IndexError when processing CRyPTIC samples
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philipwfowler commented
I see 113 failures with the following Traceback, VCF attached.
site.05.subj.PMOP-0632.lab.MOP-197.iso.1.v0.12.4.per_sample.vcf.gz
Traceback (most recent call last):
File "/home/ubuntu/.local/bin/gnomonicus", line 122, in <module>
mutations, referenceGenes = populateMutations(vcfStem, options.output_dir, diff,
File "/home/ubuntu/.local/lib/python3.10/site-packages/gnomonicus/gnomonicus_lib.py", line 388, in populateMutations
x = minority_population_mutations(diffs, resistanceCatalogue)
File "/home/ubuntu/.local/lib/python3.10/site-packages/gnomonicus/gnomonicus_lib.py", line 666, in minority_population_mutations
mutations = diff.minor_populations(interpretation=minor_type)
File "/home/ubuntu/.local/lib/python3.10/site-packages/gumpy/difference.py", line 839, in minor_populations
return self.gene2.minority_populations_GARC(interpretation=interpretation, reference=self.gene1)
File "/home/ubuntu/.local/lib/python3.10/site-packages/gumpy/gene.py", line 217, in minority_populations_GARC
pos = self.gene_position[self.nucleotide_number == population[0]][0]
IndexError: index 0 is out of bounds for axis 0 with size 0