# RNAVAR nf-core pipeline: error on multiqc module

**URL:** <https://community.seqera.io/t/rnavar-nf-core-pipeline-error-on-multiqc-module/2355>\
**Category:** Ask for help\
**Tags:** nextflow, nf-core\
**Created:** [September 4, 2025, 1:26pm UTC](https://community.seqera.io/t/rnavar-nf-core-pipeline-error-on-multiqc-module/2355 "2025-09-04T13:26:26Z")\
**Posts on this page:** 7\
**Page:** 1

<div class="post-metadata">

**Author:** ![marcelcosta](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/marcelcosta/32/1180_2.png) [@marcelcosta](https://community.seqera.io/u/marcelcosta)\
**Post date:** [September 4, 2025, 1:26pm UTC](https://community.seqera.io/t/rnavar-nf-core-pipeline-error-on-multiqc-module/2355/1 "2025-09-04T13:26:26Z")

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Hello!

I’m trying to run the [rna-var]() pipeline on mouse RNAseq data.

However, I am getting the following error affecting the `multiqc module`:

```bash
.command.sh: line 11: 42 Illegal instruction (core dumped) multiqc --force --config multiqc_config.yml .

```

I am launching the pipeline with this command:

```bash
NXF_VER=25.04.6 nextflow run nf-core/rnavar \
        --input samplesheet_rnavar.csv \
        --outdir PROCESSING_rnavar \
        --genome GRCm38 \
        --skip_baserecalibration \
        -profile apptainer

```

I am using this configuration:

```bash
process.executor = 'slurm'
executor.queueSize = 5
process.memory = '64 GB'
process.cpus = 8
apptainer.enabled = true

```

Does anyone know if I can change any configuration or solve anything?

Thanks!

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<div class="post-metadata">

**Author:** ![matthdsm](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/matthdsm/32/96_2.png) [@matthdsm](https://community.seqera.io/u/matthdsm)\
**Post date:** [September 4, 2025, 5:19pm UTC](https://community.seqera.io/t/rnavar-nf-core-pipeline-error-on-multiqc-module/2355/2 "2025-09-04T17:19:11Z")

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I’m guessing you’re trying to run this on an ARM mac using docker?

I suggest updating the multiqc module. There was a known issue with v1.30, which should be fixed if you use the latest image.

Xref [1.29 AMD docker container breaks on M4 ARM architecture with hardware virtualization · Issue #3238 · MultiQC/MultiQC · GitHub](https://github.com/MultiQC/MultiQC/issues/3238)

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<div class="post-metadata">

**Author:** ![marcelcosta](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/marcelcosta/32/1180_2.png) [@marcelcosta](https://community.seqera.io/u/marcelcosta)\
**Post date:** [September 5, 2025, 7:57am UTC](https://community.seqera.io/t/rnavar-nf-core-pipeline-error-on-multiqc-module/2355/3 "2025-09-05T07:57:49Z")

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Hi!

Thanks for answering!

> [@matthdsm](#):
>
> I’m guessing you’re trying to run this on an ARM mac using docker?

No, I am using apptainer in an HPC with an x86\_64 architecture and Intel processors.

> [@matthdsm](#):
>
> I suggest updating the multiqc module. There was a known issue with v1.30, which should be fixed if you use the latest image.

I am calling directly the rnavar pipeline from github repo and I see that is using v1.29. I don’t know if I am able to use another version of this module along the pipeline. Or maybe I should download it and make the changes manually and locally.

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<div class="post-metadata">

**Author:** ![matthdsm](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/matthdsm/32/96_2.png) [@matthdsm](https://community.seqera.io/u/matthdsm)\
**Post date:** [September 5, 2025, 9:00am UTC](https://community.seqera.io/t/rnavar-nf-core-pipeline-error-on-multiqc-module/2355/4 "2025-09-05T09:00:33Z")

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Can you try again by running the dev version? Just add `-r dev` to the command

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<div class="post-metadata">

**Author:** ![marcelcosta](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/marcelcosta/32/1180_2.png) [@marcelcosta](https://community.seqera.io/u/marcelcosta)\
**Post date:** [September 5, 2025, 11:51am UTC](https://community.seqera.io/t/rnavar-nf-core-pipeline-error-on-multiqc-module/2355/5 "2025-09-05T11:51:02Z")

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Hi @matthdsm,

Using the dev version solved the issue! Do you think I should report that to their github?

Thanks for your help!

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<div class="post-metadata">

**Author:** ![matthdsm](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/matthdsm/32/96_2.png) [@matthdsm](https://community.seqera.io/u/matthdsm)\
**Post date:** [September 5, 2025, 12:07pm UTC](https://community.seqera.io/t/rnavar-nf-core-pipeline-error-on-multiqc-module/2355/6 "2025-09-05T12:07:35Z")

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No need, this fix is already in dev and will integrated in the next release

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<div class="post-metadata">

**Author:** ![system](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/system/32/2402_2.png) [@system](https://community.seqera.io/u/system)\
**Post date:** [September 12, 2025, 12:07pm UTC](https://community.seqera.io/t/rnavar-nf-core-pipeline-error-on-multiqc-module/2355/7 "2025-09-12T12:07:53Z")

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