search

KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
110 stars 27 forks source link

OC stalling on mapper #153

Closed katelynmullen closed 6 months ago

katelynmullen commented 1 year ago

Screenshot 2023-05-16 at 12 27 24 PM Reposting as a new issue in case my response on the downtime thread was missed. I tried reinstalling mapper and oc entirely and neither worked. I tried a test again this morning with the one patient I sent you and it successfully ran in 43 seconds. However, when I tried to cat a file of commands for 88 patients, gene mapper stalled. Then I tried to rerun the single patient again, but the gene mapper continued to stall. Can someone please assist? Thanks!

kmoad commented 1 year ago

After talking with Kateyln, this appears to be an a issue with mapper multiprocessing and small input files. Can be worked-around by adding --mp 1 to the oc run command.

Working to reproduce and fix the underlying issue.