DRAM fails in Pfam step #2
Description
Hi,
After two hours of execution, I get this error message:
2020-02-20 09:01:34.157973: Annotation started
0:00:00.015948: 293 fastas found
0:00:00.200998: Retrieved database locations and descriptions
0:00:00.201027: Annotating OX3.63.fa.edit
0:00:00.204969: Filtering fasta
0:00:00.567192: Calling genes with prodigal
0:01:02.343928: Turning genes from prodigal to mmseqs2 db
0:01:05.671204: Getting hits from kofam
0:17:22.857032: Getting forward best hits from uniref
1:59:58.829147: Getting reverse best hits from uniref
2:01:09.718439: Getting descriptions of hits from uniref
2:02:49.837900: Getting forward best hits from peptidase
2:03:04.585179: Getting reverse best hits from peptidase
2:03:10.425246: Getting descriptions of hits from peptidase
2:03:13.396760: Getting hits from pfam
Traceback (most recent call last):
File "/home/daniel/miniconda3/envs/dram/bin/DRAM.py", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/domus/h1/daniel/dev/DRAM/scripts/DRAM.py", line 172, in
args.func(**args_dict)
File "/domus/h1/daniel/dev/DRAM/mag_annotator/annotate_bins.py", line 871, in annotate_bins
genes_called, threads, verbose))
File "/domus/h1/daniel/dev/DRAM/mag_annotator/annotate_bins.py", line 741, in annotate_fasta
db_handler=db_handler, threads=threads, verbose=verbose))
File "/domus/h1/daniel/dev/DRAM/mag_annotator/annotate_bins.py", line 192, in run_mmseqs_pfam
str(threads)], verbose=verbose)
File "/domus/h1/daniel/dev/DRAM/mag_annotator/utils.py", line 34, in run_process
stderr=stderr).stdout.decode(errors='ignore')
File "/home/daniel/miniconda3/envs/dram/lib/python3.7/subprocess.py", line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['mmseqs', 'search', 'annotation/working_dir/OX3.63.fa.edit/tmp/gene.mmsdb', '/crex/proj/sllstore2017037/nobackup/data/DRAM_data/pfam.mmspro', 'annotation/working_dir/OX3.63.fa.edit/tmp/pfam.mmsdb', 'annotation/working_dir/OX3.63.fa.edit/tmp/tmp', '-k', '5', '-s', '7', '--threads', '16']' returned non-zero exit status 1.