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