\r\n['Kdpa_yiya', 'Kdpi_yi', 'Kdpi_yiya', 'Kdpa_ya', 'Kdpa_pi', 'Kpi_i', 'Kpi_ya', 'Kpa_i', 'Kpa_yi', 'Kp_pd1', 'KMp_pd1', 'Ka_shp', 'Kd1_shp', 'Kd2_shp', 'Kdp_cp2', 'Kp_cd28', 'KMp_cd28', 'Kdp_cd28', 'KMdp_cd28', 'Ka_pi3k', 'Kd_pi3k', 'Kp_cd3', 'KMp_cd3', 'Kdp_cd3', 'KMdp_cd3', 'Ka_zap', 'Kd_zap', 'Kp1_zap', 'Kp2_zap', 'Kp_lat', 'Ka_gads', 'Kd_gads', 'Ka_slp', 'Kd_slp', 'Kp_slp', 'perc_SHP2_bound'] \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"LCK_P_LCKyi_inh\" in default compartment\r\nInfo: single compartment model: locating \"LCK_P_LCKya_act\" in default compartment\r\nInfo: single compartment model: locating \"LCKya_P_LCKyiya_act\" in default compartment\r\nInfo: single compartment model: locating \"LCKyi_P_LCKpi_inh\" in default compartment\r\nInfo: single compartment model: locating \"LCKyiya_DP_LCKyi\" in default compartment\r\nInfo: single compartment model: locating \"LCKya_DP_LCKi\" in default compartment\r\nInfo: single compartment model: locating \"LCKyi_DP_LCKi\" in default compartment\r\nInfo: single compartment model: locating \"LCKyiya_DP_LCKya\" in default compartment\r\nInfo: single compartment model: locating \"LCKpi_DP_LCKyi\" in default compartment\r\nInfo: single compartment model: locating \"PD1_P_PD1p1_act\" in default compartment\r\nInfo: single compartment model: locating \"PD1p1_P_PD1p2_act\" in default compartment\r\nInfo: single compartment model: locating \"PD1p1_Bd_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"PD1p2_Bd_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"CP2_Diss_SHP2_PD1p1\" in default compartment\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "rbapy": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.201855, + "exception": { + "message": "`/root/in/Theinmozhi_2018.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmposscluog/./Theinmozhi_2018.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` may be invalid.\r\n - The model file `Theinmozhi_2018.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-7 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKinactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ZAP70 / (ZAP70 + ZAP70i + ZAP70a1 + ZAP70a2) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'PI3K / (PI3Kb + PI3K) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '6e-6 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'SHP2 / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'CPactive / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Cell * Equation_for_PD1_activation(Kp_pd1, LCKactive, PD1, KMp_pd1, PD1p1, PD1p2, LCKt, k)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD3z_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD28_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_SHP2_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_PI3K_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_ZAP70_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y315' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y93' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y505' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y394' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LAT_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_active' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_inactive' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_switch' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ModelValue_0' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` may be invalid.\r\n - Variable `p1_perc_PI3K_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` may be invalid.\r\n - Variable `p2_perc_ZAP70_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` may be invalid.\r\n - Variable `p3_perc_LCK_active_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` may be invalid.\r\n - Variable `p3_perc_LCK_inactive_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` may be invalid.\r\n - Variable `p4_SLP76a_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` may be invalid.\r\n - Variable `p5_ZAP70a2_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` may be invalid.\r\n - Variable `auto_dg_for_task2_CPactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` may be invalid.\r\n - Variable `auto_dg_for_task2_LATt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` may be invalid.\r\n - Variable `auto_dg_for_task2_k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` may be invalid.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` may be invalid.\r\n - Variable `auto_dg_for_task2_Cell__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_7_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_8_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_9_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_10_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Theinmozhi_2018.sedml` may be invalid.\r\n - Model `model` may be invalid.\r\n - The model file `Theinmozhi_2018.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1.2e-7 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '2.4e-5 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKinactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCKactive / (LCKi + LCKpi + LCKya + LCKyi + LCKyiya) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ZAP70 / (ZAP70 + ZAP70i + ZAP70a1 + ZAP70a2) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'PI3K / (PI3Kb + PI3K) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '6e-6 * ModelValue_0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'SHP2 / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'CPactive / (SHP2 + CPactive) * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Cell * Equation_for_PD1_activation(Kp_pd1, LCKactive, PD1, KMp_pd1, PD1p1, PD1p2, LCKt, k)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD3z_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CD28_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_SHP2_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_PI3K_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_ZAP70_free' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y315' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ZAP70_phos_Y93' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y505' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_phos_Y394' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LAT_phosphorylated' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_active' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'perc_LCK_inactive' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'LCK_switch' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ModelValue_0' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_PI3K_free_1_task2` may be invalid.\r\n - Variable `p1_perc_PI3K_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_ZAP70_free_1_task2` may be invalid.\r\n - Variable `p2_perc_ZAP70_free_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_active_1_task2` may be invalid.\r\n - Variable `p3_perc_LCK_active_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `perc_LCK_inactive_2_task2` may be invalid.\r\n - Variable `p3_perc_LCK_inactive_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `SLP76a_1_task2` may be invalid.\r\n - Variable `p4_SLP76a_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `ZAP70a2_1_task2` may be invalid.\r\n - Variable `p5_ZAP70a2_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKt` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CPactive` may be invalid.\r\n - Variable `auto_dg_for_task2_CPactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kb` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kb__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PI3Kt` may be invalid.\r\n - Variable `auto_dg_for_task2_PI3Kt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70t` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATt` may be invalid.\r\n - Variable `auto_dg_for_task2_LATt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSt` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76t` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3t` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3t__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKinactive` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKinactive__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpi_yiya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpi_yiya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdpa_pi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdpa_pi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpi_ya` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpi_ya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_i` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kpa_yi` may be invalid.\r\n - Variable `auto_dg_for_task2_Kpa_yi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_k` may be invalid.\r\n - Variable `auto_dg_for_task2_k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_pd1` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_pd1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd1_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd1_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd2_shp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd2_shp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cp2` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cp2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd28` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd28__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_pi3k` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_pi3k__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_Kdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_KMdp_cd3` may be invalid.\r\n - Variable `auto_dg_for_task2_KMdp_cd3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp1_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp1_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp2_zap` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp2_zap__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_lat` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_lat__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_gads` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_gads__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Ka_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Ka_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kd_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kd_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Kp_slp` may be invalid.\r\n - Variable `auto_dg_for_task2_Kp_slp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_bound` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_bound__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3z_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3z_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_perc_SHP2_free` may be invalid.\r\n - Variable `auto_dg_for_task2_perc_SHP2_free__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y315` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y315__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70_phos_Y93` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70_phos_Y93__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y505` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y505__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_phos_Y394` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_phos_Y394__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LAT_phosphorylated` may be invalid.\r\n - Variable `auto_dg_for_task2_LAT_phosphorylated__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_switch` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_switch__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ModelValue_0` may be invalid.\r\n - Variable `auto_dg_for_task2_ModelValue_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Cell` may be invalid.\r\n - Variable `auto_dg_for_task2_Cell__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKyi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKyi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCK_P_LCKya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCK_P_LCKya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_P_LCKyiya_act` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_P_LCKyiya_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_P_LCKpi_inh` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKya_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKya_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyi_DP_LCKi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyi_DP_LCKi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKyiya_DP_LCKya` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKyiya_DP_LCKya__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LCKpi_DP_LCKyi` may be invalid.\r\n - Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1_P_PD1p1_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1_P_PD1p1_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_P_PD1p2_act` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_P_PD1p2_act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p1_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p1_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_PD1p2_Bd_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_PD1p2_Bd_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_Diss_SHP2_PD1p1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP2_DP_CP1` may be invalid.\r\n - Variable `auto_dg_for_task2_CP2_DP_CP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CP1_Diss_PD1_SHP2` may be invalid.\r\n - Variable `auto_dg_for_task2_CP1_Diss_PD1_SHP2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28i_P_CD28a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28i_P_CD28a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_DP_CD28i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_DP_CD28i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD28a_Bd_PI3K` may be invalid.\r\n - Variable `auto_dg_for_task2_CD28a_Bd_PI3K__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3i_P_CD3a` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3i_P_CD3a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_DP_CD3i` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_DP_CD3i__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CD3a_Bd_ZAP70` may be invalid.\r\n - Variable `auto_dg_for_task2_CD3a_Bd_ZAP70__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70i_P_ZAP70a1` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70i_P_ZAP70a1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ZAP70a1_P_ZAP70a2` may be invalid.\r\n - Variable `auto_dg_for_task2_ZAP70a1_P_ZAP70a2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATi_P_LATa` may be invalid.\r\n - Variable `auto_dg_for_task2_LATi_P_LATa__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_LATa_Bd_GADS` may be invalid.\r\n - Variable `auto_dg_for_task2_LATa_Bd_GADS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_GADSa_Bd_SLP76` may be invalid.\r\n - Variable `auto_dg_for_task2_GADSa_Bd_SLP76__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SLP76i_P_SLC76a` may be invalid.\r\n - Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_6_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_7_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_8_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_9_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `plot_10_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "smoldyn": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", + "log_yml": {}, + "detailed_error_log": {} + }, + "tellurium": { + "exception_message": "", + "log_yml": { + "duration": 2.683102, + "exception": null, + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmp8k26xsn5/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Theinmozhi_2018.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmp8k26xsn5/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Output `plot_6_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_7_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_8_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_9_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `plot_10_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n\r\n", + "sedDocuments": [ + { + "duration": 2.162615, + "exception": null, + "location": "Theinmozhi_2018.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 5 plots:\r\n Theinmozhi_2018.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 120 data sets\r\n Plots (5):\r\n plot_10_task2: 1 curves\r\n plot_6_task2: 1 curves\r\n plot_7_task2: 1 curves\r\n plot_8_task2: 2 curves\r\n plot_9_task2: 1 curves\r\n\r\nExecuting SED-ML file 1: Theinmozhi_2018.sedml ...\r\n Found 1 tasks and 6 outputs:\r\n Tasks:\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_10_task2`\r\n `plot_6_task2`\r\n `plot_7_task2`\r\n `plot_8_task2`\r\n `plot_9_task2`\r\n Executing task 1: `task2`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 6 outputs ...\r\n Generating output 1: `plot_6_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `plot_7_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `plot_8_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `plot_9_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 5: `plot_10_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 6: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.271984, + "exception": null, + "id": "plot_6_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p2_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.212757, + "exception": null, + "id": "plot_7_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p3_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p3_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.365539, + "exception": null, + "id": "plot_8_task2", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning:\r\n\r\n\u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p4_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.21375, + "exception": null, + "id": "plot_9_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p5_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.207144, + "exception": null, + "id": "plot_10_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_PI3K_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_ZAP70_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_LCK_active", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_LCK_inactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKpi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CPactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3K", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3Kb", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3Kt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKinactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_yiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpi_yi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpi_yiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_ya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_pi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpi_i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpi_ya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpa_i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpa_yi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_pd1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_pd1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd1_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd2_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cp2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMdp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_pi3k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_pi3k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMdp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp1_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp2_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_lat", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_gads", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_gads", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_SHP2_bound", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3z_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_SHP2_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70_phos_Y315", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70_phos_Y93", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_phos_Y505", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_phos_Y394", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LAT_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_switch", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ModelValue_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_P_LCKyi_inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_P_LCKya_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya_P_LCKyiya_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi_P_LCKpi_inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya_DP_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya_DP_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi_DP_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya_DP_LCKya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKpi_DP_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1_P_PD1p1_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1_P_PD1p2_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1_Bd_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p2_Bd_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2_Diss_SHP2_PD1p1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2_DP_CP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP1_Diss_PD1_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28i_P_CD28a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a_DP_CD28i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a_Bd_PI3K", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3i_P_CD3a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a_DP_CD3i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a_Bd_ZAP70", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70i_P_ZAP70a1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a1_P_ZAP70a2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATi_P_LATa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATa_Bd_GADS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSa_Bd_SLP76", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76i_P_SLC76a", + "status": "SUCCEEDED" + } + ], + "duration": 0.195382, + "exception": null, + "id": "autogen_report_for_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": null, + "duration": 0.277226, + "exception": null, + "id": "task2", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: 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Variable `auto_dg_for_task2_Kp2_zap__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kp_pd1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKyi_P_LCKpi_inh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CP1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD28a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_PD1p2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LATa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SLP76i_P_SLC76a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ModelValue_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kd_gads__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_KMp_cd3__x` 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Variable `auto_dg_for_task2_Kdp_cd3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CD3a__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Kdp_cp2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p2_perc_ZAP70_free_1_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ZAP70t__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_LCKpi_DP_LCKyi__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mModel `model` may be invalid.\r\n - The model file `/tmp/tmp8k26xsn5/./Theinmozhi_2018.xml` has warnings.\r\n - 13 warnings of type SBML unit consistency (99505). The following is the first warning at line 2568, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'LCK_switch' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 15 warnings of type Modeling practice (80701). The following is the first warning at line 1946, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning:\r\n\r\n\u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mAlgorithm parameter with KiSAO id 'KISAO_0000216' was ignored because it is not supported. Parameter must have one of the following KiSAO ids:\r\n - KISAO_0000209: relative_tolerance (relative tolerance)\r\n - KISAO_0000211: absolute_tolerance (absolute tolerance)\r\n - KISAO_0000571: absolute_tolerance_adjustment_factor (absolute tolerance adjustment factor)\r\n - KISAO_0000220: maximum_bdf_order (Maximum Backward Differentiation Formula (BDF) order)\r\n - KISAO_0000219: maximum_adams_order (Maximum Adams order)\r\n - KISAO_0000415: maximum_num_steps (Maximum number of steps)\r\n - KISAO_0000467: maximum_time_step (Maximum time step)\r\n - KISAO_0000485: minimum_time_step (Minimum time step)\r\n - KISAO_0000559: initial_time_step (Initial time step)\r\n - KISAO_0000671: stiff (Stiff)\r\n - KISAO_0000670: multiple_steps (Multiple steps)\u001b[0m\r\n\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "vcell": { + "exception_message": "Command '-i '/root/in/Theinmozhi_2018.omex' -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1", + "log_yml": { + "duration": 6, + "exception": null, + "output": "Processing Theinmozhi_2018.sedml. Done", + "sedDocuments": [ + { + "duration": null, + "exception": { + "message": "Unable to initialize bioModel for the given selection cannot set float node to NaNcannot set float node to NaNFailure executing the sed document.", + "type": "RuntimeException" + }, + "location": "Theinmozhi_2018.sedml", + "output": "Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating HDF5 file...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "QUEUED" + } + ], + "duration": null, + "exception": null, + "id": "plot_6_task2", + "output": null, + "skipReason": null, + "status": "QUEUED" + }, + { + "curves": [ + { + "id": "p2_curve_1_task2", + "status": "QUEUED" + } + ], + "duration": null, + "exception": null, + "id": "plot_7_task2", + "output": null, + "skipReason": null, + "status": "QUEUED" + }, + { + "curves": [ + { + "id": "p3_curve_1_task2", + "status": "QUEUED" + }, + { + "id": "p3_curve_2_task2", + "status": "QUEUED" + } + ], + "duration": null, + "exception": null, + "id": "plot_8_task2", + "output": null, + "skipReason": null, + "status": "QUEUED" + }, + { + "curves": [ + { + "id": "p4_curve_1_task2", + "status": "QUEUED" + } + ], + "duration": null, + "exception": null, + "id": "plot_9_task2", + "output": null, + "skipReason": null, + "status": "QUEUED" + }, + { + "curves": [ + { + "id": "p5_curve_1_task2", + "status": "QUEUED" + } + ], + "duration": null, + "exception": null, + "id": "plot_10_task2", + "output": null, + "skipReason": null, + "status": "QUEUED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "QUEUED" + }, + { + "id": "autogen_task2_perc_PI3K_free", + "status": "QUEUED" + }, + { + "id": "autogen_task2_perc_ZAP70_free", + "status": "QUEUED" + }, + { + "id": "autogen_task2_perc_LCK_active", + "status": "QUEUED" + }, + { + "id": "autogen_task2_perc_LCK_inactive", + "status": "QUEUED" + }, + { + "id": "autogen_task2_SLP76a", + "status": "QUEUED" + }, + { + "id": "autogen_task2_ZAP70a2", + "status": "QUEUED" + }, + { + "id": "autogen_task2_LCKi", + "status": "QUEUED" + }, + { + "id": "autogen_task2_LCKyi", + "status": "QUEUED" + }, + { + "id": "autogen_task2_LCKya", + "status": "QUEUED" + }, + { + "id": "autogen_task2_LCKyiya", + "status": "QUEUED" + }, + { + "id": "autogen_task2_LCKpi", + "status": "QUEUED" + }, + { + "id": "autogen_task2_LCKt", + "status": "QUEUED" + }, + { + "id": "autogen_task2_LCKactive", + "status": "QUEUED" + }, + { + "id": "autogen_task2_PD1", + "status": "QUEUED" + }, + { + "id": "autogen_task2_PD1p1", + "status": "QUEUED" + }, + { + "id": "autogen_task2_PD1p2", + "status": "QUEUED" + }, + { + "id": "autogen_task2_CP1", + "status": "QUEUED" + }, + { + "id": "autogen_task2_SHP2", + "status": "QUEUED" + }, + { + "id": "autogen_task2_CP2", + "status": "QUEUED" + }, + { + "id": "autogen_task2_CPactive", + "status": "QUEUED" + }, + { + "id": "autogen_task2_CD28a", + "status": "QUEUED" + }, + { + "id": "autogen_task2_CD28i", + "status": "QUEUED" + }, + { + "id": "autogen_task2_PI3K", + "status": "QUEUED" + }, + { + "id": "autogen_task2_PI3Kb", + "status": "QUEUED" + }, + { + "id": "autogen_task2_CD28t", + "status": "QUEUED" + }, + { + "id": "autogen_task2_CD3a", + "status": "QUEUED" + }, + { + "id": "autogen_task2_CD3i", + "status": "QUEUED" + }, + { + "id": "autogen_task2_ZAP70a1", + "status": "QUEUED" + }, + 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"ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpsc9ck7p3/./Theinmozhi_2018.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + } +} \ No newline at end of file diff --git a/BioModels/BIOMD0000000724/tests/results_remote.json b/BioModels/BIOMD0000000724/tests/results_remote.json new file mode 100644 index 00000000..04b59548 --- /dev/null +++ b/BioModels/BIOMD0000000724/tests/results_remote.json @@ -0,0 +1,3984 @@ +{ + "amici": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc64e10bb4455d6187637", + "download": "https://api.biosimulations.org/results/674dc64e10bb4455d6187637/download", + "logs": "https://api.biosimulations.org/logs/674dc64e10bb4455d6187637?includeOutput=true", + "log_yml": { + "duration": 2.773027, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Cannot turn parameter ModelValue_0 into a constant/fixed parameter since it either has an initial assignment or is the target of an assignment or rate rule.\n \n target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='LCK_switch'] is not a valid XPath to an attribute of a model element", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 2.257669, + "exception": { + "message": "The SED document did not execute successfully:\n\n Cannot turn parameter ModelValue_0 into a constant/fixed parameter since it either has an initial assignment or is the target of an assignment or rate rule.\n\n target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='LCK_switch'] is not a valid XPath to an attribute of a model element", + "type": "SedmlExecutionError" + }, + "location": "Theinmozhi_2018.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 5 plots:\r\n Theinmozhi_2018.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 120 data sets\r\n Plots (5):\r\n plot_10_task2: 1 curves\r\n plot_6_task2: 1 curves\r\n plot_7_task2: 1 curves\r\n plot_8_task2: 2 curves\r\n plot_9_task2: 1 curves\r\n\r\nExecuting SED-ML file 1: Theinmozhi_2018.sedml ...\r\n Found 2 tasks and 6 outputs:\r\n Tasks:\r\n `task1`\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_10_task2`\r\n `plot_6_task2`\r\n `plot_7_task2`\r\n `plot_8_task2`\r\n `plot_9_task2`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 6 outputs ...\r\n Generating output 1: `plot_6_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `plot_7_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `plot_8_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `plot_9_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 5: `plot_10_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 6: `autogen_report_for_task2` ... \u001b[36mqueued\u001b[0m\r\n Executing task 2: `task2`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 6 outputs ...\r\n Generating output 1: `plot_6_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `plot_7_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `plot_8_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `plot_9_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 5: `plot_10_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 6: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SKIPPED" + } + ], + "duration": 0.10247, + "exception": null, + "id": "plot_6_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "p2_curve_1_task2", + "status": "SKIPPED" + } + ], + "duration": 0.098795, + "exception": null, + "id": "plot_7_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "p3_curve_1_task2", + "status": "SKIPPED" + }, + { + "id": "p3_curve_2_task2", + "status": "SKIPPED" + } + ], + "duration": 0.103154, + "exception": null, + "id": "plot_8_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "p4_curve_1_task2", + "status": "SKIPPED" + } + ], + "duration": 0.108454, + "exception": null, + "id": "plot_9_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "p5_curve_1_task2", + "status": "SKIPPED" + } + ], + "duration": 0.102384, + "exception": null, + "id": "plot_10_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_perc_PI3K_free", + "status": "SKIPPED" + }, + { + "id": 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"status": "SKIPPED" + }, + { + "id": "autogen_task2_Kpi_ya", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kpa_i", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kpa_yi", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_k", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kp_pd1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_KMp_pd1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Ka_shp", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kd1_shp", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kd2_shp", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kdp_cp2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kp_cd28", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_KMp_cd28", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Kdp_cd28", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_KMdp_cd28", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Ka_pi3k", + "status": "SKIPPED" + }, + { + "id": 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}, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "boolnet": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc653ef911d5d45259ac2", + "download": "https://api.biosimulations.org/results/674dc653ef911d5d45259ac2/download", + "logs": "https://api.biosimulations.org/logs/674dc653ef911d5d45259ac2?includeOutput=true", + "log_yml": { + "duration": 0.301955, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cbmpy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc655261553b9bc253e9b", + "download": "https://api.biosimulations.org/results/674dc655261553b9bc253e9b/download", + "logs": 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Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cobrapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc658261553b9bc253ea0", + "download": "https://api.biosimulations.org/results/674dc658261553b9bc253ea0/download", + "logs": "https://api.biosimulations.org/logs/674dc658261553b9bc253ea0?includeOutput=true", + "log_yml": { + "duration": 0.254102, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "copasi": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc65aef911d5d45259acd", + "download": "https://api.biosimulations.org/results/674dc65aef911d5d45259acd/download", + "logs": "https://api.biosimulations.org/logs/674dc65aef911d5d45259acd?includeOutput=true", + "log_yml": { + "duration": 2.764347, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 2.259948, + "exception": null, + "location": "Theinmozhi_2018.