Command not found

[me-orlov]

Description of the bug

Hello everyone,

A year ago I have successfully installed nextflow and used the scrnaseq pipeline. Today I have tried to run the basic test for the rnaseq pipeline, and I am getting an error (127) that says either the fastq or the trim_galore command cannot be found. Which command it is depends on the run. They switch if I retry. The error persists regardless of whether I use singularity (what I used a year ago), docker (installed today) or apptainer (also installed today). I have even tried an install of nextflow as a dedicated conda environment, and am still getting the same error. I would be very grateful if someone could help me shed some light on this, as these pipelines are a great tool. Thank you in advance!

Command used and terminal output

nextflow run nf-core/rnaseq -profile test, docker --outdir ~/Bioinformatics/BulkRnaSeqNfTest

-[nf-core/rnaseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)` terminated with an error exit status (127)

Command executed:

  [ ! -f  RAP1_UNINDUCED_REP1.fastq.gz ] && ln -s SRR6357073_1.fastq.gz RAP1_UNINDUCED_REP1.fastq.gz
  trim_galore \
      --fastqc_args '-t 2' \
      --cores 1 \
      --gzip \
      RAP1_UNINDUCED_REP1.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:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 4: trim_galore: command not found

Work dir:
  /home/mgoiko/work/6f/9d1d0c3b77e45f3166fe47dc09ece3

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

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

Relevant files

System information

Ubuntu 22.04.4 LTS

[me-orlov]

Hello everyone, I have finally sorted out the issue. Want to leave this up for people in case it helps someone. If you are getting the error, please make sure there is no space between the words in

profile -test,docker

[drpatelh]

Great you figured it out and thanks for confirming here for everyones benefit!