Bamsort Failed with "AttributeError"

lkuang · June 23, 2022, 6:16am

It failed when run bamsort.

The cmd used:
pbrun bamsort --ref fix_WYDT04_HiFiasm_genome.fa --in-bam DY90_rmdup.bam --out-bam output.bam --sort-order coordinate

PS: haplotypecaller , deepvariant , rna_gatk , etc. can be run correctly.

Thanks for any advice.

gburnett · June 23, 2022, 8:45pm

I was just able to replicate your error. I am submitting a bug to our engineering team.

Thank you for your patience.

lkuang · July 1, 2022, 5:24am

Hi @gburnett, Does this issue also exist in PB3.8?

lkuang · August 5, 2022, 10:03am

Hi, @gburnett What is the status of this bug.

gburnett · August 5, 2022, 5:58pm

This is fixed in the latest version of Parabricks 3.8.1. You should be able to download it from the trial portal.

Thanks!