Hi all, the MultiQC runs on my pipeline are timing out and exit with error status (140). This problem occurs when running the pipeline with test data on the HPC with a singularity MultiQC container. The same pipeline runs fine locally with the docker MultiQC container. The MultiQC process runs for the entire allocated time, fails, and then does the same on the retry attempt. The logs don't give any particular information towards the cause -

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

/// MultiQC 🔍 v1.26

            config | Loading config settings from: multiqc_config.yml
       file_search | Search path: /SAN/reuterlab/Expevol_analysis/poolseqfreq/work/98/ef8879f64bcc095499c7786873d26f

    custom_content | abhilesh-poolseqfreq-summary: Found 1 sample (html)
    custom_content | abhilesh-poolseqfreq-methods-description: Found 1 sample (html)
            fastqc | Found 2 reports
          cutadapt | Found 1 reports
            fastqc | Found 2 reports
            preseq | Found 1 reports
            picard | Found 1 MarkDuplicates reports
          samtools | Found 1 stats reports
          samtools | Found 1 flagstat reports
          samtools | Found 1 idxstats reports
          samtools | Found 1 coverage reports
     write_results | Rendering plots. Export plots to formats png, svg, pdf is requested, so it might take a while. To disable plot export, set `export_plots: false` in config, or remove the `--export-plots` command line flag

Have you tried doing what it suggests in the log? Disabling plot export?

Yes, it results in the same timeout and error problem. Only happens when using the singularity container on the HPC. Works fine with the docker container on a M2 Mac

Can you paste the verbose log (

-v

) from when it's disabled please?