Sarek test run unable to find docker image

C2i-PeterChung commented 2 months ago

Description of the bug

I am new to nextlfow sarek pipeline, I tried to use docker as profile to test run the sarek pipeline but it had error. is this the docker issue ? how can I download back that bwa version, I tried to write config file to implement the bwa images but it isn't work. Please advice. Thanks.

Command used and terminal output

command:
nextflow run nf-core/sarek -r 3.4.1 -profile test,docker --outdir test_result

Output:
[nf-core/sarek] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX (genome.fasta)'

Caused by:
  Process `NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX (genome.fasta)` terminated with an error exit status (125)

Command executed:

  mkdir bwa
  bwa \
      index \
       \
      -p bwa/genome \
      genome.fasta

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX":
      bwa: $(echo $(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*$//')
  END_VERSIONS

Command exit status:
  125

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/bwa:0.7.17--hed695b0_7' locally
  0.7.17--hed695b0_7: Pulling from biocontainers/bwa
  docker: [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of quay.io/biocontainers/bwa:0.7.17--hed695b0_7 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/.
  See 'docker run --help'.

Work dir:
  /data2/peter/HHGPHK/bam_files/work/1e/6a22d245cdb00e6ceb0bd0edaa18d6

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

Relevant files

I don't have relevant files, I just followed the https://nf-co.re/docs/usage/introduction

To test that everything is working properly, try running the tests for your pipeline of interest in the terminal: nextflow run nf-core/sarek -r 3.4.1 -profile test,docker --outdir test_result

System information

  N E X T F L O W
  version 23.10.1 build 5891
  created 12-01-2024 22:01 UTC (13-01-2024 06:01 HKST)
  cite doi:10.1038/nbt.3820
  http://nextflow.io

Liunx 5.15.0-106-generic

Distributor ID: Ubuntu Description: Ubuntu 22.04.4 LTS Release: 22.04 Codename: jammy

maxulysse commented 2 months ago

Hi @C2i-PeterChung, I'm afraid the latest version of Docker has some issues dealing with biocontainers. Can you either try a less recent version, or singularity instead?

C2i-PeterChung commented 1 month ago

@maxulysse Thanks for your comment, I downgraded the docker and nextflow

  N E X T F L O W
  version 23.10.0 build 5889
  created 15-10-2023 15:07 UTC (23:07 HKST)
  cite doi:10.1038/nbt.3820
  http://nextflow.io

Docker version 20.10.24, build 297e128

the test pipeline is work, ran successfully. but when i tried on the my samples, it isnt work again.

nextflow -bg run nf-core/sarek -r 3.4.0 -params-file params_samplesheet_F54.json -profile docker

`Workflow execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: 125.

The full error message was:

Error executing process > 'NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (120660)'

Caused by: Process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (120660) terminated with an error exit status (125)

Command executed:

gatk --java-options "-Xmx3276M -XX:-UsePerfData" \ ApplyBQSR \ --input 120660.converted.cram \ --output 120660_chr18_47019913-54536574.recal.cram \ --reference Homo_sapiens_assembly38.fasta \ --bqsr-recal-file 120660.recal.table \ --intervals chr18_47019913-54536574.bed \ --tmp-dir . \

cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR": gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.(GATK) v//; s/ .$//') END_VERSIONS

Command exit status: 125

Command output: (empty)

Command error: docker: Error response from daemon: failed to create endpoint nxf-KB7uWAKUF0MjLaJT0g9n3HcB on network bridge: failed to add the host (veth6c6efa2) <=> sandbox (vethc1f5ac4) pair interfaces: cannot allocate memory. time="2024-05-16T14:54:58+08:00" level=error msg="error waiting for container: context canceled"

Work dir: /data/hhgphk/run2/work/21/e4610a04eb25030ca10ce4bc0d8336

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line`

nf-core / sarek