Command error: `touch: .command.trace: Permission denied` when running on docker

Nextflow Help
1

Hi,

I have been trying to run several nf-core pipelines using docker and test profile in my local ubuntu machine.
I have docker-desktop installed and running.
I also added the user to the docker group. So I can run docker as non-root user.

For example: I run rnaseq pipeline with the command:

nextflow run nf-core/rnaseq -profile test,docker --outdir test_run -r 3.14.0

I am getting following error:

-[nf-core/rnaseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)` terminated with an error exit status (1)

Command executed:

  [ ! -f  WT_REP2_1.fastq.gz ] && ln -s SRR6357072_1.fastq.gz WT_REP2_1.fastq.gz
  [ ! -f  WT_REP2_2.fastq.gz ] && ln -s SRR6357072_2.fastq.gz WT_REP2_2.fastq.gz
  trim_galore \
      --fastqc_args '-t 2' \
      --cores 1 \
      --paired \
      --gzip \
      WT_REP2_1.fastq.gz \
      WT_REP2_2.fastq.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE":
      trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//')
      cutadapt: $(cutadapt --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

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

Work dir:
  /home/arriyaz/temp/nextflow-practice/work/1d/f49845a12800d622ab339e74ab7172

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

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

Here is the log file:
nextflow.log (87.5 KB)

I am getting same error for other workflow also (e.g., mnaseseq, viralintegration)

2

Hello @arriyaz.

According to your nextflow.log file, you’re running Nextflow 23.10.1. I tried to simulate what you’re doing on macOS and on Linux with nextflow run nf-core/rnaseq -profile test,docker --outdir test_run -r 3.14.0. In both environments, the pipeline ran just fine. I attached a printscreen below showing FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE with WT_REP2 succeeded, differently from the same sample in your run that failed.

Captura de Tela 2024-05-06 às 23.52.18
Captura de Tela 2024-05-06 às 23.52.182060×56 104 KB

Based on that, I believe your problem is related to some Docker configuration and not Nextflow.

3

Hi, I have the same problem.
Are you able to solve it?

I run your workflow and demo workflow with simmilar errors. Have you figure out what could be the problem. I tried to run it in Debian and ubuntu, with docker rootless and with the normal docker without luck.

I send the .nextflow.log for:

nextflow run nf-core/demo -r dev -profile test,docker --outdir testDemo

nextflow.log (26,2 KB)