Entering edit mode
3.0 years ago
cmirchan
▴
10
I am using HaplotypeCaller (GATK v4.1.4.1) via a Snakemake workflow on GCP Kubernetes. I am running into an issue of HaplotypeCaller reporting that only 1 thread is available, despite the fact that more are available. I'm not sure if this is a known issue with GCP instances, but I have tried different machine types to no avail. In the HaplotypeCaller logs, I see these messages:
18:46:31.968 INFOIntelPairHmm - Available threads: 1
18:46:31.968 INFOIntelPairHmm - Requested threads: 3
18:46:31.969 WARNIntelPairHmm - Using 1 available threads, but 3 were requested
So for some reason HaplotypeCaller is only recognizing 1 thread available, even though the instance has more. I would appreciate any advice on how to fix this, or what I may be missing.
