MultiQC timing out

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1

When running

nextflow run nf-core/mag -profile docker,test -r 3.4.0

on my M1 Mac, I’m finding MultiQC is just hanging after it gets to

.command.log:

WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

/// MultiQC 🔍 v1.27

            config | Loading config settings from: multiqc_config.yml
     version_check | MultiQC Version v1.28 now available!
       file_search | Search path: /Users/mahpa906/Documents/Projects/nf-cascade/work/ed/a9417924b3891ba4edf6dcecd130ba
       file_search | Only using modules: fastqc, fastp, adapterremoval, trimmomatic, porechop, filtlong, fastqc, bowtie2, bowtie2, kraken, kraken, quast, bowtie2, custom_content, quast, busco, prokka

            fastqc | Found 6 reports
             fastp | Found 3 reports
            fastqc | Found 6 reports
           bowtie2 | Found 3 reports
            kraken | Found 2 reports
             quast | Found 4 reports
           bowtie2 | Found 8 reports
    custom_content | nf-core-mag-methods-description: Found 1 sample (html)
    custom_content | nf-core-mag-summary: Found 1 sample (html)
             quast | Found 19 reports
             busco | Found 19 reports
            prokka | Found 19 logs
       file_search | Only using modules: fastqc, fastp, fastqc, bowtie2, kraken, quast, bowtie2, quast, busco, prokka, nf-core-mag-methods-description, nf-core-mag-summary
     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
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MultiQC v1.28 is also timing out.

Asking on the nf-core #mag forum, i simply got it was not supposed to happen.

2

It’s likely the static plot generation, that seems to hang in some contexts.

We just merged a time out to gracefully handle these, might help?

3

What’s the best way to test, or should I just wait for release? There’s no hurry on my side.

4

I can confirm that I observed this hang behaviour on my Apple M1 yesterday with MultiQC 1.28.

5

@mahesh.binzerpanchal see https://docs.seqera.io/multiqc/getting_started/installation:

Pip (dev version)

pip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC.git

Then run normally.

6

Thanks. It looks like that fixed it.

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