runnin VEP in a docker using jupyterlab notebook

Juan Fernandez

Hello,

I am trying to run VEP in a docker using jupyterlab but I am unable to read mount the /mnt/project/result folder to read the vcf, here is the code I am using

# Define input file from previous step
VCF_FILE="file-GygvyfQJ8jp7jV677Z1b6Z0k"
VCFPREFIX="merged_chr5_80654652_80876815"
CMD="docker load -i /mnt/project/vep_docker/ensembl_vep_docker.tar && \
         docker run -v /mnt/project/result:/data:ro -v /mnt/project/vep_docker/cache:/vep_cache \
                    ensemblorg/ensembl-vep \
                    vep -i /data/merged_chr5_80654652_80876815.filtered.vcf.gz \
                        -o ${VCFPREFIX}_vep113_annotated.vcf.gz \
                        --cache --dir_cache /vep_cache/ --offline --vcf --force_overwrite"
# Submit DNAnexus job
runid=$(dx run swiss-army-knife \
    -iin="/vep_docker/ensembl_vep_docker.tar" \
    -iin="file-GygvyfQJ8jp7jV677Z1b6Z0k"
    -icmd="${CMD}" \
    --name="${VCFPREFIX}_vep113_annotated.vcf.gz" \
    --instance-type=mem2_ssd1_v2_x4 \
    --destination=results/ \
    --yes --brief)

echo “✅ Submitted dx job with ID: ${runid}”

However, after running this I get the following error after the job failed:

+ eval 'docker load -i /mnt/project/vep_docker/ensembl_vep_docker.tar && docker run -v /mnt/project/result:/data:ro -v /mnt/project/vep_docker/cache:/vep_cache ensemblorg/ensembl-vep vep -i /data/merged_chr5_80654652_80876815.filtered.vcf.gz -o merged_chr5_80654652_80876815_vep113_annotated.vcf.gz --cache --dir_cache /vep_cache/ --offline --vcf --force_overwrite'
++ docker load -i /mnt/project/vep_docker/ensembl_vep_docker.tar
Loaded image: ensemblorg/ensembl-vep:latest
++ docker run -v /mnt/project/result:/data:ro -v /mnt/project/vep_docker/cache:/vep_cache ensemblorg/ensembl-vep vep -i /data/merged_chr5_80654652_80876815.filtered.vcf.gz -o merged_chr5_80654652_80876815_vep113_annotated.vcf.gz --cache --dir_cache /vep_cache/ --offline --vcf --force_overwrite
docker: Error response from daemon: error while creating mount source path '/mnt/project/result': mkdir /mnt/project/result: read-only file system.

Comments

1 comment

  • Comment author
    Yuanyuan Ye

    Hi, have you solved the problem?

    0

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