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 5 plots:\r\n Theinmozhi_2018.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 120 data sets\r\n Plots (5):\r\n plot_10_task2: 1 curves\r\n plot_6_task2: 1 curves\r\n plot_7_task2: 1 curves\r\n plot_8_task2: 2 curves\r\n plot_9_task2: 1 curves\r\n\r\nExecuting SED-ML file 1: Theinmozhi_2018.sedml ...\r\n Found 1 tasks and 6 outputs:\r\n Tasks:\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_10_task2`\r\n `plot_6_task2`\r\n `plot_7_task2`\r\n `plot_8_task2`\r\n `plot_9_task2`\r\n Executing task 1: `task2`\r\n Executing simulation ...woohoo!\r\nwoohoo!\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 6 outputs ...\r\n Generating output 1: `plot_6_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `plot_7_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `plot_8_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `plot_9_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 5: `plot_10_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 6: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.431834, + "exception": null, + "id": "plot_6_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p2_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.144277, + "exception": null, + "id": "plot_7_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p3_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p3_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.159484, + "exception": null, + "id": "plot_8_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p4_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.131023, + "exception": null, + "id": "plot_9_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p5_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.126484, + "exception": null, + "id": "plot_10_task2", + "output": "", + "skipReason": null, + 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"status": "SKIPPED" + }, + { + "id": "autogen_task2_CP1_Diss_PD1_SHP2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD28i_P_CD28a", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD28a_DP_CD28i", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD28a_Bd_PI3K", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD3i_P_CD3a", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD3a_DP_CD3i", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CD3a_Bd_ZAP70", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ZAP70i_P_ZAP70a1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ZAP70a1_P_ZAP70a2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LATi_P_LATa", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_LATa_Bd_GADS", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_GADSa_Bd_SLP76", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SLP76i_P_SLC76a", + "status": "SKIPPED" + } + ], + "duration": 0.059872, + "exception": null, + "id": 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named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "opencor": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc667ef911d5d45259ae3", + "download": "https://api.biosimulations.org/results/674dc667ef911d5d45259ae3/download", + "logs": "https://api.biosimulations.org/logs/674dc667ef911d5d45259ae3?includeOutput=true", + "log_yml": { + "duration": 0.070162, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpmn01a13j/./Theinmozhi_2018.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pyneuroml": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc66910bb4455d618766d", + "download": "https://api.biosimulations.org/results/674dc66910bb4455d618766d/download", + "logs": "https://api.biosimulations.org/logs/674dc66910bb4455d618766d?includeOutput=true", + "log_yml": { + "duration": 0.078418, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pysces": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc66b10bb4455d6187671", + "download": "https://api.biosimulations.org/results/674dc66b10bb4455d6187671/download", + "logs": "https://api.biosimulations.org/logs/674dc66b10bb4455d6187671?includeOutput=true", + "log_yml": { + "duration": 5.360377, + "exception": null, + "output": "libtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified in the user configuration file, set \"matplotlib_backend = \" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems *\r\n* http://pysces.sourceforge.net *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", + "sedDocuments": [ + { + "duration": 4.704026, + "exception": null, + "location": "Theinmozhi_2018.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 5 plots:\r\n Theinmozhi_2018.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 120 data sets\r\n Plots (5):\r\n plot_10_task2: 1 curves\r\n plot_6_task2: 1 curves\r\n plot_7_task2: 1 curves\r\n plot_8_task2: 2 curves\r\n plot_9_task2: 1 curves\r\n\r\nExecuting SED-ML file 1: Theinmozhi_2018.sedml ...\r\n Found 1 tasks and 6 outputs:\r\n Tasks:\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_10_task2`\r\n `plot_6_task2`\r\n `plot_7_task2`\r\n `plot_8_task2`\r\n `plot_9_task2`\r\n Executing task 1: `task2`\r\n Executing simulation ...Info: single compartment model: locating \"CP2_DP_CP1\" in default compartment\r\nInfo: single compartment model: locating \"CP1_Diss_PD1_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"CD28i_P_CD28a\" in default compartment\r\nInfo: single compartment model: locating \"CD28a_DP_CD28i\" in default compartment\r\nInfo: single compartment model: locating \"CD28a_Bd_PI3K\" in default compartment\r\nInfo: single compartment model: locating \"CD3i_P_CD3a\" in default compartment\r\nInfo: single compartment model: locating \"CD3a_DP_CD3i\" in default compartment\r\nInfo: single compartment model: locating \"CD3a_Bd_ZAP70\" in default compartment\r\nInfo: single compartment model: locating \"ZAP70i_P_ZAP70a1\" in default compartment\r\nInfo: single compartment model: locating \"ZAP70a1_P_ZAP70a2\" in default compartment\r\nInfo: single compartment model: locating \"LATi_P_LATa\" in default compartment\r\nInfo: single compartment model: locating \"LATa_Bd_GADS\" in default compartment\r\nInfo: single compartment model: locating \"GADSa_Bd_SLP76\" in default compartment\r\nInfo: single compartment model: locating \"SLP76i_P_SLC76a\" in default compartment\r\nWriting file: /tmp/tmppsz5bkq_.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpf_2pl9st.xml\r\nout: /tmp/tmppsz5bkq_.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmppsz5bkq_.psc loading ..... \r\nParsing file: /tmp/tmppsz5bkq_.psc\r\nWarning: species \"LCKinactive\" (fixed) does not occur in any reaction\r\nWarning: species \"CD3t\" (fixed) does not occur in any reaction\r\nWarning: species \"SLP76t\" (fixed) does not occur in any reaction\r\nWarning: species \"GADSt\" (fixed) does not occur in any reaction\r\nWarning: species \"LATt\" (fixed) does not occur in any reaction\r\nWarning: species \"ZAP70t\" (fixed) does not occur in any reaction\r\nWarning: species \"PI3Kt\" (fixed) does not occur in any reaction\r\nWarning: species \"CD28t\" (fixed) does not occur in any reaction\r\nWarning: species \"CPactive\" (fixed) does not occur in any reaction\r\nWarning: species \"LCKactive\" (fixed) does not occur in any reaction\r\nWarning: species \"LCKt\" (fixed) does not occur in any reaction\r\nInfo: \"CD28t\" has been initialised but does not occur in a rate equation\r\nInfo: \"PI3Kt\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70t\" has been initialised but does not occur in a rate equation\r\nInfo: \"LATt\" has been initialised but does not occur in a rate equation\r\nInfo: \"GADSt\" has been initialised but does not occur in a rate equation\r\nInfo: \"SLP76t\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD3t\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCKinactive\" has been initialised but does not occur in a rate equation\r\nInfo: \"Kdpa_yiya\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_SHP2_bound\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD3z_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD28_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_SHP2_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_PI3K_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_ZAP70_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70_phos_Y315\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70_phos_Y93\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_phos_Y505\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_phos_Y394\" has been initialised but does not occur in a rate equation\r\nInfo: \"LAT_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_LCK_active\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_LCK_inactive\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_switch\" has been initialised but does not occur in a rate equation\r\nInfo: \"ModelValue_0\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . . . done.\r\nCalculating K matrix . . . . . . . . . . . done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 101 points: 0.15407371520996094\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 6 outputs ...\r\n Generating output 1: `plot_6_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `plot_7_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `plot_8_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `plot_9_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 5: `plot_10_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 6: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.31045, + "exception": null, + "id": "plot_6_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p2_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.146464, + "exception": null, + "id": "plot_7_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p3_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p3_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.17892, + "exception": null, + "id": "plot_8_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p4_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.130808, + "exception": null, + "id": "plot_9_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p5_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.127922, + "exception": null, + "id": "plot_10_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_PI3K_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_ZAP70_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_LCK_active", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_LCK_inactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKpi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CPactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3K", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3Kb", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3Kt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKinactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_yiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpi_yi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpi_yiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_ya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_pi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpi_i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpi_ya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpa_i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpa_yi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_pd1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_pd1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd1_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd2_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cp2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMdp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_pi3k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_pi3k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMdp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp1_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp2_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_lat", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_gads", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_gads", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_SHP2_bound", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3z_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_SHP2_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70_phos_Y315", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70_phos_Y93", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_phos_Y505", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_phos_Y394", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LAT_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_switch", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ModelValue_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_P_LCKyi_inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_P_LCKya_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya_P_LCKyiya_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi_P_LCKpi_inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya_DP_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya_DP_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi_DP_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya_DP_LCKya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKpi_DP_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1_P_PD1p1_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1_P_PD1p2_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1_Bd_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p2_Bd_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2_Diss_SHP2_PD1p1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2_DP_CP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP1_Diss_PD1_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28i_P_CD28a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a_DP_CD28i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a_Bd_PI3K", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3i_P_CD3a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a_DP_CD3i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a_Bd_ZAP70", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70i_P_ZAP70a1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a1_P_ZAP70a2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATi_P_LATa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATa_Bd_GADS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSa_Bd_SLP76", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76i_P_SLC76a", + "status": "SUCCEEDED" + } + ], + "duration": 0.196404, + "exception": null, + "id": "autogen_report_for_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": null, + "duration": 3.152147, + "exception": null, + "id": "task2", + "output": "Check SBML support is at action level 2\r\nSBML file is L2V4\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmphhfyi34z.xml\r\n*******************************************************************\r\n\r\nParameter units ignored for parameters:\r\n['Kdpa_yiya', 'Kdpi_yi', 'Kdpi_yiya', 'Kdpa_ya', 'Kdpa_pi', 'Kpi_i', 'Kpi_ya', 'Kpa_i', 'Kpa_yi', 'Kp_pd1', 'KMp_pd1', 'Ka_shp', 'Kd1_shp', 'Kd2_shp', 'Kdp_cp2', 'Kp_cd28', 'KMp_cd28', 'Kdp_cd28', 'KMdp_cd28', 'Ka_pi3k', 'Kd_pi3k', 'Kp_cd3', 'KMp_cd3', 'Kdp_cd3', 'KMdp_cd3', 'Ka_zap', 'Kd_zap', 'Kp1_zap', 'Kp2_zap', 'Kp_lat', 'Ka_gads', 'Kd_gads', 'Ka_slp', 'Kd_slp', 'Kp_slp', 'perc_SHP2_bound'] \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"LCK_P_LCKyi_inh\" in default compartment\r\nInfo: single compartment model: locating \"LCK_P_LCKya_act\" in default compartment\r\nInfo: single compartment model: locating \"LCKya_P_LCKyiya_act\" in default compartment\r\nInfo: single compartment model: locating \"LCKyi_P_LCKpi_inh\" in default compartment\r\nInfo: single compartment model: locating \"LCKyiya_DP_LCKyi\" in default compartment\r\nInfo: single compartment model: locating \"LCKya_DP_LCKi\" in default compartment\r\nInfo: single compartment model: locating \"LCKyi_DP_LCKi\" in default compartment\r\nInfo: single compartment model: locating \"LCKyiya_DP_LCKya\" in default compartment\r\nInfo: single compartment model: locating \"LCKpi_DP_LCKyi\" in default compartment\r\nInfo: single compartment model: locating \"PD1_P_PD1p1_act\" in default compartment\r\nInfo: single compartment model: locating \"PD1p1_P_PD1p2_act\" in default compartment\r\nInfo: single compartment model: locating \"PD1p1_Bd_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"PD1p2_Bd_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"CP2_Diss_SHP2_PD1p1\" in default compartment\r\nInfo: single compartment model: locating \"CP2_DP_CP1\" in default compartment\r\nInfo: single compartment model: locating \"CP1_Diss_PD1_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"CD28i_P_CD28a\" in default compartment\r\nInfo: single compartment model: locating \"CD28a_DP_CD28i\" in default compartment\r\nInfo: single compartment model: locating \"CD28a_Bd_PI3K\" in default compartment\r\nInfo: single compartment model: locating \"CD3i_P_CD3a\" in default compartment\r\nInfo: single compartment model: locating \"CD3a_DP_CD3i\" in default compartment\r\nInfo: single compartment model: locating \"CD3a_Bd_ZAP70\" in default compartment\r\nInfo: single compartment model: locating \"ZAP70i_P_ZAP70a1\" in default compartment\r\nInfo: single compartment model: locating \"ZAP70a1_P_ZAP70a2\" in default compartment\r\nInfo: single compartment model: locating \"LATi_P_LATa\" in default compartment\r\nInfo: single compartment model: locating \"LATa_Bd_GADS\" in default compartment\r\nInfo: single compartment model: locating \"GADSa_Bd_SLP76\" in default compartment\r\nInfo: single compartment model: locating \"SLP76i_P_SLC76a\" in default compartment\r\nWriting file: /tmp/tmpq4zmjtzv.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmphhfyi34z.xml\r\nout: /tmp/tmpq4zmjtzv.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpq4zmjtzv.psc loading ..... \r\nParsing file: /tmp/tmpq4zmjtzv.psc\r\nWarning: species \"LCKinactive\" (fixed) does not occur in any reaction\r\nWarning: species \"CD3t\" (fixed) does not occur in any reaction\r\nWarning: species \"SLP76t\" (fixed) does not occur in any reaction\r\nWarning: species \"GADSt\" (fixed) does not occur in any reaction\r\nWarning: species \"LATt\" (fixed) does not occur in any reaction\r\nWarning: species \"ZAP70t\" (fixed) does not occur in any reaction\r\nWarning: species \"PI3Kt\" (fixed) does not occur in any reaction\r\nWarning: species \"CD28t\" (fixed) does not occur in any reaction\r\nWarning: species \"CPactive\" (fixed) does not occur in any reaction\r\nWarning: species \"LCKactive\" (fixed) does not occur in any reaction\r\nWarning: species \"LCKt\" (fixed) does not occur in any reaction\r\nInfo: \"CD28t\" has been initialised but does not occur in a rate equation\r\nInfo: \"PI3Kt\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70t\" has been initialised but does not occur in a rate equation\r\nInfo: \"LATt\" has been initialised but does not occur in a rate equation\r\nInfo: \"GADSt\" has been initialised but does not occur in a rate equation\r\nInfo: \"SLP76t\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD3t\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCKinactive\" has been initialised but does not occur in a rate equation\r\nInfo: \"Kdpa_yiya\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_SHP2_bound\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD3z_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"CD28_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_SHP2_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_PI3K_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_ZAP70_free\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70_phos_Y315\" has been initialised but does not occur in a rate equation\r\nInfo: \"ZAP70_phos_Y93\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_phos_Y505\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_phos_Y394\" has been initialised but does not occur in a rate equation\r\nInfo: \"LAT_phosphorylated\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_LCK_active\" has been initialised but does not occur in a rate equation\r\nInfo: \"perc_LCK_inactive\" has been initialised but does not occur in a rate equation\r\nInfo: \"LCK_switch\" has been initialised but does not occur in a rate equation\r\nInfo: \"ModelValue_0\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . . . done.\r\nCalculating K matrix . . . . . . . . . . . done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 101 points: 0.17607879638671875\r\nCheck SBML support is at action level 2\r\nSBML file is L2V4\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpf_2pl9st.xml\r\n*******************************************************************\r\n\r\nParameter units ignored for parameters:\r\n['Kdpa_yiya', 'Kdpi_yi', 'Kdpi_yiya', 'Kdpa_ya', 'Kdpa_pi', 'Kpi_i', 'Kpi_ya', 'Kpa_i', 'Kpa_yi', 'Kp_pd1', 'KMp_pd1', 'Ka_shp', 'Kd1_shp', 'Kd2_shp', 'Kdp_cp2', 'Kp_cd28', 'KMp_cd28', 'Kdp_cd28', 'KMdp_cd28', 'Ka_pi3k', 'Kd_pi3k', 'Kp_cd3', 'KMp_cd3', 'Kdp_cd3', 'KMdp_cd3', 'Ka_zap', 'Kd_zap', 'Kp1_zap', 'Kp2_zap', 'Kp_lat', 'Ka_gads', 'Kd_gads', 'Ka_slp', 'Kd_slp', 'Kp_slp', 'perc_SHP2_bound'] \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"LCK_P_LCKyi_inh\" in default compartment\r\nInfo: single compartment model: locating \"LCK_P_LCKya_act\" in default compartment\r\nInfo: single compartment model: locating \"LCKya_P_LCKyiya_act\" in default compartment\r\nInfo: single compartment model: locating \"LCKyi_P_LCKpi_inh\" in default compartment\r\nInfo: single compartment model: locating \"LCKyiya_DP_LCKyi\" in default compartment\r\nInfo: single compartment model: locating \"LCKya_DP_LCKi\" in default compartment\r\nInfo: single compartment model: locating \"LCKyi_DP_LCKi\" in default compartment\r\nInfo: single compartment model: locating \"LCKyiya_DP_LCKya\" in default compartment\r\nInfo: single compartment model: locating \"LCKpi_DP_LCKyi\" in default compartment\r\nInfo: single compartment model: locating \"PD1_P_PD1p1_act\" in default compartment\r\nInfo: single compartment model: locating \"PD1p1_P_PD1p2_act\" in default compartment\r\nInfo: single compartment model: locating \"PD1p1_Bd_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"PD1p2_Bd_SHP2\" in default compartment\r\nInfo: single compartment model: locating \"CP2_Diss_SHP2_PD1p1\" in default compartment\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "rbapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc66def911d5d45259af7", + "download": "https://api.biosimulations.org/results/674dc66def911d5d45259af7/download", + "logs": "https://api.biosimulations.org/logs/674dc66def911d5d45259af7?includeOutput=true", + "log_yml": { + "duration": 0.251659, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Theinmozhi_2018.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "smoldyn": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc66f10bb4455d6187678", + "download": "https://api.biosimulations.org/results/674dc66f10bb4455d6187678/download", + "logs": "https://api.biosimulations.org/logs/674dc66f10bb4455d6187678?includeOutput=true", + "log_yml": { + "duration": 0.062385, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "tellurium": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc67110bb4455d6187681", + "download": "https://api.biosimulations.org/results/674dc67110bb4455d6187681/download", + "logs": "https://api.biosimulations.org/logs/674dc67110bb4455d6187681?includeOutput=true", + "log_yml": { + "duration": 3.978802, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 3.347017, + "exception": null, + "location": "Theinmozhi_2018.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 5 plots:\r\n Theinmozhi_2018.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 120 data sets\r\n Plots (5):\r\n plot_10_task2: 1 curves\r\n plot_6_task2: 1 curves\r\n plot_7_task2: 1 curves\r\n plot_8_task2: 2 curves\r\n plot_9_task2: 1 curves\r\n\r\nExecuting SED-ML file 1: Theinmozhi_2018.sedml ...\r\n Found 2 tasks and 6 outputs:\r\n Tasks:\r\n `task1`\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_10_task2`\r\n `plot_6_task2`\r\n `plot_7_task2`\r\n `plot_8_task2`\r\n `plot_9_task2`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 6 outputs ...\r\n Generating output 1: `plot_6_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `plot_7_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `plot_8_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `plot_9_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 5: `plot_10_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 6: `autogen_report_for_task2` ... \u001b[36mqueued\u001b[0m\r\n Executing task 2: `task2`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 6 outputs ...\r\n Generating output 1: `plot_6_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `plot_7_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `plot_8_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `plot_9_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 5: `plot_10_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 6: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.139389, + "exception": null, + "id": "plot_6_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p2_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.143154, + "exception": null, + "id": "plot_7_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p3_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p3_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.148739, + "exception": null, + "id": "plot_8_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p4_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.138961, + "exception": null, + "id": "plot_9_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p5_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.144982, + "exception": null, + "id": "plot_10_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_PI3K_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_ZAP70_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_LCK_active", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_LCK_inactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKpi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CPactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3K", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3Kb", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3Kt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKinactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_yiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpi_yi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpi_yiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_ya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdpa_pi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpi_i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpi_ya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpa_i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kpa_yi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_pd1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_pd1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd1_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd2_shp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cp2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMdp_cd28", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_pi3k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_pi3k", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kdp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_KMdp_cd3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp1_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp2_zap", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_lat", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_gads", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_gads", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Ka_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kd_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Kp_slp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_SHP2_bound", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3z_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_SHP2_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70_phos_Y315", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70_phos_Y93", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_phos_Y505", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_phos_Y394", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LAT_phosphorylated", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_switch", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ModelValue_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_P_LCKyi_inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCK_P_LCKya_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya_P_LCKyiya_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi_P_LCKpi_inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya_DP_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya_DP_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi_DP_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya_DP_LCKya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKpi_DP_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1_P_PD1p1_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1_P_PD1p2_act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1_Bd_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p2_Bd_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2_Diss_SHP2_PD1p1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2_DP_CP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP1_Diss_PD1_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28i_P_CD28a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a_DP_CD28i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a_Bd_PI3K", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3i_P_CD3a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a_DP_CD3i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a_Bd_ZAP70", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70i_P_ZAP70a1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a1_P_ZAP70a2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATi_P_LATa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATa_Bd_GADS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSa_Bd_SLP76", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76i_P_SLC76a", + "status": "SUCCEEDED" + } + ], + "duration": 0.213115, + "exception": null, + "id": "autogen_report_for_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.377119, + "exception": null, + "id": "task1", + "output": "", + "simulatorDetails": [ + { + "key": "method", + "value": "simulate" + }, + { + "key": "solver", + "value": "cvode" + }, + { + "key": "relative_tolerance", + "value": 1e-06 + }, + { + "key": "absolute_tolerance", + "value": 1e-12 + }, + { + "key": "stiff", + "value": true + }, + { + "key": "maximum_bdf_order", + "value": 5 + }, + { + "key": "maximum_adams_order", + "value": 12 + }, + { + "key": "maximum_num_steps", + "value": 10000 + }, + { + "key": "maximum_time_step", + "value": 0.0 + }, + { + "key": "minimum_time_step", + "value": 0.0 + }, + { + "key": "initial_time_step", + "value": 0.0 + }, + { + "key": "multiple_steps", + "value": false + }, + { + "key": "variable_step_size", + "value": false + }, + { + "key": "max_output_rows", + "value": 100000 + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "algorithm": null, + "duration": 0.322538, + "exception": null, + "id": "task2", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "vcell": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc674261553b9bc253ed9", + "download": "https://api.biosimulations.org/results/674dc674261553b9bc253ed9/download", + "logs": "https://api.biosimulations.org/logs/674dc674261553b9bc253ed9?includeOutput=true", + "log_yml": { + "duration": 15, + "exception": null, + "output": "Processing Theinmozhi_2018.sedml. Done", + "sedDocuments": [ + { + "duration": null, + "exception": null, + "location": "Theinmozhi_2018.sedml", + "output": "Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating CSV file... Done. Generating HDF5 file...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "plot_6_task2", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p2_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "plot_7_task2", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p3_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p3_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "plot_8_task2", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p4_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "plot_9_task2", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "p5_curve_1_task2", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "plot_10_task2", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_PI3K_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_ZAP70_free", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_LCK_active", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_perc_LCK_inactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKyiya", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKpi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LCKactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PD1p2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CP2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CPactive", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3K", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3Kb", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD28t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3a", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70a1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_PI3Kt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ZAP70t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATi", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_LATt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76i", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SLP76t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CD3t", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_GADSa", + "status": 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A mathematical model for cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells

