sample["RO"] TypeError

[MikeWLloyd]

I have been running with success, but one sample has thrown an error in the normalise.py script:

mity 1.2.0
mity runall
Running FreeBayes in sensitive mode
Traceback (most recent call last):
  File "/usr/local/bin/mity", line 33, in <module>
    main()
  File "/usr/local/bin/mity", line 29, in main
    args.func(args)
  File "/usr/local/lib/python3.12/site-packages/mitylib/commands.py", line 427, in _cmd_runall
    call.Call(
  File "/usr/local/lib/python3.12/site-packages/mitylib/call.py", line 70, in __init__
    self.run()
  File "/usr/local/lib/python3.12/site-packages/mitylib/call.py", line 93, in run
    self.run_normalise()
  File "/usr/local/lib/python3.12/site-packages/mitylib/call.py", line 104, in run_normalise
    Normalise(
  File "/usr/local/lib/python3.12/site-packages/mitylib/normalise.py", line 59, in __init__
    self.run()
  File "/usr/local/lib/python3.12/site-packages/mitylib/normalise.py", line 73, in run
    self.run_filtering()
  File "/usr/local/lib/python3.12/site-packages/mitylib/normalise.py", line 90, in run_filtering
    variant = self.add_filter(variant)
              ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/mitylib/normalise.py", line 282, in add_filter
    if int(sample["RO"]) > 0:
       ^^^^^^^^^^^^^^^^^
TypeError: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'

[trentzz]

Hi @MikeWLloyd,

Thanks for your issue. We have had a similar issue previously here (issue 66). They ended up having a malformed CRAM file.

To help debug this issue, please read this previous reply from me and follow these steps.

Thank you!
Trent Zeng

[MikeWLloyd]

The BAM I am using was freshly mapped by BWA and passed directly to Mity. This sample has mean coverage of 25x, but it isn't evenly distributed. I suspect the coverage issue might be the cause. I am going to run with --keep and see what I can find. I will post the vcfs etc., if I am able.

[MikeWLloyd]

The command I used is:

apptainer exec --no-home --pid -B /projects quay.io-biocontainers-mity-2.0.0--pyhdfd78af_0.img mity runall  --keep   --prefix AFG6.mity     --reference mm10     --min_vaf 0.01     --contig MT     --custom-reference-fasta Mus_musculus.GRCm38.dna.MT.fa     --custom-reference-genome Mus_musculus.GRCm38.dna.primary_assembly.genome     AFG6_mt.mba_dedup_sortsam.bam

The BAM input and the VCF outputs are here: https://thejacksonlaboratory.box.com/s/du28tn5gmgfipt4d2duskw6t4zz86xb8