search

Illumina / Cyrius

A tool to genotype CYP2D6 with WGS data
Other
46 stars 5 forks source link

TypeError: 'NoneType' object cannot be interpreted as an integer #41

Open anh151 opened 7 months ago

anh151 commented 7 months ago

Hello, I have been able to succesffully run Cyrius on many samples. However, one sample I get the error shown below. Any thoughts on the cause? PyPGx and Aldy were both able to call this sample as 2x2/4.

!python3 {cyrius_path} -m {manifest_file} -p cyrius_1152285 -g 38 -o cyrius_results
INFO:root:Processing sample 1152285 at 2023-11-13 15:07:38.992327
Traceback (most recent call last):
  File "/home/jupyter/workspaces/pharmacogenomichaplotypecharacterization/bin/Cyrius/star_caller.py", line 562, in <module>
    main()
  File "/home/jupyter/workspaces/pharmacogenomichaplotypecharacterization/bin/Cyrius/star_caller.py", line 530, in main
    bam_name, call_parameters, threads, count_file, reference_fasta, index_name=index_name
  File "/home/jupyter/workspaces/pharmacogenomichaplotypecharacterization/bin/Cyrius/star_caller.py", line 362, in d6_star_caller
    bamfile, cnvtag, haplotype_db["g.42127526C>T_g.42127556T>C"]
  File "/home/jupyter/workspaces/pharmacogenomichaplotypecharacterization/bin/Cyrius/caller/call_variants.py", line 339, in call_var42127526_var42127556
    for _ in range(var7526_cn):
TypeError: 'NoneType' object cannot be interpreted as an integer

Thanks, Andrew