Skip to content

running error when changed the window size #29

@HippoYI

Description

@HippoYI

Hi Mitchell,
I was doing comparison of the centromere sequence of two species. When I set the parameters to “window: 500, cooler_window: 600, mm_f: 1000” the program went well. But the monomer sequence of my centromere was ~36bp, so I want to change the window size to a smaller one. After the parameters were set to "window: 32, cooler_window: 100, mm_f: 1000", I got the following errors:

Error in rule aln_prep:
jobid: 8
input: results/Agig_CEN5_Afim_cen4.32.fasta
output: temp/Agig_CEN5_Afim_cen4.32.1000.ref_0.fasta.mmi
log: logs/aln_prep.Agig_CEN5_Afim_cen4.32.1000.ref_0.log (check log file(s) for error details)
conda-env: /Users/hippo/Documents/JH_StainedGlass_analysis/Agig_CEN5_Afim_cen4/.snakemake/conda/18f28c24ae197bbcc7e830a560e33b11_
shell:
minimap2 -f 1000 -s 6 -a --no-pairing -k21 --sr -A2 -B8 -O12,32 -E2,1 -r100 -g100 --heap-sort=yes -X -w11 -e0 -d temp/Agig_CEN5_Afim_cen4.32.1000.ref_0.fasta.mmi results/Agig_CEN5_Afim_cen4.32.fasta 2> logs/aln_prep.Agig_CEN5_Afim_cen4.32.1000.ref_0.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-08-04T113517.379978.snakemake.log

And the logs/aln_prep.Agig_CEN5_Afim_cen4.32.1000.ref_0.log file had only one line:
[ERROR] unknown option in "-w11"

I don't know if I got this error when the smaller window size was set up, and how to solve this, could you help me out? Thanks!

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions