Replies: 3 comments
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It is working well when used >=2 CPUs but still failing when using only 1 CPU. |
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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. |
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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 KarchinLab/open-cravat-modules-karchinlab@69c352d. Please update to mutation_assessor version 3.1.1 ( The error handling is fixed here d2b6b59 and that fix will be out in the next release. This will prevent similar errors from stopping annotator execution. |
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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!
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