Missing jszip.min.js when generating report (MultiQC v1.18)

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1

I am encountering an issue when running MultiQC on FastQC reports. The report is generated, but I receive the following error:

Could not include file ‘assets/js/packages/jszip.min.js’: [Errno 2] No such file or directory: ‘/tmp/tmpXXXX/assets/js/packages/jszip.min.js’

MultiQC output:

Report : multiqc_report.html Data : multiqc_data MultiQC complete

Details:

MultiQC version: v1.18

Installed using: sudo install (system-wide installation)

OS: Ubuntu (Linux)

Running inside: standard terminal (not conda/venv)

The HTML report is created, but I am concerned that some assets may not be properly embedded.

Questions

?Is this caused by an incomplete installation

?Is this related to system-wide installation with sudo

?Would reinstalling inside a virtual environment (venv or conda) resolve the issue

Thank you for your help.

2

Hi @mahsa

You’re making this easy for me with the questions at the end!

  1. Yes
  2. Possibly
  3. Very likely

There’s definitely something weird going on with your installation, I can think of no reason why you’d have asset files within your /tmp directory. And using sudo is generally a big no-no.

While you’re at it, I’d recommend upgrading to the latest version, version 1.18 is 2.5 years old now.

Hope that helps!

3

Thank you very much for your clarification and for pointing out the installation issue. I really appreciate your help.

I have one additional question. When I tried to install MultiQC using pip install multiqc, I received the following error:

error: externally-managed-environment This environment is externally managed.

It suggests that the Python installation is managed by the system (Debian/Ubuntu) and recommends using apt, a virtual environment, or --break-system-packages.

Could you please clarify why this happens when using pip?
Is this related to PEP 668 restrictions in newer Ubuntu/Debian versions?

4

Hi @mahsa,

There are many answers to this question. As you said, trying to install with your system Python is almost always problematic and you should definitely not do that.

I would instead try to use any of the following options:

  • Docker / Singularity (if running within a pipeline)
  • Astral’s uv (uv tool install multiqc)
  • Conda (miniforge)
  • Python virtual environments

In all cases, MultiQC won’t be trying to install into / use your system version of Python and you shouldn’t get these conflicts.

Phil

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