Closed tkmamidi closed 10 months ago
It is working well when used >=2 CPUs but still failing when using only 1 CPU.
I've been able to recreate this and am working on a diagnosis. It seems like it's the combination of mutation_assessor and --mp 1. Multiprocessing issues are a bit tricky to diagnose, but I'll keep you updated as it's worked on.
This turned out to be an issue with bothe the mutation_assessor annotator, and some poor error handling by the main package. The annotator is fixed by this commit https://github.com/KarchinLab/open-cravat-modules-karchinlab/commit/69c352d9dc5eb6baa4bbe049fcebd82387b11756.
Please update to mutation_assessor version 3.1.1 (oc module update mutation_assessor
).
The error handling is fixed here https://github.com/KarchinLab/open-cravat/commit/d2b6b59400fac6fdd09373d09166ac84db7858c6 and that fix will be out in the next release. This will prevent similar errors from stopping annotator execution.
I'm currently using v2.4.1 and some annotation columns are missing from the output when using only 1 CPU. Upon investigation, I found that
aggregator
step started before all theAnnotators
are finished running.Here's an example -
Here,
aggregator
step started beforemutation_assessor
finished running.Can someone please help me with solving this? Thank you!