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Pipeline stalls after genomicsdbimport #40

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nvnieuwk opened this issue Jan 4, 2023 · 4 comments
Closed

Pipeline stalls after genomicsdbimport #40

nvnieuwk opened this issue Jan 4, 2023 · 4 comments
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nvnieuwk commented Jan 4, 2023

Description of the bug

When running a multi family run, the pipeline stalls after genomicsdbimport until all families have been run through genomicsdbimport

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dev version on the 4th of January 2023
@nvnieuwk nvnieuwk added the bug Something isn't working label Jan 4, 2023
@nvnieuwk nvnieuwk self-assigned this Jan 4, 2023
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nvnieuwk commented Jan 4, 2023

Doesn't seem to be stalling but just skipping after genomicsdbimport. Only had this happen once on the HPC...

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nvnieuwk commented Jan 5, 2023 •
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Possibly fixed in #42

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nvnieuwk commented Jan 5, 2023

I was able to recreate the issue using the stub run on the HPC 🥳

@nvnieuwk nvnieuwk closed this as completed Jan 5, 2023
@nvnieuwk nvnieuwk reopened this Jan 5, 2023
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nvnieuwk commented Jan 5, 2023

Issue found: It was a meta id parsing error in the BED_SCATTER_GROOVY subwf. It couldn't handle the . present in the family names. Should be fixed in #44

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