Index error mid way through run.

[alexanderchang1]

Hi,

I'm trying to run treeomics on the mutect2 data and ran into the following error.

tail teeomics.log

2024-03-21 23:19:50,340 treeomics.utils.vcf_parser:103 WARNING: Unrecognized filter value: contamination
2024-03-21 23:19:50,341 treeomics.utils.vcf_parser:103 WARNING: Unrecognized filter value: normal_artifact
2024-03-21 23:19:50,342 treeomics.utils.vcf_parser:103 WARNING: Unrecognized filter value: weak_evidence
2024-03-21 23:19:50,343 treeomics.utils.vcf_parser:103 WARNING: Unrecognized filter value: normal_artifact
2024-03-21 23:19:50,345 treeomics.utils.vcf_parser:103 WARNING: Unrecognized filter value: weak_evidence
2024-03-21 23:19:50,346 treeomics.utils.vcf_parser:103 WARNING: Unrecognized filter value: normal_artifact
2024-03-21 23:19:50,347 treeomics.utils.vcf_parser:103 WARNING: Unrecognized filter value: normal_artifact
2024-03-21 23:19:50,349 treeomics.utils.vcf_parser:262 INFO: Read sample AUR_AFE5_AUR_AFE5_NT1 with 21622 variants from file /bgfs/alee/LO_LAB/Personal/Alexander_Chang/alc376/wholebody_phylo/mutect_treeomics_test/AUR-AFE5-TTM4_vs_AUR-AFE5-NT1.mutect2.filtered.vcf.
2024-03-21 23:19:50,350 treeomics.utils.vcf_parser:262 INFO: Read sample AUR_AFE5_AUR_AFE5_TTM4 with 21622 variants from file /bgfs/alee/LO_LAB/Personal/Alexander_Chang/alc376/wholebody_phylo/mutect_treeomics_test/AUR-AFE5-TTM4_vs_AUR-AFE5-NT1.mutect2.filtered.vcf.
2024-03-21 23:19:50,367 treeomics.patient:714 INFO: Start processing of 10 samples.

tail error output file

    considered_samples=included_samples, wes_filtering=args.wes_filtering, artifacts=common_vars)
  File "/bgfs/alee/LO_LAB/Personal/Alexander_Chang/alc376/wholebody_phylo/treeomics/treeomics/patient.py", line 628, in read_vcf_directory
    artifacts=artifacts)
  File "/bgfs/alee/LO_LAB/Personal/Alexander_Chang/alc376/wholebody_phylo/treeomics/treeomics/patient.py", line 739, in _process_samples
    status = self._add_variant(tmp_vars, fpr, artifacts, wes_filtering=wes_filtering)
  File "/bgfs/alee/LO_LAB/Personal/Alexander_Chang/alc376/wholebody_phylo/treeomics/treeomics/patient.py", line 1031, in _add_variant
    filter_variant(mut_key, Filter.MIN_VAR_COV)
  File "/bgfs/alee/LO_LAB/Personal/Alexander_Chang/alc376/wholebody_phylo/treeomics/treeomics/patient.py", line 1009, in filter_variant
    del self.sample_coverages[sa_name][-1]
IndexError: list assignment index out of range

Do you have any idea how to fix this or what was causing the error?