ZeroDivisionError - Kraken2 module breaks when you have 0 unclassified reads

[drpatelh]

I tested with MultiQC v1.10.1. Creating a fresh folder with just the file below and running multiqc . should reproduce the error below:

[ERROR  ] multiqc : Oops! The 'kraken' MultiQC module broke... 
    Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues 
    If possible, please include a log file that triggers the error - the last file found was:
      ./hCoV-19_2021.kraken2.report.txt
  ============================================================
  Module kraken raised an exception: Traceback (most recent call last):
    File "/usr/local/lib/python3.9/site-packages/multiqc/multiqc.py", line 594, in run
      output = mod()
    File "/usr/local/lib/python3.9/site-packages/multiqc/modules/kraken/kraken.py", line 70, in __init__
      self.sum_sample_counts()
    File "/usr/local/lib/python3.9/site-packages/multiqc/modules/kraken/kraken.py", line 237, in sum_sample_counts
      row["counts_rooted"] / self.kraken_sample_total_readcounts[s_name]
  ZeroDivisionError: division by zero

The log above didn't point to the erroring file but the correct one is attached below:

test.kraken2.report.txt

[ewels]

The log above didn't point to the erroring file

Yes it did?

the last file found was:
      ./hCoV-19_2021.kraken2.report.txt

[ewels]

ah you mean the one it pointed to was not actually the one that caused the error maybe? Yeah that happens sometimes.

[ewels]

Fixed - should be solved in 1.11dev.

Thanks for providing the test data, I thought I fixed it in a about 2 lines but when I tested it, turned out to be a little more involved. Should now work though I think 👍🏻

[drpatelh]

Thanks for the quick fix 🙇🏽

[ewels]

Oops sorry, just realised that my force-push didn't go through last night. Should now be in place in 3cb88c4 so should now work 🤞🏻