GWAS hanging up on runJob stage

I’m testing a linear mixed model regression on 10,000 rows of chr22 with 100,000 samples.

It’s being run on a dataproc cluster configured with 72 cpu cores. It’s been over 10 hours since the initial command was run.

Is it typically the case that the runJob stage hangs in Pending for a significant period of time?


What platform are you running your regression on?
If you are running on GCP, and using preemptibles, this could be partially the reason that you have this issue.

Unless if this has been solved since!

thanks for the reply!

don’t know what happened, but I updated the hail version and it seems to be working fine now.

Glad to hear this! :slight_smile: