I am still having issues with MULTIQC running on the cluster with a singularity container. Now, it's failing with an exit code 140. Reading up a bit about it, sounds like it might be experiencing memory issues? The MULTIQC module is defined with the

process_single

label. What could be causing these issues? Here's the log from the pipeline run -

eb-18 05:08:29.099 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=ABHILESH_POOLSEQFREQ:POOLSEQFREQ:MULTIQC; work-dir=/SAN/reuterlab/Expevol_analysis/poolseqfreq/work/22/cb812868c886fa3baf1eac891980e2
  error [nextflow.exception.ProcessFailedException]: Process `ABHILESH_POOLSEQFREQ:POOLSEQFREQ:MULTIQC` terminated with an error exit status (140)
Feb-18 05:08:33.683 [TaskFinalizer-6] ERROR nextflow.processor.TaskProcessor - Error executing process > 'ABHILESH_POOLSEQFREQ:POOLSEQFREQ:MULTIQC'

Caused by:
  Process `ABHILESH_POOLSEQFREQ:POOLSEQFREQ:MULTIQC` terminated with an error exit status (140)


Command executed:

  multiqc \
      --force \
       \
      --config multiqc_config.yml \
       \
       \
       \
       \
       \
      .
  
  cat <<-END_VERSIONS > versions.yml
  "ABHILESH_POOLSEQFREQ:POOLSEQFREQ:MULTIQC":
      multiqc: $( multiqc --version | sed -e "s/multiqc, version //g" )
  END_VERSIONS

Command exit status:
  140

Command output:
  (empty)

Command error:
  WARNING: While bind mounting '/SAN/reuterlab/Expevol_analysis/poolseqfreq:/SAN/reuterlab/Expevol_analysis/poolseqfreq': destination is already in the mount point list

Work dir:
  /SAN/reuterlab/Expevol_analysis/poolseqfreq/work/22/cb812868c886fa3baf1eac891980e2

Container:
  /home/adhawanj/.singularity/pull/depot.galaxyproject.org-singularity-multiqc-1.26--pyhdfd78af_0.img

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

Does it work if you try to run it interactively in the work directory?

I was having issues with running MultiQC standalone with the singularity container (bind mounts for the reports directory not working fine) but I did manage to run MultiQC by itself using singularity with just the FastQC results and that completed quickly and successfully. I've been getting different errors running MultiQC as part of the pipeline. Sometimes, its error code 140, other times MultiQC times out without completing both in the first attempt and the auto-retry

I would try with just a

pip install multiqc

locally if you can, or conda. As vanilla an install as possible.