stat /opt/somaticseq/utilities/split_mergedBed.py: no such file or directory error

[jeongmeani]

Hi,

using Somatciseq version 3.4.0, i analysis WES data. so far t have worked fine, but today some error occurs.

in docker space, running vardict like below script

#!/bin/bash

#$ -o /data/projects/konyang/WES/03.Variant/1-2.Somaticseq_lofreq/pair/KY009-BL1.KY009-TT1/logs #$ -e /data/projects/konyang/WES/03.Variant/1-2.Somaticseq_lofreq/pair/KY009-BL1.KY009-TT1/logs #$ -S /bin/bash #$ -l h_vmem=14G set -e

echo -e "Start at date +"%Y/%m/%d %H:%M:%S"" 1>&2

docker run --rm -v /:/mnt -u $UID --memory 14G --cpu-shares 2048 lethalfang/somaticseq:latest \ /opt/somaticseq/utilities/split_mergedBed.py \ -infile /mnt//data/projects/konyang/WES/03.Variant/1-2.Somaticseq_lofreq/pair/KY009-BL1.KY009-TT1/genome.bed -outfile /mnt//data/projects/konyang/WES/03.Varia

docker run --rm -v /:/mnt -u $UID --memory 14G --cpu-shares 2048 lethalfang/vardictjava:1.7.0 bash -c \ "/opt/VarDict-1.7.0/bin/VarDict \ -G /mnt//data/ref/hg19/hg19.rm.superconfig.fa \ -f 0.05 -h \ -b '/mnt//data/projects/konyang/WES/02.BAM/6.Lofreq_indel/KY009 TT1.BQSR.lofreqIndel.bam|/mnt//data/projects/konyang/WES/02.BAM/6.Lofreq_indel/KY009-BL1.BQSR. -Q 1 -c 1 -S 2 -E 3 -g 4 /mnt//data/projects/konyang/WES/03.Variant/1-2.Somaticseq_lofreq/pair/KY009-BL1.KY009-TT1/split_regions.bed ` > /mnt//data/projects/konyang/WES/03.Variant/1-2.Somaticseq_lofreq/pair/KY009-BL1.KY009-TT1/vardict.var"

docker run --rm -v /:/mnt -u $UID --memory 14G --cpu-shares 2048 lethalfang/vardictjava:1.7.0 \ bash -c "cat /mnt//data/projects/konyang/WES/03.Variant/1-2.Somaticseq_lofreq/pair/KY009-BL1.KY009-TT1/vardict.var | awk'NR!=1' | /opt/VarDict/testsomatic.R > /mnt//data/projects/konyang/WES/03.Variant/1-2.Somaticseq_lofreq/pair/KY009-BL1.KY009-TT1/VarDict.vcf"`

echo -e "Done atdate +"%Y/%m/%d %H:%M:%S"" 1>&2

but it returns error message

container_linux.go:247: starting container process caused "exec: \"/opt/somaticseq/utilities/split_mergedBed.py\": stat >/opt/Bed.py: no such file or directory"

docker: Error response from daemon: oci runtime error: container_linux.go:247: starting container process caused "exec: >\"/opedBed.py\": stat /opt/somaticseq/utilities/split_mergedBed.py: no such file or directory".

is this docker problem?

Best Regards.

Jeongmin

[litaifang]

I see. The problem is that in the latest docker image, I moved somaticseq/utilities into somaticseq/somaticseq/utilities to avoid potential namespace conflict, but the script is pulling lethalfang/somaticseq:latest while I should have used the same version as the version in the package, i.e., lethalfang/somaticseq:3.4.0. It never caused a problem until now. I think in all future versions, I'll fix the docker image version to the package version (they are actually already fixed, though I forgot when I did that). For you though, I'm pretty sure if you manually change "latest" to "3.4.0", and reinstall, it'll fix the problem. I think there are two such instances:

• utilities/dockered_pipelines/create_tumor_normal_run_scripts.py
• utilities/dockered_pipelines/create_tumor_only_run_scripts.py

The lines are out.write( 'docker run --rm -v /:/mnt -u $UID --memory {MEM}G lethalfang/somaticseq:{VERSION} \\\n'.format(MEM=mem, VERSION='latest') )

[jeongmeani]

OK!

Thank you for quick response and solution.

i have changed the version part of script, it works!

Thank you again.

Best Regards.

Jeongmin

[litaifang]

Older version pulling latest docker image: already solved as latest version will pull the docker image with the same version as the software version. For older installation, the solution may be manual.