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SBIMB / StellarPGx

Calling star alleles in highly polymorphic pharmacogenes (e.g. CYP450 genes) by leveraging genome graph-based variant detection.
MIT License
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File _var_1/chr10/094935000-094990000.vcf.gz not created #10

Closed NTNguyen13 closed 2 years ago

NTNguyen13 commented 2 years ago

Describe the bug Run StellarPGx with docker implementation on CYP2C9 gene. I have run StellarPGx for around 1000 samples with different genes (CYP2D6, CYP2C19, etc.) with no problem, but with CYP2C9, it always stuck at this step (different runs stuck at different samples). I checked the working directory and found that the file _var_1/chr10/094935000-094990000.vcf.gz is not created in the previous process, so that it will fail at this step.

To Reproduce nextflow run main.nf -profile standard --build hg38 --gene cyp2c9

Screenshots image

twesigomwedavid commented 2 years ago

@NTNguyen13,

Thanks a lot for spotting this issue. It should be now fixed by 471cb5bd383ecec7a6f7fad25b8d4aa83f1588cd

David

NTNguyen13 commented 2 years ago

thank you very much!