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EpoRActJAK2 + SOCS3 + SOCS3Eqc + SOCS3Inh + p2EpoRpJAK2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cyt + + Function_for_v_6 + DeaEpoRJAKActSHP1 + SHP1Act + SHP1ActEpoR + p1EpoRpJAK2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cyt + + Function_for_v_7 + DeaEpoRJAKActSHP1 + SHP1Act + SHP1ActEpoR + p2EpoRpJAK2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cyt + + Function_for_v_8 + DeaEpoRJAKActSHP1 + SHP1Act + SHP1ActEpoR + p12EpoRpJAK2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cyt + + Function_for_v_11 + EpoRpJAK2 + SHP1 + SHP1ActEpoR + p12EpoRpJAK2 + p1EpoRpJAK2 + p2EpoRpJAK2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cyt + SHP1Dea + SHP1Act + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cyt + + Function_for_v_13 + EpoRpJAK2 + SOCS3 + SOCS3Eqc + SOCS3Inh + STAT5 + STAT5ActJAK2 + p12EpoRpJAK2 + p1EpoRpJAK2 + p2EpoRpJAK2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cyt + + Function_for_v_14 + CIS + CISEqc + CISInh + SOCS3 + SOCS3Eqc + SOCS3Inh + STAT5 + STAT5ActEpoR + p12EpoRpJAK2 + p1EpoRpJAK2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Function_for_v_15 + STAT5Imp + cyt + pSTAT5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Function_for_v_16 + STAT5Exp + npSTAT5 + nuc + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nuc + + Function_for_v_17 + ActD + CISRNAEqc + CISRNATurn + npSTAT5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nuc + CISRNADelay + CISnRNA1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Function_for_v_19 + CISRNADelay + CISnRNA2 + nuc + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cyt + CISRNATurn + CISRNA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cyt + + Function_for_v_21 + CISEqc + CISRNA + CISTurn + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cyt + CISTurn + CIS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Function_for_v_23 + ActD + SOCS3Eqc + SOCS3Turn + cyt + npSTAT5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cyt + SOCS3Turn + SOCS3 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cyt + + Function_for_v_25 + SOCS3Eqc + SOCS3EqcOE + SOCS3Turn + SOCS3oe + + + + + + + + \ No newline at end of file diff --git a/BioModels/BIOMD0000001077/tests/d1_plots_local/amici_plot_2_task2.pdf b/BioModels/BIOMD0000001077/tests/d1_plots_local/amici_plot_2_task2.pdf new file mode 100644 index 00000000..986d5df5 Binary files /dev/null and b/BioModels/BIOMD0000001077/tests/d1_plots_local/amici_plot_2_task2.pdf differ diff --git a/BioModels/BIOMD0000001077/tests/d1_plots_local/copasi_plot_2_task2.pdf 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b/BioModels/BIOMD0000001077/tests/results_compatibility_biosimulators.md new file mode 100644 index 00000000..e403e10e --- /dev/null +++ b/BioModels/BIOMD0000001077/tests/results_compatibility_biosimulators.md @@ -0,0 +1,23 @@ +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------|:-------------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with AMICI.

