MultiQC is not plotting Mean and Median coverage for Qualimap

[CuriusScientist]

Description of the bug:

MultiQC is not plotting Mean and Median coverage for Qualimap, which is surely present as shown by the Qualimap report for one of the samples

MultiQC run details (please complete the following):

• Command used to run MultiQC: multiqc ./
• MultiQC Version: MultiQC v1.8
• Quyalimap Version: v.2.2.2-dev
• Operating System: Ubuntu
• Python Version: Python 3.7.3
• Method of MultiQC installation: Conda

Additional context

[ewels]

Thanks for this @CuriusScientist - I think that there is something wrong with this code. See also https://github.com/ewels/MultiQC/issues/1082

I'm away for Christmas holidays now but @apeltzer (who wrote the new code for the mean coverage calculation) is hoping to have a look. Otherwise I'll look in to this as soon as I get a chance.

Is it possible for you to attach one of these Qualimap reports? The more examples we have where this is failing the better.

Thanks,

Phil

[apeltzer]

Hi @CuriusScientist ! I'll communicate the bugfixing in the other thread - if you want / can share some data, please do 👍

[apeltzer]

Please see #1085 for a proposed fix for this.

[CuriusScientist]

@ewels @apeltzer I see that you have fixed and merged the branch "apeltzer:fix-qualimap" #1085

In order to get the latest version, I followed the following steps

• Downloaded MultiQC from github

• Ran successfully "pip install MultiQC-master.zip"
  Successfully built multiqc
  Installing collected packages: multiqc
  Successfully installed multiqc-1.9.dev0

• multiqc ./
  [INFO ] multiqc : This is MultiQC v1.9.dev0
  [INFO ] multiqc : Template : default
  [WARNING] multiqc : You are running MultiQC with Python 2.7.16
  [WARNING] multiqc : Please upgrade! MultiQC will soon drop support for Python < 3.6
  [INFO ] multiqc : Searching : /Users/nitinsharma/Documents/00_Work_Projects/ULP-WGS_Bravo/QualiMap
  Searching 801 files.. [####################################] 100%
  [INFO ] qualimap : Found 8 BamQC reports
  [INFO ] multiqc : Compressing plot data
  [INFO ] multiqc : Report : multiqc_report.html
  [INFO ] multiqc : Data : multiqc_data
  [INFO ] multiqc : MultiQC complete

But I can't get the mean coverage

what am I missing here

[ewels]

Hi @CuriusScientist,

No need to download like that, you can just run pip install --upgrade --force-reinstall git+https://github.com/ewels/MultiQC.git (readme, docs).

Can you please attach a single Qualimap report where this isn't working so that we can replicate your problem? In my testing for #1085 the fix worked fine.

Thanks,

Phil

[CuriusScientist]

@ewels what files shall I send you in order for you check if there is an error or if I am doing something wrong

[apeltzer]

The multiqc_report.html would be great to see :+1:

[CuriusScientist]

multiqc.zip

@apeltzer .html files are not supported by Github so I have added all the files and zipped it

[apeltzer]

Can you also share the genome_results.txt files from QualiMap?

[CuriusScientist]

genome_results1.txt
genome_results2.txt
genome_results3.txt
genome_results4.txt

@apeltzer I have attached 4 sample files. I think that should be good enough but do let me know if you need anything else

[apeltzer]

Found the problem. The regex doesn't work if its too low coverage. I'll push a fix in a separate PR for you to test and also include one of your example files in the MultiQC_TestData repository.

[apeltzer]

Would be cool to get the other test files (html report, etc pp from qualimap too to include in the testdata).

[ewels]

Hopefully fixed now ✅ Thanks both!