QualiMap mean coverage

[BaiqiFu]

Description of bug:
Qualimap: mean coverage computation for general statistics seems incorrect.

MultiQC Error log:
MultiQC Report:

QualiMap Report (CG_R):

File that triggers the error:
see example_data.zip

MultiQC run details (please complete the following):

• Command used to run MultiQC: /data1/software/python/3.8.0/bin/multiqc --force --filename xx --outdir . bamqc/*_bamqc
• MultiQC Version: [MultiQC v1.8]
• Operating System: [CentOS 7]
• Python Version: [Python 3.8.0]
• Method of MultiQC installation: [pip]

[ewels]

Hmm, @apeltzer - any ideas what is going on here?

[apeltzer]

Not really but I can check - code doesn't show this behaviour easily...

[apeltzer]

Ok, just so to give an update on this one here. I double-checked using the https://github.com/ewels/MultiQC_TestData/tree/master/data/modules/qualimap testdata:

QualiMap Report:

MultiQC Report:

Other sample:

As QualiMap doesn't provide median values, I can't compare these directly to what it computes but the outputs don't look weird/off for me 👎

Maybe QualiMap produces slightly different output now and didn't in the past? Need to check that too...

[apeltzer]

Please see #1085 for a proposed fix for this.

[BaiqiFu]

Hello!

Thank you very much for your reply！

But this bug seems to still exist in my other projects.

BamQC:
bamqc.zip

MultiQC:
multiqc.zip

Command:

/data1/software/python/3.8.0/bin/multiqc --force --filename wheat_multi-bamqc --outdir multiqc bamqc/*_bamqc

MultiQC Version:

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

2. https://github.com/apeltzer/MultiQC/tree/fix-qualimap

The above two versions are not correct.

So how do I choose the version?

[ewels]

Hi @BaiqiFu,

The PR to fix this was only merged a few weeks ago - I'm not entirely sure which version you were running, but either way it seems fixed to me now. See an example report that I just generated with the latest version of the code using your bamqc.zip data: multiqc_report.html.zip

This should now work with the latest v1.9dev code (the install command 1 from your post above will install this now), and will be released properly soon.

Let me know if you're still having problems,

Phil

[BaiqiFu]

Hi

Now I am using the v1.9，this version works very well without problems!
Thank you very much for your work!

[ewels]

Ok great! Thanks for letting us know :)