Docker Error while running nf-core/rnaseq pipeline

Question

[eesha28112001]

I have run a nf-core pipeline with the following parameters:

 nextflow run nf-core/rnaseq -r 3.10.1 
--input samplesheet.csv 
--outdir outputlatest 
--fasta chr22_with_ERCC92.fa 
-profile docker 
--gtf chr22_with_ERCC92.gtf 
--skip_multiqc true  
--skip_dupradar true 
--skip_stringtie true 
--aligner star_salmon 
--pseudo_aligner salmon 
--max_memory 3.5GB 
--max_cpus 4

Receiving an error related to docker as follows:

-[nf-core/rnaseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)` terminated with an error exit status (125)

Command executed:

  check_samplesheet.py \
      samplesheet.csv \
      samplesheet.valid.csv

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  125

Command output:
  (empty)

Command error:
  docker: Error response from daemon: mkdir /var/lib/docker/overlay2/9cda2dc8109540d8effde76ee6908db2e1b9003432ed6479f54a7a9b837ba7ea-init: read-only file system.
  See 'docker run --help'.

Work dir:
  /home/eesha/work/7f/d95c0812ea0079c37470fc50622537

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

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

What could be the solution to this? How can I change Docker settings in order to execute the pipeline smoothly?

Answer 1

[ATpoint]

read-only file system

You must make sure that the output destination is writable.

[eesha28112001]

How do I do that?

[barslmn]

It may be caused by docker installation or maybe user groups. Can you run docker run hello-world without problems?

[eesha28112001]

No, it gives an error as follows:

Unable to find image 'hello-world:latest' locally docker: Error response from daemon: error creating temporary lease: write /var/lib/desktop-containerd/daemon/io.containerd.metadata.v1.bolt/meta.db: read-only file system: unknown. See 'docker run --help'.

[barslmn]

You got some docker troubleshooting to do. Try reinstalling according to official documentation: https://docs.docker.com/engine/install/ After that follow their post installation instructions: https://docs.docker.com/engine/install/linux-postinstall/

[eesha28112001]

Okay, will do this! Using a Ubuntu subsystem on Windows so maybe it had something to do with that :(

[ATpoint]

No it doesn't. If you setup Docker correctly it works fine on WSL just as on native Linux, I use Docker on WSL2 all the time without problems. Try to purge the existing Docker and make a fresh install, following the linked manuals. It should work.