SED-ML and SBML are compatible with AMICI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='epo_level'] is not a valid XPath to an attribute of a model element

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='epo_level'] is not a valid XPath to an attribute of a model element

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

Only BNGL, SED-ML are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with CBMPy.

SED-ML and SBML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with COBRApy.

SED-ML and SBML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with COPASI.

SED-ML and SBML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with GillesPy2.

SED-ML and SBML are compatible with GillesPy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with LibSBMLSim.

SED-ML and SBML are compatible with LibSBMLSim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with MASSpy.

SED-ML and SBML are compatible with MASSpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Could not load MassModel 'Adlung2021___Cell_to_cell_variability_in_JAK2_STAT5_pathway'

target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='epo_level'] cannot be changed by XML manipulation, as the target is not an attribute of a model element

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

Only CellML, SED-ML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with PySCeS.

SED-ML and SBML are compatible with PySCeS.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

Only RBApy, SED-ML are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.
- Simulation `sim1` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

Only Smoldyn, SED-ML are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with Tellurium.

SED-ML and SBML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may not be compatibe with VCell.

BNGL, SED-ML and SBML are compatible with VCell.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| plot | | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

Only XPP, SED-ML are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/BioModels/BIOMD0000001077/tests/results_local.json b/BioModels/BIOMD0000001077/tests/results_local.json new file mode 100644 index 00000000..c3ea3529 --- /dev/null +++ b/BioModels/BIOMD0000001077/tests/results_local.json @@ -0,0 +1,2015 @@ +{ + "amici": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/amici' returned non-zero exit status 1", + "log_yml": { + "duration": 19.877325, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='epo_level'] is not a valid XPath to an attribute of a model element", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 19.468539, + "exception": { + "message": "The SED document did not execute successfully:\n\n target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='epo_level'] is not a valid XPath to an attribute of a model element", + "type": "SedmlExecutionError" + }, + "location": "Adlung2021 _model_jakstat_pa.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 1 plots:\r\n Adlung2021 _model_jakstat_pa.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 71 data sets\r\n Plots (1):\r\n plot_2_task2: 2 curves\r\n\r\nExecuting SED-ML file 1: Adlung2021 _model_jakstat_pa.sedml ...\r\n Found 2 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_2_task2`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_2_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_report_for_task2` ... \u001b[36mqueued\u001b[0m\r\n Executing task 2: `task2`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_2_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SKIPPED" + }, + { + "id": "p1_curve_2_task2", + "status": "SKIPPED" + } + ], + "duration": 0.224991, + "exception": null, + "id": "plot_2_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_measuralbe_pSTAT5", + "status": "SKIPPED" + }, + { + "id": "autogen_task2__pSTAT5_Total_STAT5", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_EpoRJAK2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_EpoRpJAK2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_p1EpoRpJAK2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_p2EpoRpJAK2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_p12EpoRpJAK2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SHP1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SHP1Act", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_STAT5", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_pSTAT5", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_npSTAT5", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CISnRNA1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CISnRNA2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CISRNA", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CIS", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SOCS3", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_ActD", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CISEqc", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CISInh", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CISRNADelay", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CISRNAEqc", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CISRNATurn", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_CISTurn", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_DeaEpoRJAKActSHP1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_EpoRActJAK2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_JAK2ActEpo", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SHP1ActEpoR", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SHP1Dea", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SOCS3Eqc", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SOCS3EqcOE", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SOCS3Inh", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SOCS3Turn", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_SOCS3oe", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_STAT5ActEpoR", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_STAT5ActJAK2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_STAT5Exp", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_STAT5Imp", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_epo_level", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_init_EpoRJAK2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_init_SHP1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_init_STAT5", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Epo", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_Total_STAT5", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_cyt", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_nuc", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v1_v_0", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v2_v_1", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v3_v_2", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v4_v_3", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v5_v_4", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v6_v_5", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v7_v_6", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v8_v_7", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v9_v_8", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v12_v_11", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v13_v_12", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v14_v_13", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v15_v_14", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v16_v_15", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v17_v_16", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v18_v_17", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v19_v_18", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v20_v_19", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v21_v_20", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v22_v_21", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v23_v_22", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v24_v_23", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v25_v_24", + "status": "SKIPPED" + }, + { + "id": "autogen_task2_v26_v_25", + "status": "SKIPPED" + } + ], + "duration": 0.07207, + "exception": null, + "id": "autogen_report_for_task2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": "KISAO_0000496", + "duration": 18.465958, + "exception": null, + "id": "task1", + "output": "", + "simulatorDetails": [ + { + "key": "solver", + "value": "amici.amici.CVodeSolver" + }, + { + "key": "method", + "value": "amici.swig_wrappers.runAmiciSimulation" + }, + { + "key": "arguments", + "value": {} + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "algorithm": null, + "duration": 0.050769, + "exception": { + "message": "target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='epo_level'] is not a valid XPath to an attribute of a model element", + "type": "ValueError" + }, + "id": "task2", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "brian2": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.055226, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpe0rhutg5/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n [py.warnings]\r\npyNeuroML >>> WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpe0rhutg5/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "bionetgen": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", + "log_yml": { + "duration": 0.168358, + "exception": { + "message": "`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmph3rp0u03/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` has warnings.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNA__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` has warnings.\r\n - Variable `auto_dg_for_task2_CIS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` has warnings.\r\n - Variable `auto_dg_for_task2_ActD__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` has warnings.\r\n - Variable `auto_dg_for_task2_CISInh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISTurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` has warnings.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` has warnings.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` has warnings.\r\n - Variable `auto_dg_for_task2_epo_level__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` has warnings.\r\n - Variable `auto_dg_for_task2_Epo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` has warnings.\r\n - Variable `auto_dg_for_task2_cyt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` has warnings.\r\n - Variable `auto_dg_for_task2_nuc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` has warnings.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` has warnings.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` has warnings.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` has warnings.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` has warnings.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` has warnings.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` has warnings.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` has warnings.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` has warnings.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` has warnings.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` has warnings.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` has warnings.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` has warnings.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` has warnings.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` has warnings.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` has warnings.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` has warnings.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` has warnings.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` has warnings.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` has warnings.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` has warnings.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` has warnings.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` has warnings.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` has warnings.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` has warnings.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNA__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` has warnings.\r\n - Variable `auto_dg_for_task2_CIS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` has warnings.\r\n - Variable `auto_dg_for_task2_ActD__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` has warnings.\r\n - Variable `auto_dg_for_task2_CISInh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISTurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` has warnings.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` has warnings.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` has warnings.\r\n - Variable `auto_dg_for_task2_epo_level__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` has warnings.\r\n - Variable `auto_dg_for_task2_Epo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` has warnings.\r\n - Variable `auto_dg_for_task2_cyt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` has warnings.\r\n - Variable `auto_dg_for_task2_nuc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` has warnings.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` has warnings.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` has warnings.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` has warnings.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` has warnings.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` has warnings.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` has warnings.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` has warnings.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` has warnings.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` has warnings.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` has warnings.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` has warnings.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` has warnings.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` has warnings.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` has warnings.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` has warnings.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` has warnings.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` has warnings.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` has warnings.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` has warnings.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` has warnings.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` has warnings.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` has warnings.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` has warnings.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "boolnet": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", + "log_yml": { + "duration": 0.177739, + "exception": { + "message": "`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp3ztexqvf/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` may be invalid.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_SHP1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_STAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'epo_level' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'STAT5 + pSTAT5 + 0.275 * npSTAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_0(Epo, EpoRJAK2, JAK2ActEpo, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_1(DeaEpoRJAKActSHP1, EpoRpJAK2, SHP1Act, SHP1ActEpoR)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_2(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_3(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_4(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_5(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_6(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_7(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_8(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p12EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_11(EpoRpJAK2, SHP1, SHP1ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SHP1Dea * SHP1Act' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_13(EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActJAK2, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_14(CIS, CISEqc, CISInh, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_15(STAT5Imp, cyt, pSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_16(STAT5Exp, npSTAT5, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * Function_for_v_17(ActD, CISRNAEqc, CISRNATurn, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * CISRNADelay * CISnRNA1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_19(CISRNADelay, CISnRNA2, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISRNATurn * CISRNA' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_21(CISEqc, CISRNA, CISTurn)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISTurn * CIS' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_23(ActD, SOCS3Eqc, SOCS3Turn, cyt, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SOCS3Turn * SOCS3' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_25(SOCS3Eqc, SOCS3EqcOE, SOCS3Turn, SOCS3oe)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISInh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNADelay' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNAEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNATurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISTurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'DeaEpoRJAKActSHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'EpoRActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'JAK2ActEpo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1Dea' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Eqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3EqcOE' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Inh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Turn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3oe' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Exp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Imp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'epo_level' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_EpoRJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_SHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Epo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Total_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'measuralbe_pSTAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id '_pSTAT5_Total_STAT5' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` may be invalid.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNA__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` may be invalid.\r\n - Variable `auto_dg_for_task2_CIS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` may be invalid.\r\n - Variable `auto_dg_for_task2_ActD__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` may be invalid.\r\n - Variable `auto_dg_for_task2_CISInh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISTurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` may be invalid.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` may be invalid.\r\n - Variable `auto_dg_for_task2_epo_level__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` may be invalid.\r\n - Variable `auto_dg_for_task2_Epo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` may be invalid.\r\n - Variable `auto_dg_for_task2_cyt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` may be invalid.\r\n - Variable `auto_dg_for_task2_nuc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` may be invalid.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` may be invalid.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` may be invalid.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` may be invalid.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` may be invalid.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` may be invalid.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` may be invalid.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` may be invalid.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` may be invalid.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` may be invalid.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` may be invalid.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` may be invalid.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` may be invalid.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` may be invalid.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` may be invalid.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` may be invalid.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` may be invalid.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` may be invalid.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` may be invalid.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` may be invalid.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` may be invalid.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` may be invalid.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` may be invalid.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` may be invalid.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` may be invalid.\r\n - Model `model` may be invalid.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_SHP1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_STAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'epo_level' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'STAT5 + pSTAT5 + 0.275 * npSTAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_0(Epo, EpoRJAK2, JAK2ActEpo, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_1(DeaEpoRJAKActSHP1, EpoRpJAK2, SHP1Act, SHP1ActEpoR)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_2(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_3(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_4(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_5(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_6(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_7(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_8(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p12EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_11(EpoRpJAK2, SHP1, SHP1ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SHP1Dea * SHP1Act' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_13(EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActJAK2, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_14(CIS, CISEqc, CISInh, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_15(STAT5Imp, cyt, pSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_16(STAT5Exp, npSTAT5, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * Function_for_v_17(ActD, CISRNAEqc, CISRNATurn, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * CISRNADelay * CISnRNA1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_19(CISRNADelay, CISnRNA2, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISRNATurn * CISRNA' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_21(CISEqc, CISRNA, CISTurn)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISTurn * CIS' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_23(ActD, SOCS3Eqc, SOCS3Turn, cyt, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SOCS3Turn * SOCS3' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_25(SOCS3Eqc, SOCS3EqcOE, SOCS3Turn, SOCS3oe)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISInh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNADelay' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNAEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNATurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISTurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'DeaEpoRJAKActSHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'EpoRActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'JAK2ActEpo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1Dea' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Eqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3EqcOE' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Inh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Turn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3oe' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Exp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Imp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'epo_level' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_EpoRJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_SHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Epo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Total_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'measuralbe_pSTAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id '_pSTAT5_Total_STAT5' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` may be invalid.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNA__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` may be invalid.\r\n - Variable `auto_dg_for_task2_CIS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` may be invalid.\r\n - Variable `auto_dg_for_task2_ActD__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` may be invalid.\r\n - Variable `auto_dg_for_task2_CISInh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISTurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` may be invalid.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` may be invalid.\r\n - Variable `auto_dg_for_task2_epo_level__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` may be invalid.\r\n - Variable `auto_dg_for_task2_Epo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` may be invalid.\r\n - Variable `auto_dg_for_task2_cyt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` may be invalid.\r\n - Variable `auto_dg_for_task2_nuc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` may be invalid.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` may be invalid.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` may be invalid.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` may be invalid.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` may be invalid.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` may be invalid.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` may be invalid.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` may be invalid.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` may be invalid.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` may be invalid.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` may be invalid.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` may be invalid.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` may be invalid.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` may be invalid.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` may be invalid.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` may be invalid.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` may be invalid.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` may be invalid.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` may be invalid.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` may be invalid.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` may be invalid.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` may be invalid.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` may be invalid.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` may be invalid.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cbmpy": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.241068, + "exception": { + "message": "`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpqh1x7s4u/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` has warnings.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNA__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` has warnings.\r\n - Variable `auto_dg_for_task2_CIS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` has warnings.\r\n - Variable `auto_dg_for_task2_ActD__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` has warnings.\r\n - Variable `auto_dg_for_task2_CISInh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISTurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` has warnings.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` has warnings.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` has warnings.\r\n - Variable `auto_dg_for_task2_epo_level__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` has warnings.\r\n - Variable `auto_dg_for_task2_Epo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` has warnings.\r\n - Variable `auto_dg_for_task2_cyt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` has warnings.\r\n - Variable `auto_dg_for_task2_nuc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` has warnings.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` has warnings.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` has warnings.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` has warnings.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` has warnings.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` has warnings.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` has warnings.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` has warnings.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` has warnings.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` has warnings.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` has warnings.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` has warnings.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` has warnings.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` has warnings.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` has warnings.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` has warnings.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` has warnings.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` has warnings.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` has warnings.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` has warnings.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` has warnings.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` has warnings.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` has warnings.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` has warnings.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` has warnings.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNA__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` has warnings.\r\n - Variable `auto_dg_for_task2_CIS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` has warnings.\r\n - Variable `auto_dg_for_task2_ActD__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` has warnings.\r\n - Variable `auto_dg_for_task2_CISInh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISTurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` has warnings.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` has warnings.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` has warnings.\r\n - Variable `auto_dg_for_task2_epo_level__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` has warnings.\r\n - Variable `auto_dg_for_task2_Epo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` has warnings.\r\n - Variable `auto_dg_for_task2_cyt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` has warnings.\r\n - Variable `auto_dg_for_task2_nuc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` has warnings.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` has warnings.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` has warnings.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` has warnings.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` has warnings.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` has warnings.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` has warnings.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` has warnings.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` has warnings.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` has warnings.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` has warnings.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` has warnings.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` has warnings.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` has warnings.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` has warnings.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` has warnings.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` has warnings.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` has warnings.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` has warnings.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` has warnings.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` has warnings.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` has warnings.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` has warnings.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` has warnings.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cobrapy": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.28623, + "exception": { + "message": "`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpio8mhijs/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` has warnings.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNA__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` has warnings.\r\n - Variable `auto_dg_for_task2_CIS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` has warnings.\r\n - Variable `auto_dg_for_task2_ActD__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` has warnings.\r\n - Variable `auto_dg_for_task2_CISInh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISTurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` has warnings.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` has warnings.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` has warnings.\r\n - Variable `auto_dg_for_task2_epo_level__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` has warnings.\r\n - Variable `auto_dg_for_task2_Epo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` has warnings.\r\n - Variable `auto_dg_for_task2_cyt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` has warnings.\r\n - Variable `auto_dg_for_task2_nuc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` has warnings.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` has warnings.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` has warnings.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` has warnings.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` has warnings.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` has warnings.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` has warnings.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` has warnings.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` has warnings.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` has warnings.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` has warnings.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` has warnings.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` has warnings.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` has warnings.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` has warnings.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` has warnings.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` has warnings.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` has warnings.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` has warnings.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` has warnings.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` has warnings.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` has warnings.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` has warnings.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` has warnings.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` has warnings.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNA__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` has warnings.\r\n - Variable `auto_dg_for_task2_CIS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` has warnings.\r\n - Variable `auto_dg_for_task2_ActD__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` has warnings.\r\n - Variable `auto_dg_for_task2_CISInh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISTurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` has warnings.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` has warnings.