Open schlaepferp opened 1 year ago
Something is going wrong here.
Could you please provide the file:
results/SRR10903401/20200102/variants/coverage_intervals.tsv
?
I will try to reproduce your errors to see where it come from. (Normally SNV should work: their are tested as part of our CI/CD).
Hi,
I get the same error when running V-pipe with snv: true in the config file. Did you find why ?
Thank you, Best
I'm not sure if this is intentional (read: I miss something that I should provide somewhere), or if this is a bug. I tried the same thing with other SARS reads, same behavior.
What I did:
I set up the SARS tutorial. It runs through fine.
I afterwards modified the config.yaml and changed the line
snv: false
tosnf: true
Result: It breaks the code.
Expected behavior: Either an error message telling me what is missing, or running through smoothly.
Current dump
Activating conda environment: .snakemake/conda/2db3c1462cfa3088aba362563d569612_ usage: shorah [options] shotgun [-h] [-v] -b BAM -f REF
[-a FLOAT] [-r chrm:start-stop]
[-R INT] [-x INT] [-S FLOAT] [-I]
[-p FLOAT]
[-of {csv,vcf} [{csv,vcf} ...]]
[-c INT] [-w INT] [-s INT] [-k]
[-t INT]
shorah [options] shotgun: error: argument -r/--region: expected one argument
usage: shorah [options] shotgun [-h] [-v] -b BAM -f REF
[-a FLOAT] [-r chrm:start-stop]
[-R INT] [-x INT] [-S FLOAT] [-I]
[-p FLOAT]
[-of {csv,vcf} [{csv,vcf} ...]]
[-c INT] [-w INT] [-s INT] [-k]
[-t INT]
shorah [options] shotgun: error: argument -r/--region: expected one argument
[Tue Jun 13 14:44:29 2023]
Error in rule snv:
jobid: 20
input: /home/usr1/vpipe_test_dir/V-pipe/workflow/../resources/sars-cov-2/NC_045512.2.fasta, results/SRR10903401/20200102/alignments/REF_aln.bam, results/SRR10903401/20200102/variants/coverage_intervals.tsv
output: results/SRR10903401/20200102/variants/SNVs/snvs.csv, results/SRR10903401/20200102/variants/SNVs/snvs.vcf
log: results/SRR10903401/20200102/variants/SNVs/shorah.out.log, results/SRR10903401/20200102/variants/SNVs/shorah.err.log (check log file(s) for error details)
conda-env: /home/usr1/vpipe_testdir/work/.snakemake/conda/2db3c1462cfa3088aba362563d569612
shell:
[Tue Jun 13 14:44:29 2023] Error in rule snv: jobid: 18 input: /home/usr1/vpipe_test_dir/V-pipe/workflow/../resources/sars-cov-2/NC_045512.2.fasta, results/SRR10903402/20200102/alignments/REF_aln.bam, results/SRR10903402/20200102/variants/coverage_intervals.tsv output: results/SRR10903402/20200102/variants/SNVs/snvs.csv, results/SRR10903402/20200102/variants/SNVs/snvs.vcf log: results/SRR10903402/20200102/variants/SNVs/shorah.out.log, results/SRR10903402/20200102/variants/SNVs/shorah.err.log (check log file(s) for error details) conda-env: /home/usr1/vpipe_testdir/work/.snakemake/conda/2db3c1462cfa3088aba362563d569612 shell:
Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2023-06-13T144427.023150.snakemake.log