Kaiju module works only at phylum level

[jkibilds]

Description of bug:
When I run MultiQC on table reports from Kaiju, the Kaiju module breaks if the input files have taxonomic classification at any other level than phylum.

MultiQC Error log:

[INFO   ]         multiqc : This is MultiQC v1.9
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching   : /mnt/home/juriski/projects/scratch/MiSeq_run_200529/results/kaiju1/taxa/genus
[INFO   ]           kaiju : Found 1 reports
[ERROR  ]         multiqc : Oops! The 'kaiju' 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:
    genus/Li-2020-14538-3.kaiju.genus.tsv
============================================================
Module kaiju raised an exception: Traceback (most recent call last):
  File "/home/juriski/.conda/envs/multiqc/lib/python3.6/site-packages/multiqc/multiqc.py", line 569, in run
    output = mod()
  File "/home/juriski/.conda/envs/multiqc/lib/python3.6/site-packages/multiqc/modules/kaiju/kaiju.py", line 64, in __init__
    self.kaiju_stats_table()
  File "/home/juriski/.conda/envs/multiqc/lib/python3.6/site-packages/multiqc/modules/kaiju/kaiju.py", line 105, in kaiju_stats_table
    general_data = self.kaiju_data[self.kaiju_data.keys().sorted()[0]]
AttributeError: 'dict_keys' object has no attribute 'sorted'
============================================================
[WARNING]         multiqc : No analysis results found. Cleaning up..
[INFO   ]         multiqc : MultiQC complete

File that triggers the error:
Li-2020-14538-3.kaiju.genus.txt
(I had to rename the file from .tsv to .txt because GitHub allows only certain extensions)

MultiQC run details:

• Command used to run MultiQC: multiqc -o genus/mqcout genus/
• MultiQC Version: MultiQC v1.9
• Operating System: CentOS 7
• Python Version: Python 3.6.10
• Method of MultiQC installation: conda

Additional context
I prepared Kaiju reports for the same sample at all taxonomic levels (except superkingdom) using kaiju2table and ran MultiQC on each report file separately. It produced a report and no error messages only with phylum-level input. The same is true if I use input files from https://github.com/ewels/MultiQC_TestData/tree/master/data/modules/kaiju - only the three example files at phylum level work.

[ewels]

Aha, good spot - thank you! This was a very last-minute addition to the v1.9 release by @noirot.

Any thoughts @noirot? Do you think you could add a fix for this please?

We can add this test data to MultiQC_TestData once we have a fix (not before though, as it will cause all MultiQC tests to start failing).

Thanks,

Phil

[noirot]

Oh weird ! Yes I'll have a look.

[ewels]

@jkibilds - should now be fixed in v1.10dev. Let us know if you find any problems, thanks for reporting!

Phil

[jkibilds]

Now it works with reports from all taxonomic levels, thanks!