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` has warnings.\r\n - Variable `auto_dg_for_task2_epo_level__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` has warnings.\r\n - Variable `auto_dg_for_task2_Epo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` has warnings.\r\n - Variable `auto_dg_for_task2_cyt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` has warnings.\r\n - Variable `auto_dg_for_task2_nuc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` has warnings.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` has warnings.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` has warnings.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` has warnings.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` has warnings.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` has warnings.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` has warnings.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` has warnings.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` has warnings.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` has warnings.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` has warnings.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` has warnings.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` has warnings.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` has warnings.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` has warnings.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` has warnings.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` has warnings.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` has warnings.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` has warnings.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` has warnings.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` has warnings.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` has warnings.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` has warnings.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` has warnings.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "copasi": { + "exception_message": "", + "log_yml": { + "duration": 1.598433, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp8th35q9z/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp8th35q9z/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 1.225818, + "exception": null, + "location": "Adlung2021 _model_jakstat_pa.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 1 plots:\r\n Adlung2021 _model_jakstat_pa.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 71 data sets\r\n Plots (1):\r\n plot_2_task2: 2 curves\r\n\r\nExecuting SED-ML file 1: Adlung2021 _model_jakstat_pa.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_2_task2`\r\n Executing task 1: `task2`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_2_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p1_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.419649, + "exception": null, + "id": "plot_2_task2", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_measuralbe_pSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2__pSTAT5_Total_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p1EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p2EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p12EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1Act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_pSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_npSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISnRNA1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISnRNA2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNA", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CIS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ActD", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISEqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISInh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNADelay", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNAEqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNATurn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISTurn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_DeaEpoRJAKActSHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRActJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_JAK2ActEpo", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1ActEpoR", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1Dea", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Eqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3EqcOE", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Turn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3oe", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5ActEpoR", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5ActJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5Exp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5Imp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_epo_level", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_EpoRJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_SHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Epo", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Total_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_cyt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_nuc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v1_v_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v2_v_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v3_v_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v4_v_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v5_v_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v6_v_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v7_v_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v8_v_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v9_v_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v12_v_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v13_v_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v14_v_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v15_v_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v16_v_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v17_v_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v18_v_17", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v19_v_18", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v20_v_19", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v21_v_20", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v22_v_21", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v23_v_22", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v24_v_23", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v25_v_24", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v26_v_25", + "status": "SUCCEEDED" + } + ], + "duration": 0.276758, + "exception": null, + "id": "autogen_report_for_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": null, + "duration": 0.293335, + "exception": null, + "id": "task2", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task2_STAT5Imp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v1_v_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v6_v_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v16_v_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v7_v_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v25_v_24__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v5_v_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_p1EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_nuc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SOCS3oe__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Total_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SOCS3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v21_v_20__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISnRNA2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_STAT5Exp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISRNA__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CIS__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_STAT5ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISRNATurn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISEqc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable 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- XPath could not be validated.\r\n- Variable `auto_dg_for_task2_JAK2ActEpo__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v18_v_17__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_init_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SOCS3Inh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p1__pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v13_v_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v20_v_19__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_init_EpoRJAK2__x` has warnings.\r\n - XPath could not be 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XPath could not be validated.\r\n- Variable `auto_dg_for_task2_p12EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SOCS3Turn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v4_v_3__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `model` may be invalid.\r\n - The model file `/tmp/tmp8th35q9z/tmp9g246j9k.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `model` may be invalid.\r\n - The model file `/tmp/tmp8th35q9z/tmpq117yqur.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "gillespy2": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.179067, + "exception": { + "message": "`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpg4zwjpv2/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` has warnings.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNA__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` has warnings.\r\n - Variable `auto_dg_for_task2_CIS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` has warnings.\r\n - Variable `auto_dg_for_task2_ActD__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` has warnings.\r\n - Variable `auto_dg_for_task2_CISInh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISTurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` has warnings.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` has warnings.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` has warnings.\r\n - Variable `auto_dg_for_task2_epo_level__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` has warnings.\r\n - Variable `auto_dg_for_task2_Epo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` has warnings.\r\n - Variable `auto_dg_for_task2_cyt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` has warnings.\r\n - Variable `auto_dg_for_task2_nuc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` has warnings.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` has warnings.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` has warnings.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` has warnings.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` has warnings.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` has warnings.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` has warnings.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` has warnings.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` has warnings.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` has warnings.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` has warnings.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` has warnings.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` has warnings.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` has warnings.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` has warnings.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` has warnings.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` has warnings.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` has warnings.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` has warnings.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` has warnings.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` has warnings.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` has warnings.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` has warnings.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` has warnings.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` has warnings.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNA__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` has warnings.\r\n - Variable `auto_dg_for_task2_CIS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` has warnings.\r\n - Variable `auto_dg_for_task2_ActD__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` has warnings.\r\n - Variable `auto_dg_for_task2_CISInh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISTurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` has warnings.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` has warnings.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` has warnings.\r\n - Variable `auto_dg_for_task2_epo_level__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` has warnings.\r\n - Variable `auto_dg_for_task2_Epo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` has warnings.\r\n - Variable `auto_dg_for_task2_cyt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` has warnings.\r\n - Variable `auto_dg_for_task2_nuc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` has warnings.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` has warnings.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` has warnings.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` has warnings.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` has warnings.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` has warnings.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` has warnings.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` has warnings.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` has warnings.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` has warnings.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` has warnings.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` has warnings.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` has warnings.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` has warnings.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` has warnings.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` has warnings.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` has warnings.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` has warnings.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` has warnings.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` has warnings.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` has warnings.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` has warnings.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` has warnings.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` has warnings.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "ginsim": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.182057, + "exception": { + "message": "`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpa7t2lxxp/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` may be invalid.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_SHP1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_STAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'epo_level' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'STAT5 + pSTAT5 + 0.275 * npSTAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_0(Epo, EpoRJAK2, JAK2ActEpo, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_1(DeaEpoRJAKActSHP1, EpoRpJAK2, SHP1Act, SHP1ActEpoR)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_2(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_3(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_4(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_5(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_6(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_7(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_8(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p12EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_11(EpoRpJAK2, SHP1, SHP1ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SHP1Dea * SHP1Act' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_13(EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActJAK2, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_14(CIS, CISEqc, CISInh, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_15(STAT5Imp, cyt, pSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_16(STAT5Exp, npSTAT5, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * Function_for_v_17(ActD, CISRNAEqc, CISRNATurn, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * CISRNADelay * CISnRNA1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_19(CISRNADelay, CISnRNA2, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISRNATurn * CISRNA' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_21(CISEqc, CISRNA, CISTurn)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISTurn * CIS' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_23(ActD, SOCS3Eqc, SOCS3Turn, cyt, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SOCS3Turn * SOCS3' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_25(SOCS3Eqc, SOCS3EqcOE, SOCS3Turn, SOCS3oe)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISInh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNADelay' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNAEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNATurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISTurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'DeaEpoRJAKActSHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'EpoRActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'JAK2ActEpo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1Dea' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Eqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3EqcOE' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Inh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Turn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3oe' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Exp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Imp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'epo_level' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_EpoRJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_SHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Epo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Total_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'measuralbe_pSTAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id '_pSTAT5_Total_STAT5' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` may be invalid.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNA__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` may be invalid.\r\n - Variable `auto_dg_for_task2_CIS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` may be invalid.\r\n - Variable `auto_dg_for_task2_ActD__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` may be invalid.\r\n - Variable `auto_dg_for_task2_CISInh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISTurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` may be invalid.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` may be invalid.\r\n - Variable `auto_dg_for_task2_epo_level__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` may be invalid.\r\n - Variable `auto_dg_for_task2_Epo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` may be invalid.\r\n - Variable `auto_dg_for_task2_cyt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` may be invalid.\r\n - Variable `auto_dg_for_task2_nuc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` may be invalid.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` may be invalid.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` may be invalid.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` may be invalid.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` may be invalid.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` may be invalid.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` may be invalid.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` may be invalid.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` may be invalid.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` may be invalid.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` may be invalid.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` may be invalid.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` may be invalid.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` may be invalid.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` may be invalid.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` may be invalid.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` may be invalid.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` may be invalid.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` may be invalid.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` may be invalid.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` may be invalid.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` may be invalid.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` may be invalid.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` may be invalid.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` may be invalid.\r\n - Model `model` may be invalid.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_SHP1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_STAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'epo_level' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'STAT5 + pSTAT5 + 0.275 * npSTAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_0(Epo, EpoRJAK2, JAK2ActEpo, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_1(DeaEpoRJAKActSHP1, EpoRpJAK2, SHP1Act, SHP1ActEpoR)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_2(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_3(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_4(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_5(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_6(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_7(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_8(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p12EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_11(EpoRpJAK2, SHP1, SHP1ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SHP1Dea * SHP1Act' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_13(EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActJAK2, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_14(CIS, CISEqc, CISInh, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_15(STAT5Imp, cyt, pSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_16(STAT5Exp, npSTAT5, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * Function_for_v_17(ActD, CISRNAEqc, CISRNATurn, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * CISRNADelay * CISnRNA1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_19(CISRNADelay, CISnRNA2, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISRNATurn * CISRNA' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_21(CISEqc, CISRNA, CISTurn)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISTurn * CIS' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_23(ActD, SOCS3Eqc, SOCS3Turn, cyt, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SOCS3Turn * SOCS3' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_25(SOCS3Eqc, SOCS3EqcOE, SOCS3Turn, SOCS3oe)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISInh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNADelay' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNAEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNATurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISTurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'DeaEpoRJAKActSHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'EpoRActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'JAK2ActEpo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1Dea' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Eqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3EqcOE' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Inh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Turn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3oe' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Exp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Imp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'epo_level' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_EpoRJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_SHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Epo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Total_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'measuralbe_pSTAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id '_pSTAT5_Total_STAT5' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` may be invalid.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNA__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` may be invalid.\r\n - Variable `auto_dg_for_task2_CIS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` may be invalid.\r\n - Variable `auto_dg_for_task2_ActD__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` may be invalid.\r\n - Variable `auto_dg_for_task2_CISInh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISTurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` may be invalid.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` may be invalid.\r\n - Variable `auto_dg_for_task2_epo_level__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` may be invalid.\r\n - Variable `auto_dg_for_task2_Epo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` may be invalid.\r\n - Variable `auto_dg_for_task2_cyt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` may be invalid.\r\n - Variable `auto_dg_for_task2_nuc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` may be invalid.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` may be invalid.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` may be invalid.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` may be invalid.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` may be invalid.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` may be invalid.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` may be invalid.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` may be invalid.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` may be invalid.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` may be invalid.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` may be invalid.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` may be invalid.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` may be invalid.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` may be invalid.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` may be invalid.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` may be invalid.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` may be invalid.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` may be invalid.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` may be invalid.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` may be invalid.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` may be invalid.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` may be invalid.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` may be invalid.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` may be invalid.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "libsbmlsim": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.17365, + "exception": { + "message": "`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpc5gfiv71/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` may be invalid.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_SHP1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_STAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'epo_level' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'STAT5 + pSTAT5 + 0.275 * npSTAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_0(Epo, EpoRJAK2, JAK2ActEpo, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_1(DeaEpoRJAKActSHP1, EpoRpJAK2, SHP1Act, SHP1ActEpoR)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_2(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_3(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_4(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_5(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_6(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_7(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_8(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p12EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_11(EpoRpJAK2, SHP1, SHP1ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SHP1Dea * SHP1Act' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_13(EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActJAK2, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_14(CIS, CISEqc, CISInh, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_15(STAT5Imp, cyt, pSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_16(STAT5Exp, npSTAT5, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * Function_for_v_17(ActD, CISRNAEqc, CISRNATurn, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * CISRNADelay * CISnRNA1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_19(CISRNADelay, CISnRNA2, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISRNATurn * CISRNA' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_21(CISEqc, CISRNA, CISTurn)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISTurn * CIS' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_23(ActD, SOCS3Eqc, SOCS3Turn, cyt, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SOCS3Turn * SOCS3' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_25(SOCS3Eqc, SOCS3EqcOE, SOCS3Turn, SOCS3oe)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISInh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNADelay' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNAEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNATurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISTurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'DeaEpoRJAKActSHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'EpoRActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'JAK2ActEpo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1Dea' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Eqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3EqcOE' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Inh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Turn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3oe' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Exp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Imp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'epo_level' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_EpoRJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_SHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Epo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Total_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'measuralbe_pSTAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id '_pSTAT5_Total_STAT5' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` may be invalid.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNA__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` may be invalid.\r\n - Variable `auto_dg_for_task2_CIS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` may be invalid.\r\n - Variable `auto_dg_for_task2_ActD__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` may be invalid.\r\n - Variable `auto_dg_for_task2_CISInh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISTurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` may be invalid.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` may be invalid.\r\n - Variable `auto_dg_for_task2_epo_level__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` may be invalid.\r\n - Variable `auto_dg_for_task2_Epo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` may be invalid.\r\n - Variable `auto_dg_for_task2_cyt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` may be invalid.\r\n - Variable `auto_dg_for_task2_nuc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` may be invalid.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` may be invalid.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` may be invalid.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` may be invalid.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` may be invalid.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` may be invalid.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` may be invalid.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` may be invalid.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` may be invalid.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` may be invalid.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` may be invalid.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` may be invalid.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` may be invalid.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` may be invalid.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` may be invalid.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` may be invalid.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` may be invalid.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` may be invalid.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` may be invalid.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` may be invalid.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` may be invalid.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` may be invalid.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` may be invalid.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` may be invalid.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` may be invalid.\r\n - Model `model` may be invalid.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_SHP1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_STAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'epo_level' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'STAT5 + pSTAT5 + 0.275 * npSTAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_0(Epo, EpoRJAK2, JAK2ActEpo, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_1(DeaEpoRJAKActSHP1, EpoRpJAK2, SHP1Act, SHP1ActEpoR)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_2(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_3(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_4(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_5(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_6(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_7(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_8(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p12EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_11(EpoRpJAK2, SHP1, SHP1ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SHP1Dea * SHP1Act' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_13(EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActJAK2, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_14(CIS, CISEqc, CISInh, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_15(STAT5Imp, cyt, pSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_16(STAT5Exp, npSTAT5, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * Function_for_v_17(ActD, CISRNAEqc, CISRNATurn, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * CISRNADelay * CISnRNA1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_19(CISRNADelay, CISnRNA2, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISRNATurn * CISRNA' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_21(CISEqc, CISRNA, CISTurn)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISTurn * CIS' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_23(ActD, SOCS3Eqc, SOCS3Turn, cyt, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SOCS3Turn * SOCS3' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_25(SOCS3Eqc, SOCS3EqcOE, SOCS3Turn, SOCS3oe)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISInh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNADelay' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNAEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNATurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISTurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'DeaEpoRJAKActSHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'EpoRActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'JAK2ActEpo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1Dea' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Eqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3EqcOE' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Inh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Turn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3oe' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Exp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Imp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'epo_level' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_EpoRJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_SHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Epo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Total_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'measuralbe_pSTAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id '_pSTAT5_Total_STAT5' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` may be invalid.