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I've been trying to run a minimal example of the NextFlow RNAseq pipeline, like so:

nextflow run nf-core/rnaseq -r 3.10.0 -profile test,docker --outdir /home/kai/RNASeq/rnaseq_test/test_output

However, this appears to return the error below:

Error executing process > 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)` terminated with an error exit status (1)

Command executed:

  gtf2bed \
      genome_gfp.gtf \
      > genome_gfp.bed
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED":
      perl: $(echo $(perl --version 2>&1) | sed 's/.*v\(.*\)) built.*/\1/')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  touch: .command.trace: Permission denied

Steps I've taken to potentially fix this:

  • Check if docker is running as a non-root user (my understanding is that this fixed a similar problem for another user as discussed here FileNotFoundException (Permission denied) with Nextflow and Docker) However, I haven't discounted it could still very much be a docker issue.

  • Added a beforeScript 'chmod o+rw .'directive prior the script in the nextflow module itself.

I'm using Ubuntu 22.04.2 LTS.

As always, any advice would be appreciated :)

KLM117
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  • I have quite the same problem. I think what is interesting is that all other files created by nextflow exist in this work directory (`.command.run`, `.command.sh`, ...) Is this the same for you? – Alex Mar 15 '23 at 08:05

0 Answers0