AttributeError("'NoneType' object has no attribute 'startswith'") for gene= UGT1A1

[J-Bradlee]

Hi there,

Aldy has been working fine for all the other genes however only when I try UGT1A1 do i get this error.

  Aldy v4.4 (Python 3.8.10 on Linux 5.15.0-1042-azure-x86_64-with-glibc2.29)
   (c) 2016-2023 Aldy Authors. All rights reserved.
   Free for non-commercial/academic use only.
Genotyping sample P000205.hc.vqsr.hs38.vcf.gz...
WARNING: Cannot detect genome, defaulting to hg19.
WARNING: Using VCF file. Copy-number calling is not available.
Using VCF sample P000205
ERROR: gene= UGT1A1, file= /dbfs/mnt/s3/s3/vcf/LKCGP-P000205-251422-02-04-07-G1/hs38/haplotypecaller/v4_2_5_0/P000205.hc.vqsr.hs38.vcf.gz
AttributeError("'NoneType' object has no attribute 'startswith'")
Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/aldy/__main__.py", line 122, in main
    _genotype(args.gene, output, args)
  File "/usr/local/lib/python3.8/dist-packages/aldy/__main__.py", line 443, in _genotype
    run(None)
  File "/usr/local/lib/python3.8/dist-packages/aldy/__main__.py", line 393, in run
    _ = genotype(
  File "/usr/local/lib/python3.8/dist-packages/aldy/genotype.py", line 176, in genotype
    sample = sam.Sample(gene, profile, sam_path, debug=debug)
  File "/usr/local/lib/python3.8/dist-packages/aldy/sam.py", line 116, in __init__
    self._make_coverage(norm, muts)
  File "/usr/local/lib/python3.8/dist-packages/aldy/sam.py", line 482, in _make_coverage
    self.coverage = Coverage(
  File "/usr/local/lib/python3.8/dist-packages/aldy/coverage.py", line 50, in __init__
    if not (indel_coverage and op.startswith("ins")):
AttributeError: 'NoneType' object has no attribute 'startswith'

wondering if anyone else has run into this issue?

[J-Bradlee]

Fixed this by specifiying the reference genome. --genome hg38