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNA__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` may be invalid.\r\n - Variable `auto_dg_for_task2_CIS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` may be invalid.\r\n - Variable `auto_dg_for_task2_ActD__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` may be invalid.\r\n - Variable `auto_dg_for_task2_CISInh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISTurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` may be invalid.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` may be invalid.\r\n - Variable `auto_dg_for_task2_epo_level__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` may be invalid.\r\n - Variable `auto_dg_for_task2_Epo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` may be invalid.\r\n - Variable `auto_dg_for_task2_cyt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` may be invalid.\r\n - Variable `auto_dg_for_task2_nuc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` may be invalid.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` may be invalid.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` may be invalid.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` may be invalid.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` may be invalid.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` may be invalid.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` may be invalid.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` may be invalid.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` may be invalid.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` may be invalid.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` may be invalid.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` may be invalid.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` may be invalid.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` may be invalid.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` may be invalid.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` may be invalid.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` may be invalid.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` may be invalid.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` may be invalid.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` may be invalid.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` may be invalid.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` may be invalid.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` may be invalid.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` may be invalid.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "masspy": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.190694, + "exception": { + "message": "`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mSedmlFeatureNotSupportedWarning\u001b[0m: \u001b[33m`/tmp/tmp6thjs41z/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` has warnings.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNA__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` has warnings.\r\n - Variable `auto_dg_for_task2_CIS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` has warnings.\r\n - Variable `auto_dg_for_task2_ActD__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` has warnings.\r\n - Variable `auto_dg_for_task2_CISInh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISTurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` has warnings.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` has warnings.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` has warnings.\r\n - Variable `auto_dg_for_task2_epo_level__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` has warnings.\r\n - Variable `auto_dg_for_task2_Epo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` has warnings.\r\n - Variable `auto_dg_for_task2_cyt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` has warnings.\r\n - Variable `auto_dg_for_task2_nuc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` has warnings.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` has warnings.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` has warnings.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` has warnings.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` has warnings.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` has warnings.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` has warnings.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` has warnings.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` has warnings.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` has warnings.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` has warnings.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` has warnings.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` has warnings.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` has warnings.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` has warnings.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` has warnings.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` has warnings.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` has warnings.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` has warnings.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` has warnings.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` has warnings.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` has warnings.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` has warnings.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` has warnings.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Task `task2` has warnings.\r\n - Changes has warnings.\r\n - Change 1 has warnings.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` has warnings.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` has warnings.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` has warnings.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNA__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` has warnings.\r\n - Variable `auto_dg_for_task2_CIS__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` has warnings.\r\n - Variable `auto_dg_for_task2_ActD__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` has warnings.\r\n - Variable `auto_dg_for_task2_CISInh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` has warnings.\r\n - Variable `auto_dg_for_task2_CISTurn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` has warnings.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` has warnings.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` has warnings.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` has warnings.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` has warnings.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` has warnings.\r\n - Variable `auto_dg_for_task2_epo_level__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` has warnings.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` has warnings.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` has warnings.\r\n - Variable `auto_dg_for_task2_Epo__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` has warnings.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` has warnings.\r\n - Variable `auto_dg_for_task2_cyt__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` has warnings.\r\n - Variable `auto_dg_for_task2_nuc__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` has warnings.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` has warnings.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` has warnings.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` has warnings.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` has warnings.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` has warnings.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` has warnings.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` has warnings.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` has warnings.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` has warnings.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` has warnings.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` has warnings.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` has warnings.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` has warnings.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` has warnings.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` has warnings.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` has warnings.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` has warnings.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` has warnings.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` has warnings.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` has warnings.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` has warnings.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` has warnings.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` has warnings.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` has warnings.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` has warnings.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "netpyne": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "log_yml": { + "duration": 0.068732, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "neuron": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "log_yml": { + "duration": 0.051391, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpo0_8uk4z/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "opencor": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "log_yml": { + "duration": 0.082354, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpsr8mlzqf/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pyneuroml": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "log_yml": { + "duration": 0.048488, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpsteg234i/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pysces": { + "exception_message": "", + "log_yml": { + "duration": 1.871207, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpva5tuf5m/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpva5tuf5m/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 1.505052, + "exception": null, + "location": "Adlung2021 _model_jakstat_pa.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 1 plots:\r\n Adlung2021 _model_jakstat_pa.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 71 data sets\r\n Plots (1):\r\n plot_2_task2: 2 curves\r\n\r\nExecuting SED-ML file 1: Adlung2021 _model_jakstat_pa.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_2_task2`\r\n Executing task 1: `task2`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nInfo: multiple compartments defined but reaction v1_v_0 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v2_v_1 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v3_v_2 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v4_v_3 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v5_v_4 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v6_v_5 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v7_v_6 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v8_v_7 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v9_v_8 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v12_v_11 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v13_v_12 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v14_v_13 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v15_v_14 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v16_v_15 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v17_v_16 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v18_v_17 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v19_v_18 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v20_v_19 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v21_v_20 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v22_v_21 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v23_v_22 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v24_v_23 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v25_v_24 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v26_v_25 is not located in any of them.\r\nWriting file: /tmp/tmpf_ofvalt.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpp1_hf3ub.xml\r\nout: /tmp/tmpf_ofvalt.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmpf_ofvalt.psc loading ..... \r\nParsing file: /tmp/tmpf_ofvalt.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"epo_level\" has been initialised but does not occur in a rate equation\r\nInfo: \"init_EpoRJAK2\" has been initialised but does not occur in a rate equation\r\nInfo: \"init_SHP1\" has been initialised but does not occur in a rate equation\r\nInfo: \"init_STAT5\" has been initialised but does not occur in a rate equation\r\nInfo: \"Total_STAT5\" has been initialised but does not occur in a rate equation\r\nInfo: \"measuralbe_pSTAT5\" has been initialised but does not occur in a rate equation\r\nInfo: \"_pSTAT5_Total_STAT5\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . . . done.\r\nCalculating K matrix . . . . . . . . . . . done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 301 points: 0.09762334823608398\r\nCheck SBML support is at action level 2\r\nSBML file is L2V4\r\nInfo: multiple compartments defined but reaction v1_v_0 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v2_v_1 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v3_v_2 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v4_v_3 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v5_v_4 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v6_v_5 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v7_v_6 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v8_v_7 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v9_v_8 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v12_v_11 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v13_v_12 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v14_v_13 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v15_v_14 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v16_v_15 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v17_v_16 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v18_v_17 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v19_v_18 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v20_v_19 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v21_v_20 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v22_v_21 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v23_v_22 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v24_v_23 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v25_v_24 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v26_v_25 is not located in any of them.\r\nWriting file: /tmp/tmpb2_l5eav.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmp9vw1a79a.xml\r\nout: /tmp/tmpb2_l5eav.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmpb2_l5eav.psc loading ..... \r\nParsing file: /tmp/tmpb2_l5eav.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"epo_level\" has been initialised but does not occur in a rate equation\r\nInfo: \"init_EpoRJAK2\" has been initialised but does not occur in a rate equation\r\nInfo: \"init_SHP1\" has been initialised but does not occur in a rate equation\r\nInfo: \"init_STAT5\" has been initialised but does not occur in a rate equation\r\nInfo: \"Total_STAT5\" has been initialised but does not occur in a rate equation\r\nInfo: \"measuralbe_pSTAT5\" has been initialised but does not occur in a rate equation\r\nInfo: \"_pSTAT5_Total_STAT5\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . . . done.\r\nCalculating K matrix . . . . . . . . . . . done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 301 points: 0.038018226623535156\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_2_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p1_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.27036, + "exception": null, + "id": "plot_2_task2", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_measuralbe_pSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2__pSTAT5_Total_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p1EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p2EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p12EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1Act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_pSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_npSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISnRNA1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISnRNA2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNA", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CIS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ActD", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISEqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISInh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNADelay", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNAEqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNATurn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISTurn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_DeaEpoRJAKActSHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRActJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_JAK2ActEpo", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1ActEpoR", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1Dea", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Eqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3EqcOE", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Turn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3oe", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5ActEpoR", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5ActJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5Exp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5Imp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_epo_level", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_EpoRJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_SHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Epo", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Total_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_cyt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_nuc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v1_v_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v2_v_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v3_v_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v4_v_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v5_v_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v6_v_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v7_v_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v8_v_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v9_v_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v12_v_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v13_v_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v14_v_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v15_v_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v16_v_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v17_v_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v18_v_17", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v19_v_18", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v20_v_19", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v21_v_20", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v22_v_21", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v23_v_22", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v24_v_23", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v25_v_24", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v26_v_25", + "status": "SUCCEEDED" + } + ], + "duration": 0.277095, + "exception": null, + "id": "autogen_report_for_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": null, + "duration": 0.75718, + "exception": null, + "id": "task2", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task2_v20_v_19__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Epo__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_init_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CIS__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SOCS3Turn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SOCS3Inh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_STAT5ActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v9_v_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v17_v_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_p1EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v16_v_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_epo_level__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v24_v_23__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v26_v_25__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SOCS3Eqc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v23_v_22__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_p2EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v7_v_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_STAT5Imp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISTurn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_STAT5Exp__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_p12EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SOCS3EqcOE__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v22_v_21__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v6_v_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v21_v_20__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_Total_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISRNADelay__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p1_measuralbe_pSTAT5_1_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_STAT5ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_EpoRpJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v3_v_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_init_SHP1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISnRNA2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_init_EpoRJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SOCS3oe__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v2_v_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v14_v_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v1_v_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v18_v_17__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v8_v_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_EpoRActJAK2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v13_v_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_nuc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISRNAEqc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_pSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_cyt__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v25_v_24__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v15_v_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SHP1Dea__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v5_v_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISnRNA1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_JAK2ActEpo__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SOCS3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISRNATurn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_ActD__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISInh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v4_v_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_SHP1ActEpoR__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISEqc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `p1__pSTAT5_Total_STAT5_2_task2` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_CISRNA__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "rbapy": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.167536, + "exception": { + "message": "`/root/in/Adlung2021__model_jakstat_pa.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpc2oqdj6t/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` may be invalid.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_SHP1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_STAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'epo_level' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'STAT5 + pSTAT5 + 0.275 * npSTAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_0(Epo, EpoRJAK2, JAK2ActEpo, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_1(DeaEpoRJAKActSHP1, EpoRpJAK2, SHP1Act, SHP1ActEpoR)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_2(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_3(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_4(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_5(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_6(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_7(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_8(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p12EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_11(EpoRpJAK2, SHP1, SHP1ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SHP1Dea * SHP1Act' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_13(EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActJAK2, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_14(CIS, CISEqc, CISInh, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_15(STAT5Imp, cyt, pSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_16(STAT5Exp, npSTAT5, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * Function_for_v_17(ActD, CISRNAEqc, CISRNATurn, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * CISRNADelay * CISnRNA1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_19(CISRNADelay, CISnRNA2, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISRNATurn * CISRNA' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_21(CISEqc, CISRNA, CISTurn)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISTurn * CIS' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_23(ActD, SOCS3Eqc, SOCS3Turn, cyt, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SOCS3Turn * SOCS3' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_25(SOCS3Eqc, SOCS3EqcOE, SOCS3Turn, SOCS3oe)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISInh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNADelay' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNAEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNATurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISTurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'DeaEpoRJAKActSHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'EpoRActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'JAK2ActEpo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1Dea' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Eqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3EqcOE' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Inh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Turn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3oe' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Exp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Imp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'epo_level' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_EpoRJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_SHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Epo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Total_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'measuralbe_pSTAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id '_pSTAT5_Total_STAT5' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` may be invalid.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNA__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` may be invalid.\r\n - Variable `auto_dg_for_task2_CIS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` may be invalid.\r\n - Variable `auto_dg_for_task2_ActD__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` may be invalid.\r\n - Variable `auto_dg_for_task2_CISInh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISTurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` may be invalid.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` may be invalid.\r\n - Variable `auto_dg_for_task2_epo_level__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` may be invalid.\r\n - Variable `auto_dg_for_task2_Epo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` may be invalid.\r\n - Variable `auto_dg_for_task2_cyt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` may be invalid.\r\n - Variable `auto_dg_for_task2_nuc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` may be invalid.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` may be invalid.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` may be invalid.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` may be invalid.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` may be invalid.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` may be invalid.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` may be invalid.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` may be invalid.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` may be invalid.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` may be invalid.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` may be invalid.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` may be invalid.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` may be invalid.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` may be invalid.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` may be invalid.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` may be invalid.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` may be invalid.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` may be invalid.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` may be invalid.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` may be invalid.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` may be invalid.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` may be invalid.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` may be invalid.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` may be invalid.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` may be invalid.\r\n - Model `model` may be invalid.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_SHP1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_STAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'epo_level' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'STAT5 + pSTAT5 + 0.275 * npSTAT5' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pSTAT5 / Total_STAT5 * 100' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_0(Epo, EpoRJAK2, JAK2ActEpo, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_1(DeaEpoRJAKActSHP1, EpoRpJAK2, SHP1Act, SHP1ActEpoR)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_2(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_3(EpoRActJAK2, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_4(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_5(EpoRActJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_6(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_7(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_8(DeaEpoRJAKActSHP1, SHP1Act, SHP1ActEpoR, p12EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_11(EpoRpJAK2, SHP1, SHP1ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SHP1Dea * SHP1Act' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_13(EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActJAK2, p12EpoRpJAK2, p1EpoRpJAK2, p2EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_14(CIS, CISEqc, CISInh, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActEpoR, p12EpoRpJAK2, p1EpoRpJAK2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_15(STAT5Imp, cyt, pSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_16(STAT5Exp, npSTAT5, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * Function_for_v_17(ActD, CISRNAEqc, CISRNATurn, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'nuc * CISRNADelay * CISnRNA1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_19(CISRNADelay, CISnRNA2, nuc)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISRNATurn * CISRNA' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_21(CISEqc, CISRNA, CISTurn)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * CISTurn * CIS' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'Function_for_v_23(ActD, SOCS3Eqc, SOCS3Turn, cyt, npSTAT5)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * SOCS3Turn * SOCS3' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'cyt * Function_for_v_25(SOCS3Eqc, SOCS3EqcOE, SOCS3Turn, SOCS3oe)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISInh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNADelay' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNAEqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISRNATurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'CISTurn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'DeaEpoRJAKActSHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'EpoRActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'JAK2ActEpo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SHP1Dea' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Eqc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3EqcOE' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Inh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3Turn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SOCS3oe' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActEpoR' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5ActJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Exp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'STAT5Imp' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'epo_level' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_EpoRJAK2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_SHP1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'init_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Epo' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Total_STAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'measuralbe_pSTAT5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id '_pSTAT5_Total_STAT5' does not have a 'units' attribute.\r\n \r\n - Task `task2` may be invalid.\r\n - Changes may be invalid.\r\n - Change 1 may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `measuralbe_pSTAT5_1_task2` may be invalid.\r\n - Variable `p1_measuralbe_pSTAT5_1_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `_pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - Variable `p1__pSTAT5_Total_STAT5_2_task2` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p1EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p1EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p2EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p2EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_p12EpoRpJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_p12EpoRpJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Act` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Act__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_pSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_pSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_npSTAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_npSTAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA1` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISnRNA2` may be invalid.\r\n - Variable `auto_dg_for_task2_CISnRNA2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNA` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNA__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CIS` may be invalid.