docker error - docker: Error response from daemon: OCI runtime create failed: container_linux.go:349: starting container process caused "process_linux.go:319: getting the final child's pid from pipe caused \"EOF\"": unknown.

[jeongmeani]

Hi, using your docker environment and prediction script, i analysis my WES data. but about a week ago, docker often stops working while printing following message.

docker: Error response from daemon: OCI runtime create failed: container_linux.go:349: starting container process caused "process_linux.go:319: getting the final child's pid from pipe caused \"EOF\"": unknown.

i try to search solution of this error, but i could not find anything to solve it.

so do you have some ideas of this?

Best Regards

Jeongmin

[litaifang]

At which step did you receive this error? What was your command?

[jeongmeani]

at first of the almost job, i faced this error. my analysis step is ' Use BAMSurgeon to create training data - dream challenge' -> training -> prediction command is training /data/tools/SomaticSeq_install/utilities/dockered_pipelines/makeSomaticScripts.py paired \ --normal-bam /home/jmkim/somaticseq_training_twist/training_output_KN-128-001-BL1/syntheticNormal_KN-128-001-BL1.bam \ --tumor-bam /home/jmkim/somaticseq_training_twist/training_output_KN-128-001-BL1/syntheticTumor_KN-128-001-BL1.bam \ --genome-reference /data/ref/hg19/hg19.rm.superconfig.fa \ --output-directory /home/jmkim/somaticseq_training_twist/classifier_KN-128-001-BL1 \ --dbsnp-vcf /data/tools/GATK_install/bundle/hg19/dbsnp_138.hg19.vcf \ --truth-snv /home/jmkim/somaticseq_training_twist/training_output_KN-128-001-BL1/synthetic_snvs.vcf \ --truth-indel /home/jmkim/somaticseq_training_twist/training_output_KN-128-001-BL1/synthetic_indels.leftAlign.vcf \ --action 'qsub -l walltime=5:00:00' \ --threads 12 \ --run-mutect2 --run-varscan2 --run-jointsnvmix2 --run-somaticsniper --run-vardict --run-muse --run-lofreq --run-strelka2 --run-somaticseq --train-somaticseq

prediction /data/tools/SomaticSeq_install/utilities/dockered_pipelines/makeSomaticScripts.py paired \ --normal-bam /data/projects/snubh/WES/02.BAM/5.BQSR_BAM/$N_BAM \ --tumor-bam /data/projects/snubh/WES/02.BAM/5.BQSR_BAM/$T_BAM \ --genome-reference /data/ref/hg19/hg19.rm.superconfig.fa \ -outdir /data/projects/snubh/WES/03.Variant/1.Somaticseq/pair_new/$N_name'.'$T_name \ --dbsnp-vcf /data/ref/dbsnp/dbsnp_138.hg19.sortByRef.vcf \ -snvClassifier /home/jmkim/somaticseq_training_twist/classifier_KN-128-001-BL1/Ensemble.sSNV.tsv.ada.Classifier.RData \ -indelClassifier /home/jmkim/somaticseq_training_twist/classifier_KN-128-001-BL1/Ensemble.sINDEL.tsv.ada.Classifier.RData \ --action 'qsub -l walltime=100:00:00 -e '$Working_dir'/tmp3 -o '$Working_dir'/tmp3' \ --threads 12 \ --somaticseq-algorithm ada \ --exome \ --run-mutect2 --run-varscan2 --run-jointsnvmix2 --run-somaticsniper --run-muse --run-vardict --run-lofreq --run-strelka --run-somaticseq

and many outputs were not made, so i run directly merge.cmd. and print this error message.

[jmkim@penta01 KN-128-005-TF1]$ sh logs/mergeResults.2020.06.13T12.43.48. 543574.cmd

Start at 2020/06/15 09:05:06 docker: Error response from daemon: OCI runtime create failed: container_linux.g >o:349: starting container process caused "process_linux.go:319: getting the fina >l child's pid from pipe caused \"EOF\"": unknown.

a month ago, when i have used somaticseq it always work successfully. but a week ago suddenly it makes error.

Best Regards

Jeongmin

[litaifang]

Can you copy what's in logs/mergeResults.2020.06.13T12.43.48.543574.cmd?

[litaifang]

If many outputs were not made.... try run some command like docker run --rm lethalfang/somaticseq:latest ls /opt/somaticseq just to make sure docker is still working properly. Sometimes docker images may be filling up your drive.

[jeongmeani]

Ok ! Thank you. i attach logs/mergeResults.2020.06.13T12.43.48.543574.cmd. mergeResults.2020.06.13T12.43.48.543574.txt

and i ran the docker run --rm lethalfang/somaticseq:latest ls /opt/somaticseq but it print same error message..

(base) [root@penta01 somaticseq]# docker run --rm lethalfang/somaticseq:latest ls /opt/s omaticseq

docker: Error response from daemon: OCI runtime create failed: container_linux.go:349: s >tarting container process caused "process_linux.go:319: getting the final child's pid fr >om pipe caused \"EOF\"": unknown.

is my server system unstable?

Best Regards

Jeongmin

[litaifang]

I'm wondering if your local drive allocated to docker is running out of space. Try to see how many docker images are stored locally docker images See how many containers you have locally docker ps -a

Remove containers docker rm CONTAINER_ID Remove images 'docker rmi DOCKER_IMAGE`

Then try the simple docker command again docker run --rm lethalfang/somaticseq:latest ls /opt/somaticseq

[jeongmeani]

after remove some docker image and container, it works!

Thank you very much.

Best Regards

Jeongmin

[litaifang]

Docker works again after cleaning up inactive images.