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KCCG / mity

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data
MIT License
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AsertionError in mity v0.2.1 #8

Closed sjfandrews closed 3 years ago

sjfandrews commented 3 years ago

Hi I am running into the following issue when using mity v0.2.1. using the available test datasets.

singularity build mity-0.2.1.simg docker://drmjc/mity
singularity run mity-0.2.1.simg call --reference hs37d5 --out-folder-path test_out --normalise test_in/HG002.hs37d5.2x250.small.MT.RG.bam

Found dependency: /usr/local/bin/freebayes
Found dependency: /usr/local/bin/gsort
Found dependency: /usr/local/bin/tabix
Found dependency: /usr/local/bin/bgzip
Found dependency: /usr/local/bin/python
Found dependency: /usr/local/bin/mity
mity version 0.2.1
Calling mitochondrial variants
Traceback (most recent call last):
  File "/usr/local/bin/mity", line 29, in <module>
    args.func(args)
  File "/usr/local/lib/python3.7/site-packages/mitylib/commands.py", line 45, in _cmd_call
    genome = select_reference_genome(args.reference, None)
  File "/usr/local/lib/python3.7/site-packages/mitylib/util.py", line 305, in select_reference_genome
    assert len(res) == 1
AssertionError

This issue is not present in version 0.1.3

singularity build mity-0.1.3.simg docker://drmjc/mity:0.1.3
singularity run mity-0.1.3.simg call --reference hs37d5 --out-folder-path test_out --normalise 
test_in/HG002.hs37d5.2x250.small.MT.RG.bam

Found dependency: /usr/local/bin/freebayes
Found dependency: /usr/local/bin/gsort
Found dependency: /usr/local/bin/tabix
Found dependency: /usr/local/bin/bgzip
Found dependency: /usr/local/bin/python
Found dependency: /usr/local/bin/mity
mity version 0.1.3
Calling mitochondrial variants
Running FreeBayes in sensitive mode
Writing normalised vcf: test_out/HG002.hs37d5.2x250.small.MT.RG.mity.vcf.gz