\r\n - Variable `auto_dg_for_task2_CIS__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_ActD` may be invalid.\r\n - Variable `auto_dg_for_task2_ActD__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISInh` may be invalid.\r\n - Variable `auto_dg_for_task2_CISInh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNADelay` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNADelay__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNAEqc` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNAEqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISRNATurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISRNATurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_CISTurn` may be invalid.\r\n - Variable `auto_dg_for_task2_CISTurn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_DeaEpoRJAKActSHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_DeaEpoRJAKActSHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_EpoRActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_EpoRActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_JAK2ActEpo` may be invalid.\r\n - Variable `auto_dg_for_task2_JAK2ActEpo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SHP1Dea` may be invalid.\r\n - Variable `auto_dg_for_task2_SHP1Dea__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Eqc` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Eqc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3EqcOE` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3EqcOE__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Inh` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Inh__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3Turn` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3Turn__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_SOCS3oe` may be invalid.\r\n - Variable `auto_dg_for_task2_SOCS3oe__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActEpoR` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActEpoR__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5ActJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5ActJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Exp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Exp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_STAT5Imp` may be invalid.\r\n - Variable `auto_dg_for_task2_STAT5Imp__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_epo_level` may be invalid.\r\n - Variable `auto_dg_for_task2_epo_level__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_EpoRJAK2` may be invalid.\r\n - Variable `auto_dg_for_task2_init_EpoRJAK2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_SHP1` may be invalid.\r\n - Variable `auto_dg_for_task2_init_SHP1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_init_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_init_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Epo` may be invalid.\r\n - Variable `auto_dg_for_task2_Epo__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_Total_STAT5` may be invalid.\r\n - Variable `auto_dg_for_task2_Total_STAT5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_cyt` may be invalid.\r\n - Variable `auto_dg_for_task2_cyt__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_nuc` may be invalid.\r\n - Variable `auto_dg_for_task2_nuc__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v1_v_0` may be invalid.\r\n - Variable `auto_dg_for_task2_v1_v_0__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v2_v_1` may be invalid.\r\n - Variable `auto_dg_for_task2_v2_v_1__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v3_v_2` may be invalid.\r\n - Variable `auto_dg_for_task2_v3_v_2__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v4_v_3` may be invalid.\r\n - Variable `auto_dg_for_task2_v4_v_3__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v5_v_4` may be invalid.\r\n - Variable `auto_dg_for_task2_v5_v_4__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v6_v_5` may be invalid.\r\n - Variable `auto_dg_for_task2_v6_v_5__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v7_v_6` may be invalid.\r\n - Variable `auto_dg_for_task2_v7_v_6__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v8_v_7` may be invalid.\r\n - Variable `auto_dg_for_task2_v8_v_7__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v9_v_8` may be invalid.\r\n - Variable `auto_dg_for_task2_v9_v_8__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v12_v_11` may be invalid.\r\n - Variable `auto_dg_for_task2_v12_v_11__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v13_v_12` may be invalid.\r\n - Variable `auto_dg_for_task2_v13_v_12__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v14_v_13` may be invalid.\r\n - Variable `auto_dg_for_task2_v14_v_13__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v15_v_14` may be invalid.\r\n - Variable `auto_dg_for_task2_v15_v_14__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v16_v_15` may be invalid.\r\n - Variable `auto_dg_for_task2_v16_v_15__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v17_v_16` may be invalid.\r\n - Variable `auto_dg_for_task2_v17_v_16__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v18_v_17` may be invalid.\r\n - Variable `auto_dg_for_task2_v18_v_17__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v19_v_18` may be invalid.\r\n - Variable `auto_dg_for_task2_v19_v_18__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v20_v_19` may be invalid.\r\n - Variable `auto_dg_for_task2_v20_v_19__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v21_v_20` may be invalid.\r\n - Variable `auto_dg_for_task2_v21_v_20__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v22_v_21` may be invalid.\r\n - Variable `auto_dg_for_task2_v22_v_21__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v23_v_22` may be invalid.\r\n - Variable `auto_dg_for_task2_v23_v_22__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v24_v_23` may be invalid.\r\n - Variable `auto_dg_for_task2_v24_v_23__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v25_v_24` may be invalid.\r\n - Variable `auto_dg_for_task2_v25_v_24__x` may be invalid.\r\n - XPath could not be validated.\r\n - Data generator `auto_dg_for_task2_v26_v_25` may be invalid.\r\n - Variable `auto_dg_for_task2_v26_v_25__x` may be invalid.\r\n - XPath could not be validated.\r\n - Output `plot_2_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\r\n - Output `autogen_report_for_task2` may be invalid.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "smoldyn": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", + "log_yml": {}, + "detailed_error_log": {} + }, + "tellurium": { + "exception_message": "", + "log_yml": { + "duration": 1.615605, + "exception": null, + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmplbigyzh_/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` has warnings.\r\n - Model `model` has warnings.\r\n - The model file `Adlung2021 _model_jakstat_pa.xml` has warnings.\r\n - 43 warnings of type SBML unit consistency (99505). The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmplbigyzh_/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Output `plot_2_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\r\n - Output `autogen_report_for_task2` has warnings.\r\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.\u001b[0m\r\n\r\n", + "sedDocuments": [ + { + "duration": 1.046206, + "exception": null, + "location": "Adlung2021 _model_jakstat_pa.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 1 plots:\r\n Adlung2021 _model_jakstat_pa.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 71 data sets\r\n Plots (1):\r\n plot_2_task2: 2 curves\r\n\r\nExecuting SED-ML file 1: Adlung2021 _model_jakstat_pa.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_2_task2`\r\n Executing task 1: `task2`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_2_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p1_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.355131, + "exception": null, + "id": "plot_2_task2", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning:\r\n\r\n\u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_measuralbe_pSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2__pSTAT5_Total_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p1EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p2EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p12EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1Act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_pSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_npSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISnRNA1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISnRNA2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNA", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CIS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ActD", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISEqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISInh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNADelay", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNAEqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNATurn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISTurn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_DeaEpoRJAKActSHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRActJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_JAK2ActEpo", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1ActEpoR", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1Dea", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Eqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3EqcOE", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Turn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3oe", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5ActEpoR", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5ActJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5Exp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5Imp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_epo_level", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_EpoRJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_SHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Epo", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Total_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_cyt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_nuc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v1_v_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v2_v_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v3_v_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v4_v_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v5_v_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v6_v_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v7_v_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v8_v_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v9_v_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v12_v_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v13_v_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v14_v_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v15_v_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v16_v_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v17_v_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v18_v_17", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v19_v_18", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v20_v_19", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v21_v_20", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v22_v_21", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v23_v_22", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v24_v_23", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v25_v_24", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v26_v_25", + "status": "SUCCEEDED" + } + ], + "duration": 0.282932, + "exception": null, + "id": "autogen_report_for_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": null, + "duration": 0.16596, + "exception": null, + "id": "task2", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `auto_dg_for_task2_SHP1Act__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v26_v_25__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_npSTAT5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v12_v_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_init_STAT5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v19_v_18__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task2_v16_v_15__x` has 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The following is the first warning at line 1388, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'init_EpoRJAK2' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 29 warnings of type Modeling practice (80701). The following is the first warning at line 1357, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ActD' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning:\r\n\r\n\u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mAlgorithm parameter with KiSAO id 'KISAO_0000216' was ignored because it is not supported. 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Done", + "sedDocuments": [ + { + "duration": null, + "exception": { + "message": "Traceback (most recent call last): File '/usr/lib/python3.10/runpy.py', line 196, in _run_module_as_main return _run_code(code, main_globals, None, File '/usr/lib/python3.10/runpy.py', line 86, in _run_code exec(code, run_globals) File '/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py', line 397, in fire.Fire({ File '/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.10/lib/python3.10/site-packages/fire/core.py', line 141, in Fire component_trace = _Fire(component, args, parsed_flag_args, context, name) File '/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.10/lib/python3.10/site-packages/fire/core.py', line 475, in _Fire component, remaining_args = _CallAndUpdateTrace( File '/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.10/lib/python3.10/site-packages/fire/core.py', line 691, in _CallAndUpdateTrace component = fn(*varargs, **kwargs) File '/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py', line 390, in gen_plots_for_sed2d_only sns.lineplot(data=df, x=data['x'], y=series_name, ax=ax, label=(curve_id if shouldLabel else None)) File '/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.10/lib/python3.10/site-packages/seaborn/relational.py', line 618, in lineplot p = _LinePlotter( File '/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.10/lib/python3.10/site-packages/seaborn/relational.py', line 365, in __init__ super().__init__(data=data, variables=variables) File '/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.10/lib/python3.10/site-packages/seaborn/_oldcore.py', line 640, in __init__ self.assign_variables(data, variables) File '/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.10/lib/python3.10/site-packages/seaborn/_oldcore.py', line 701, in assign_variables plot_data, variables = self._assign_variables_longform( File '/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.10/lib/python3.10/site-packages/seaborn/_oldcore.py', line 938, in _assign_variables_longform raise ValueError(err) ValueError: Could not interpret value `_1_task2` for parameter `x` Failure executing the sed document.", + "type": "RuntimeException" + }, + "location": "Adlung2021 _model_jakstat_pa.sedml", + "output": "Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating CSV file... Done.", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "QUEUED" + }, + { + "id": "p1_curve_2_task2", + "status": "QUEUED" + } + ], + "duration": null, + "exception": null, + "id": "plot_2_task2", + "output": null, + "skipReason": null, + "status": "QUEUED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "QUEUED" + }, + { + "id": "autogen_task2_measuralbe_pSTAT5", + "status": "QUEUED" + }, + { + "id": "autogen_task2__pSTAT5_Total_STAT5", + "status": "QUEUED" + }, + { + "id": "autogen_task2_EpoRJAK2", + "status": "QUEUED" + }, + { + "id": "autogen_task2_EpoRpJAK2", + "status": "QUEUED" + }, + { + "id": "autogen_task2_p1EpoRpJAK2", + "status": "QUEUED" + }, + { + "id": "autogen_task2_p2EpoRpJAK2", + "status": "QUEUED" + }, + { + "id": "autogen_task2_p12EpoRpJAK2", + "status": "QUEUED" + }, + { + "id": "autogen_task2_SHP1", + "status": "QUEUED" + }, + { + "id": "autogen_task2_SHP1Act", + "status": "QUEUED" + }, + { + "id": 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"autogen_task2_init_SHP1", + "status": "QUEUED" + }, + { + "id": "autogen_task2_init_STAT5", + "status": "QUEUED" + }, + { + "id": "autogen_task2_Epo", + "status": "QUEUED" + }, + { + "id": "autogen_task2_Total_STAT5", + "status": "QUEUED" + }, + { + "id": "autogen_task2_cyt", + "status": "QUEUED" + }, + { + "id": "autogen_task2_nuc", + "status": "QUEUED" + }, + { + "id": "autogen_task2_v1_v_0", + "status": "QUEUED" + }, + { + "id": "autogen_task2_v2_v_1", + "status": "QUEUED" + }, + { + "id": "autogen_task2_v3_v_2", + "status": "QUEUED" + }, + { + "id": "autogen_task2_v4_v_3", + "status": "QUEUED" + }, + { + "id": "autogen_task2_v5_v_4", + "status": "QUEUED" + }, + { + "id": "autogen_task2_v6_v_5", + "status": "QUEUED" + }, + { + "id": "autogen_task2_v7_v_6", + "status": "QUEUED" + }, + { + "id": "autogen_task2_v8_v_7", + "status": "QUEUED" + }, + { + "id": "autogen_task2_v9_v_8", + "status": "QUEUED" + }, + { + "id": "autogen_task2_v12_v_11", + "status": "QUEUED" + }, + { + "id": 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Starting simulation... done.", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": { + "status": "FAIL", + "error_message": "Runtime Exception" + } + }, + "xpp": { + "exception_message": "Command '-i '/root/in/Adlung2021__model_jakstat_pa.omex' -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1", + "log_yml": { + "duration": 0.059965, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmplzbzn_dl/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + } +} \ No newline at end of file diff --git a/BioModels/BIOMD0000001077/tests/results_remote.json b/BioModels/BIOMD0000001077/tests/results_remote.json new file mode 100644 index 00000000..e07aa099 --- /dev/null +++ b/BioModels/BIOMD0000001077/tests/results_remote.json @@ -0,0 +1,2482 @@ +{ + "amici": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc70b10bb4455d618775b", + "download": "https://api.biosimulations.org/results/674dc70b10bb4455d618775b/download", + "logs": "https://api.biosimulations.org/logs/674dc70b10bb4455d618775b?includeOutput=true", + "log_yml": { + "duration": 33.984144, + "exception": { + "message": "The COMBINE/OMEX did not execute 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archive.\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cobrapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc71510bb4455d6187760", + "download": "https://api.biosimulations.org/results/674dc71510bb4455d6187760/download", + "logs": "https://api.biosimulations.org/logs/674dc71510bb4455d6187760?includeOutput=true", + "log_yml": { + "duration": 0.211138, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "copasi": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc717ef911d5d45259b9d", + "download": "https://api.biosimulations.org/results/674dc717ef911d5d45259b9d/download", + "logs": "https://api.biosimulations.org/logs/674dc717ef911d5d45259b9d?includeOutput=true", + "log_yml": { + "duration": 1.641921, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 1.288502, + "exception": null, + "location": "Adlung2021 _model_jakstat_pa.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 1 plots:\r\n Adlung2021 _model_jakstat_pa.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 71 data sets\r\n Plots (1):\r\n plot_2_task2: 2 curves\r\n\r\nExecuting SED-ML file 1: Adlung2021 _model_jakstat_pa.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_2_task2`\r\n Executing task 1: `task2`\r\n Executing simulation ...woohoo!\r\nwoohoo!\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_2_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p1_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.425806, + "exception": null, + "id": "plot_2_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_measuralbe_pSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2__pSTAT5_Total_STAT5", + "status": "SUCCEEDED" + }, + { + "id": 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Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", + "sedDocuments": [ + { + "duration": 1.562623, + "exception": null, + "location": "Adlung2021 _model_jakstat_pa.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 1 plots:\r\n Adlung2021 _model_jakstat_pa.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 71 data sets\r\n Plots (1):\r\n plot_2_task2: 2 curves\r\n\r\nExecuting SED-ML file 1: Adlung2021 _model_jakstat_pa.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_2_task2`\r\n Executing task 1: `task2`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nInfo: multiple compartments defined but reaction v1_v_0 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v2_v_1 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v3_v_2 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v4_v_3 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v5_v_4 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v6_v_5 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v7_v_6 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v8_v_7 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v9_v_8 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v12_v_11 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v13_v_12 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v14_v_13 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v15_v_14 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v16_v_15 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v17_v_16 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v18_v_17 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v19_v_18 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v20_v_19 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v21_v_20 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v22_v_21 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v23_v_22 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v24_v_23 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v25_v_24 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v26_v_25 is not located in any of them.\r\nWriting file: /tmp/tmpy900as0i.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmp6gzqmdi2.xml\r\nout: /tmp/tmpy900as0i.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpy900as0i.psc loading ..... \r\nParsing file: /tmp/tmpy900as0i.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"epo_level\" has been initialised but does not occur in a rate equation\r\nInfo: \"init_EpoRJAK2\" has been initialised but does not occur in a rate equation\r\nInfo: \"init_SHP1\" has been initialised but does not occur in a rate equation\r\nInfo: \"init_STAT5\" has been initialised but does not occur in a rate equation\r\nInfo: \"Total_STAT5\" has been initialised but does not occur in a rate equation\r\nInfo: \"measuralbe_pSTAT5\" has been initialised but does not occur in a rate equation\r\nInfo: \"_pSTAT5_Total_STAT5\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . . . done.\r\nCalculating K matrix . . . . . . . . . . . done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 301 points: 0.10260415077209473\r\nCheck SBML support is at action level 2\r\nSBML file is L2V4\r\nInfo: multiple compartments defined but reaction v1_v_0 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v2_v_1 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v3_v_2 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v4_v_3 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v5_v_4 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v6_v_5 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v7_v_6 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v8_v_7 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v9_v_8 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v12_v_11 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v13_v_12 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v14_v_13 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v15_v_14 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v16_v_15 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v17_v_16 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v18_v_17 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v19_v_18 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v20_v_19 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v21_v_20 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v22_v_21 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v23_v_22 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v24_v_23 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v25_v_24 is not located in any of them.\r\nInfo: multiple compartments defined but reaction v26_v_25 is not located in any of them.\r\nWriting file: /tmp/tmpbpvx7xp9.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpmmgnw416.xml\r\nout: /tmp/tmpbpvx7xp9.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpbpvx7xp9.psc loading ..... \r\nParsing file: /tmp/tmpbpvx7xp9.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"epo_level\" has been initialised but does not occur in a rate equation\r\nInfo: \"init_EpoRJAK2\" has been initialised but does not occur in a rate equation\r\nInfo: \"init_SHP1\" has been initialised but does not occur in a rate equation\r\nInfo: \"init_STAT5\" has been initialised but does not occur in a rate equation\r\nInfo: \"Total_STAT5\" has been initialised but does not occur in a rate equation\r\nInfo: \"measuralbe_pSTAT5\" has been initialised but does not occur in a rate equation\r\nInfo: \"_pSTAT5_Total_STAT5\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . . . done.\r\nCalculating K matrix . . . . . . . . . . . done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 301 points: 0.03392362594604492\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_2_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p1_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.32812, + "exception": null, + "id": "plot_2_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_measuralbe_pSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2__pSTAT5_Total_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p1EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p2EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p12EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1Act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_pSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_npSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISnRNA1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISnRNA2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNA", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CIS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ActD", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISEqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISInh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNADelay", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNAEqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNATurn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISTurn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_DeaEpoRJAKActSHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRActJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_JAK2ActEpo", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1ActEpoR", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1Dea", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Eqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3EqcOE", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Turn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3oe", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5ActEpoR", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5ActJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5Exp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5Imp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_epo_level", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_EpoRJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_SHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Epo", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Total_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_cyt", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_nuc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v1_v_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v2_v_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v3_v_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v4_v_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v5_v_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v6_v_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v7_v_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v8_v_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v9_v_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v12_v_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v13_v_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v14_v_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v15_v_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v16_v_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v17_v_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v18_v_17", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v19_v_18", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v20_v_19", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v21_v_20", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v22_v_21", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v23_v_22", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v24_v_23", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v25_v_24", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_v26_v_25", + "status": "SUCCEEDED" + } + ], + "duration": 0.281397, + "exception": null, + "id": "autogen_report_for_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": null, + "duration": 0.770676, + "exception": null, + "id": "task2", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "rbapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc72cef911d5d45259bdc", + "download": "https://api.biosimulations.org/results/674dc72cef911d5d45259bdc/download", + "logs": "https://api.biosimulations.org/logs/674dc72cef911d5d45259bdc?includeOutput=true", + "log_yml": { + "duration": 0.19761, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n - Simulation `sim1` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "smoldyn": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc72eef911d5d45259bf2", + "download": "https://api.biosimulations.org/results/674dc72eef911d5d45259bf2/download", + "logs": "https://api.biosimulations.org/logs/674dc72eef911d5d45259bf2?includeOutput=true", + "log_yml": { + "duration": 0.052547, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "tellurium": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc73010bb4455d61877b0", + "download": "https://api.biosimulations.org/results/674dc73010bb4455d61877b0/download", + "logs": "https://api.biosimulations.org/logs/674dc73010bb4455d61877b0?includeOutput=true", + "log_yml": { + "duration": 2.003138, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 1.536872, + "exception": null, + "location": "Adlung2021 _model_jakstat_pa.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 1 plots:\r\n Adlung2021 _model_jakstat_pa.sedml:\r\n Tasks (2):\r\n task1\r\n task2\r\n Reports (1):\r\n autogen_report_for_task2: 71 data sets\r\n Plots (1):\r\n plot_2_task2: 2 curves\r\n\r\nExecuting SED-ML file 1: Adlung2021 _model_jakstat_pa.sedml ...\r\n Found 2 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n `task2`\r\n Outputs:\r\n `autogen_report_for_task2`\r\n `plot_2_task2`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_2_task2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_report_for_task2` ... \u001b[36mqueued\u001b[0m\r\n Executing task 2: `task2`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_2_task2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_report_for_task2` ...", + "outputs": [ + { + "curves": [ + { + "id": "p1_curve_1_task2", + "status": "SUCCEEDED" + }, + { + "id": "p1_curve_2_task2", + "status": "SUCCEEDED" + } + ], + "duration": 0.171614, + "exception": null, + "id": "plot_2_task2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_measuralbe_pSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2__pSTAT5_Total_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p1EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p2EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_p12EpoRpJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1Act", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_pSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_npSTAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISnRNA1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISnRNA2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNA", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CIS", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_ActD", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISEqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISInh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNADelay", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNAEqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISRNATurn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_CISTurn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_DeaEpoRJAKActSHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_EpoRActJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_JAK2ActEpo", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1ActEpoR", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SHP1Dea", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Eqc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3EqcOE", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Inh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3Turn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_SOCS3oe", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5ActEpoR", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5ActJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5Exp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_STAT5Imp", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_epo_level", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_EpoRJAK2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_SHP1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_init_STAT5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Epo", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task2_Total_STAT5", + "status": 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"simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "vcell": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc733ef911d5d45259bfd", + "download": "https://api.biosimulations.org/results/674dc733ef911d5d45259bfd/download", + "logs": "https://api.biosimulations.org/logs/674dc733ef911d5d45259bfd?includeOutput=true", + "log_yml": { + "duration": 10, + "exception": null, + "output": "Processing Adlung2021 _model_jakstat_pa.sedml. 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Starting simulation... done.", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "xpp": { + "response": 201, + "view": "https://api.biosimulations.org/runs/674dc73510bb4455d61877b9", + "download": "https://api.biosimulations.org/results/674dc73510bb4455d61877b9/download", + "logs": "https://api.biosimulations.org/logs/674dc73510bb4455d61877b9?includeOutput=true", + "log_yml": { + "duration": 0.073538, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + } +} \ No newline at end of file diff --git a/BioModels/test_biomodels_compatibility_biosimulators.py b/BioModels/test_biomodels_compatibility_biosimulators.py index 9f30f049..d02cf941 100644 --- a/BioModels/test_biomodels_compatibility_biosimulators.py +++ b/BioModels/test_biomodels_compatibility_biosimulators.py @@ -164,5 +164,8 @@ def main(): if __name__ == "__main__": use_original_files = False - biomodel_id_list = ["BIOMD0000000001","BIOMD0000000138"] - main() + biomodel_id_list = ["BIOMD0000000001", + "BIOMD0000000138", + "BIOMD0000000724", + "BIOMD0000001077"] + main() \ No newline at end of file diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md index 22b1eb79..80426bb9 100644 --- a/SBML/tests/results_compatibility_biosimulators.md +++ b/SBML/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|:-------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| -|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/

