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ERROR with command: Command('bash scripts/gen_img.sh when running example case

Open OlenaMaiakovska opened this issue 1 year ago • 0 comments

Dear authors,

When I run the example provided by executing samplot-ml: snakemake -s samplot-ml-predict.smk -j 6 --use-conda --conda-frontend mamba

I get the following:

Building DAG of jobs...
Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'.
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Job stats:
job                count    min threads    max threads
---------------  -------  -------------  -------------
All                    1              1              1
AnnotateVCF            1              1              1
CreateImageList        1              1              1
CropImages             1              6              6
GenerateImages         1              6              6
PredictImages          1              6              6
total                  6              1              6

Select jobs to execute...

[Wed Mar 15 10:34:59 2023]
rule GenerateImages:
    input: /home/olena/Applications/samplot-ml/outdir/bin/gargs, /home/olena/Applications/samplot-ml/outdir/GRCh38_full_analysis_set_plus_decoy_hla.fa, /home/olena/Applications/samplot-ml/outdir/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai, /home/olena/Applications/samplot-ml/outdir/bed/HG03687-del-regions.bed
    output: /home/olena/Applications/samplot-ml/outdir/img/HG03687
    jobid: 7
    reason: Missing output files: /home/olena/Applications/samplot-ml/outdir/img/HG03687
    wildcards: sample=HG03687
    threads: 6
    resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/9136980dbd351a4c6568f0b7d9a7c082_
/home/olena/Applications/samplot-ml/workflows
scripts/gen_img.sh: line 62: samplot.py: command not found
**ERROR with command: Command('bash scripts/gen_img.sh \
    --chrom chr1 --start 934098 --end 934868 --genotyp...', , stdout[:20]: '/home/olena/Applicat', exit-code: 127, error: exit status 127, run-time: 8.538026ms)**
scripts/gen_img.sh: line 62: samplot.py: command not found
[Wed Mar 15 10:34:59 2023]
Error in rule GenerateImages:
    jobid: 7
    input: /home/olena/Applications/samplot-ml/outdir/bin/gargs, /home/olena/Applications/samplot-ml/outdir/GRCh38_full_analysis_set_plus_decoy_hla.fa, /home/olena/Applications/samplot-ml/outdir/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai, /home/olena/Applications/samplot-ml/outdir/bed/HG03687-del-regions.bed
    output: /home/olena/Applications/samplot-ml/outdir/img/HG03687
    conda-env: /home/olena/Applications/samplot-ml/workflows/.snakemake/conda/9136980dbd351a4c6568f0b7d9a7c082_
    shell:
        
        mkdir -p /home/olena/Applications/samplot-ml/outdir/img
        bash scripts/images_from_regions.sh \
            --gargs-bin /home/olena/Applications/samplot-ml/outdir/bin/gargs \
            --fasta /home/olena/Applications/samplot-ml/outdir/GRCh38_full_analysis_set_plus_decoy_hla.fa \
            --regions /home/olena/Applications/samplot-ml/outdir/bed/HG03687-del-regions.bed \
            --bam /home/olena/Applications/samplot-ml/HG03687.final.cram \
            --outdir /home/olena/Applications/samplot-ml/outdir/img/HG03687 \
            --delimiter - \
            --processes 6
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job GenerateImages since they might be corrupted:
/home/olena/Applications/samplot-ml/outdir/img/HG03687
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-03-15T103457.932841.snakemake.log

Do you have an idea what might be a reason and how can I solve it? Thank you very much in advance! Best wishes, Olena

OlenaMaiakovska avatar Mar 15 '23 09:03 OlenaMaiakovska