|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with AMICI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

| plot | plot | -|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with BioNetGen.

BNGL and SED-ML are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with BoolNet.

SED-ML and SBML-qual are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with Brian 2.

NeuroML, LEMS and SED-ML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with GillesPy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with GINsim.

SED-ML and SBML-qual are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with LibSBMLSim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with MASSpy.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with NetPyNE.

NeuroML, LEMS and SED-ML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with NEURON.

NeuroML, LEMS and SED-ML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with OpenCOR.

CellML and SED-ML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with pyNeuroML.

NeuroML, LEMS and SED-ML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with PySCeS.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with RBApy.

RBApy and SED-ML are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with Smoldyn.

SED-ML and Smoldyn are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

BNGL, SBML and SED-ML are compatible with VCell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with XPP.

SED-ML and XPP are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with AMICI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

| plot | plot | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

Only BNGL, SED-ML are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with GillesPy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with LibSBMLSim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with MASSpy.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

Only CellML, SED-ML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with PySCeS.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

Only RBApy, SED-ML are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

Only Smoldyn, SED-ML are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML, BNGL and SBML are compatible with VCell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

Only XPP, SED-ML are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_00001/tests/results_compatibility_biosimulators.md b/test_suite/test_00001/tests/results_compatibility_biosimulators.md index 9cab69c5..788e6bbf 100644 --- a/test_suite/test_00001/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_00001/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|:--------------------------------------------------------| -|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with AMICI.

SED-ML and SBML are compatible with AMICI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with BioNetGen.

SED-ML and BNGL are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with BoolNet.

SBML-qual and SED-ML are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with Brian 2.

SED-ML, LEMS and NeuroML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with CBMPy.

SED-ML and SBML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COBRApy.

SED-ML and SBML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COPASI.

SED-ML and SBML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with GillesPy2.

SED-ML and SBML are compatible with GillesPy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with GINsim.

SBML-qual and SED-ML are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with LibSBMLSim.

SED-ML and SBML are compatible with LibSBMLSim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with MASSpy.

SED-ML and SBML are compatible with MASSpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with NetPyNE.

SED-ML, LEMS and NeuroML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with NEURON.

SED-ML, LEMS and NeuroML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with OpenCOR.

SED-ML and CellML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with pyNeuroML.

SED-ML, LEMS and NeuroML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with PySCeS.

SED-ML and SBML are compatible with PySCeS.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with RBApy.

SED-ML and RBApy are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with Smoldyn.

SED-ML and Smoldyn are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with Tellurium.

SED-ML and SBML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with VCell.

SED-ML, BNGL and SBML are compatible with VCell.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with XPP.

SED-ML and XPP are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|:--------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with AMICI.

SED-ML and SBML are compatible with AMICI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

Only BNGL, SED-ML are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with CBMPy.

SED-ML and SBML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COBRApy.

SED-ML and SBML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COPASI.

SED-ML and SBML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with GillesPy2.

SED-ML and SBML are compatible with GillesPy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with LibSBMLSim.

SED-ML and SBML are compatible with LibSBMLSim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with MASSpy.

SED-ML and SBML are compatible with MASSpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

Only CellML, SED-ML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with PySCeS.

SED-ML and SBML are compatible with PySCeS.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

Only RBApy, SED-ML are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

Only Smoldyn, SED-ML are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with Tellurium.

SED-ML and SBML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with VCell.

SED-ML, BNGL and SBML are compatible with VCell.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

Only XPP, SED-ML are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_01186/tests/results_compatibility_biosimulators.md b/test_suite/test_01186/tests/results_compatibility_biosimulators.md index 6c2279b7..b03cea6b 100644 --- a/test_suite/test_01186/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_01186/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| -|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with AMICI.

SED-ML and SBML are compatible with AMICI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with BioNetGen.

SED-ML and BNGL are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with BoolNet.

SBML-qual and SED-ML are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with Brian 2.

SED-ML, LEMS and NeuroML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with CBMPy.

SED-ML and SBML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COBRApy.

SED-ML and SBML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `cobra.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/opencobra/cobrapy/issues .

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `cobra.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/opencobra/cobrapy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COPASI.

SED-ML and SBML are compatible with COPASI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with GillesPy2.

SED-ML and SBML are compatible with GillesPy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with GINsim.

SBML-qual and SED-ML are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with LibSBMLSim.

SED-ML and SBML are compatible with LibSBMLSim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with MASSpy.

SED-ML and SBML are compatible with MASSpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with NetPyNE.

SED-ML, LEMS and NeuroML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with NEURON.

SED-ML, LEMS and NeuroML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with OpenCOR.

SED-ML and CellML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with pyNeuroML.

SED-ML, LEMS and NeuroML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with PySCeS.

SED-ML and SBML are compatible with PySCeS.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with RBApy.

SED-ML and RBApy are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with Smoldyn.

SED-ML and Smoldyn are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with Tellurium.

SED-ML and SBML are compatible with Tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with VCell.

SED-ML, BNGL and SBML are compatible with VCell.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with XPP.

SED-ML and XPP are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with AMICI.

SED-ML and SBML are compatible with AMICI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

Only BNGL, SED-ML are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with CBMPy.

SED-ML and SBML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COBRApy.

SED-ML and SBML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `cobra.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/opencobra/cobrapy/issues .

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `cobra.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/opencobra/cobrapy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COPASI.

SED-ML and SBML are compatible with COPASI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with GillesPy2.

SED-ML and SBML are compatible with GillesPy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

Only SBML-qual, SED-ML are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with LibSBMLSim.

SED-ML and SBML are compatible with LibSBMLSim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with MASSpy.

SED-ML and SBML are compatible with MASSpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

Only CellML, SED-ML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

Only NeuroML, SED-ML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with PySCeS.

SED-ML and SBML are compatible with PySCeS.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

Only RBApy, SED-ML are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

Only Smoldyn, SED-ML are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with Tellurium.

SED-ML and SBML are compatible with Tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with VCell.

SED-ML, BNGL and SBML are compatible with VCell.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

Only XPP, SED-ML are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/utils/__init__.py b/utils/__init__.py index 4b8c6269..b4242165 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -227,24 +227,39 @@ def get_entry_format(file_path, file_type): return file_entry_format +def temp_sedml_file_if_not_empty(sedml_filepath, temp_sedml_filepath): + """ + If the temp_sedml_filepath is not empty, return its content, otherwise return the original content of the sedml file + """ + sedstr = "" -def add_xmlns_sbml_attribute(sedml_filepath, sbml_filepath, output_filepath=None): + if temp_sedml_filepath: + if os.path.exists(temp_sedml_filepath): + with open(temp_sedml_filepath, 'r') as file: + sedstr = file.read() + + if sedstr == "": + with open(sedml_filepath, 'r') as file: + sedstr = file.read() + + return sedstr + +def add_xmlns_sbml_attribute(sedml_filepath, sbml_filepath, temp_sedml_filepath=None): ''' add an xmlns:sbml attribute to the sedml file that matches the sbml file raise an error if the attribute is already present output fixed file to output_filepath which defaults to sedml_filepath + + If no temp_sedml_filepath is provided, the original sedml file is overwritten. ''' - # read the sedml file as a string - with open(sedml_filepath, 'r') as file: - sedstr = file.read() + sed_str = temp_sedml_file_if_not_empty(sedml_filepath, temp_sedml_filepath) - m = re.search(r']*>', sedstr) + m = re.search(r']*>', sed_str) if m == None: raise ValueError(f'Invalid SedML file: main tag not found in {sedml_filepath}') - # read the sbml file as a string to add the xmlns attribute if it is missing if "xmlns:sbml" in m.group(): raise ValueError(f'xmlns:sbml attribute already present in file {sedml_filepath}') @@ -254,13 +269,13 @@ def add_xmlns_sbml_attribute(sedml_filepath, sbml_filepath, output_filepath=None sbml_xmlns = re.search(r'xmlns="([^"]*)"', sbml_str).group(1) missing_sbml_attribute = 'xmlns:sbml="' + sbml_xmlns + '"' - sedstr = re.sub(r']*>', sedstr) @@ -293,13 +299,11 @@ def add_xmlns_fbc_attribute(sedml_filepath, sbml_filepath, temp_sedml_filepath=N fbc_xmlns = re.search(r'xmlns:fbc="([^"]*)"', sbml_str).group(1) missing_fbc_attribute = 'xmlns:fbc="' + fbc_xmlns + '"' sedstr = sedstr[:location] + ' ' + missing_fbc_attribute + sedstr[location:] - if temp_sedml_filepath == None: temp_sedml_filepath = sedml_filepath with open(temp_sedml_filepath,"w") as fout: - fout.write(sedstr) @@ -347,6 +351,24 @@ def get_temp_file(): ''' return f"tmp{random.randrange(1000000)}" +def remove_spaces_from_filename(file_path): + ''' + create another file with the same content but with filename spaces replaced by underscores + ''' + dir_name = os.path.dirname(file_path) + if ' ' in dir_name: + raise ValueError(f'File directory path should not contain spaces: {dir_name}') + old_filename = os.path.basename(file_path) + if ' ' not in old_filename: + return file_path + if ' ' in old_filename: + new_filename = old_filename.replace(' ', '_') + new_file_path = os.path.join(dir_name, new_filename) + shutil.copy(file_path, new_file_path) + return new_file_path + + + def create_omex(sedml_filepath, sbml_filepath, omex_filepath=None, silent_overwrite=True, add_missing_xmlns=True): ''' wrap a sedml and an sbml file in a combine archive omex file @@ -367,13 +389,17 @@ def create_omex(sedml_filepath, sbml_filepath, omex_filepath=None, silent_overwr os.remove(omex_filepath) tmp_sedml_filepath = get_temp_file() + if add_missing_xmlns: - if xmlns_sbml_attribute_missing(sedml_filepath): + xmlns_sbml_missing = xmlns_sbml_attribute_missing(sedml_filepath) + xmlns_fbc_missing = xmlns_fbc_attribute_missing(sbml_filepath,sedml_filepath) + if xmlns_sbml_missing: add_xmlns_sbml_attribute(sedml_filepath, sbml_filepath, tmp_sedml_filepath) - if xmlns_fbc_attribute_missing(sbml_filepath,sedml_filepath): + if xmlns_fbc_missing: add_xmlns_fbc_attribute(sedml_filepath, sbml_filepath, tmp_sedml_filepath) - - sedml_filepath = tmp_sedml_filepath + if xmlns_sbml_missing or xmlns_fbc_missing: + sedml_filepath = tmp_sedml_filepath + sbml_file_entry_format = get_entry_format(sbml_filepath, 'SBML') sedml_file_entry_format = get_entry_format(sedml_filepath, 'SEDML') @@ -397,7 +423,7 @@ def create_omex(sedml_filepath, sbml_filepath, omex_filepath=None, silent_overwr ) om.to_omex(Path(omex_filepath)) - if tmp_sedml_filepath: + if os.path.exists(tmp_sedml_filepath): os.remove(tmp_sedml_filepath) return omex_filepath @@ -529,6 +555,7 @@ def check_file_compatibility_test(engine, model_filepath, experiment_filepath): if file_extensions in engine_filetypes_tuple_list: return 'pass', (f"The file extensions {file_extensions} suggest the input file types are {filetypes_strings}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") + if 'xml' in file_extensions: model_sbml = 'sbml' in model_filepath model_sedml = 'sedml' in model_filepath @@ -536,6 +563,7 @@ def check_file_compatibility_test(engine, model_filepath, experiment_filepath): experiment_sedml = 'sedml' in experiment_filepath if model_sbml and experiment_sbml and experiment_sedml and not model_sedml: + file_types_tuple = ('sbml', 'sedml') file_types = [TYPES[i] for i in file_types_tuple] filetypes_strings = ', '.join(file_types[:-1]) + ' and ' + file_types[-1] if len(file_types) > 1 else file_types[0] @@ -543,10 +571,13 @@ def check_file_compatibility_test(engine, model_filepath, experiment_filepath): return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {filetypes_strings} which is compatible with {engine_name}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") else: return 'FAIL', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {filetypes_strings} which is not compatible with {engine_name}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") + else: + return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may not be compatibe with {engine_name}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") else: return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may not be compatibe with {engine_name}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") + def collapsible_content(content, title='Details'): """ Create a collapsible content section in markdown format @@ -609,8 +640,9 @@ def run_biosimulators_remote(engine,sedml_filepath,sbml_filepath): results_urls = biosimulations.submit_simulation_archive(\ archive_file=omex_file_name,\ sim_dict=sim_dict) - - os.remove(omex_filepath) + + if os.path.exists(omex_filepath): + os.remove(omex_filepath) return results_urls @@ -673,7 +705,8 @@ def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir='out detailed_error_log_dict['status'] = 'FAIL' detailed_error_log_dict['error_message'] = "Runtime Exception" - os.remove(omex_filepath) + if os.path.exists(omex_filepath): + os.remove(omex_filepath) return {"exception_message":exception_message,"log_yml":log_yml_dict, "detailed_error_log":detailed_error_log_dict} @@ -689,9 +722,12 @@ def biosimulators_core(engine,omex_filepath,output_dir=None): output_dir: folder to write the simulation outputs to ''' + omex_filepath_no_spaces = remove_spaces_from_filename(omex_filepath) + #directory containing omex file needs mapping into the container as the input folders - omex_dir = os.path.dirname(os.path.abspath(omex_filepath)) - omex_file = os.path.basename(os.path.abspath(omex_filepath)) + omex_dir = os.path.dirname(os.path.abspath(omex_filepath_no_spaces)) + omex_file = os.path.basename(os.path.abspath(omex_filepath_no_spaces)) + mount_in = docker.types.Mount("/root/in",omex_dir,type="bind",read_only=True) #we want the output folder to be different to the input folder @@ -705,8 +741,11 @@ def biosimulators_core(engine,omex_filepath,output_dir=None): client = docker.from_env() client.containers.run(f"ghcr.io/biosimulators/{engine}", mounts=[mount_in,mount_out], - command=f"-i /root/in/{omex_file} -o /root/out", + command=f"-i '/root/in/{omex_file}' -o /root/out", auto_remove=True) + + if os.path.exists(omex_filepath_no_spaces): + os.remove(omex_filepath_no_spaces) def test_engine(engine,filename,error_categories=error_categories): ''' @@ -1167,8 +1206,10 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir): # add xfail to engines that do not support sbml sbml_incompatible_ENGINES = [e for e in ENGINES.keys() if 'sbml' not in ENGINES[e]['formats'][0]] for e in sbml_incompatible_ENGINES: - compatibility = check_file_compatibility_test(e, sbml_filepath, sedml_filepath) - compatibility_content = f'EXPECTED FAIL

{compatibility[1]}' + engine_name = ENGINES[e]['name'] + unique_compatible_filetpyes_strings = ', '.join([TYPES[i] for i in ENGINES[e]['formats'][0] if i in list(TYPES.keys())]) + compatibility = (f"Only {unique_compatible_filetpyes_strings} are compatible with {engine_name}.") + compatibility_content = f'EXPECTED FAIL

{compatibility}' results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content, title=f'{xfail_html}') results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = f'{xfail_html}' @@ -1387,4 +1428,4 @@ def run_biosimulators_remotely_and_locally(engine_keys, d1_plots_remote_dir=d1_plots_remote_dir, test_folder=test_folder) - return results_table \ No newline at end of file + return results_table