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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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Resume annotation option #193

Open tkmamidi opened 8 months ago

tkmamidi commented 8 months ago

Is there a way to resume the annotation when it is killed/stopped before creating the database? I think it is a really good feature to continue from where it stopped instead of starting from the beginning.

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kmoad commented 8 months ago

Try using the --startat aggregator option. It should resume and pick up the annotator outputs. But it has been buggy in the past.

tkmamidi commented 5 months ago

Sorry, the question is even before finishing the annotation step. When a run is stopped cause of timeout errors, we have to rerun it from the starting step. Is there a checkpoint on how many annotators are complete and how many are pending? I'm running WGS samples with 70 annotators and it gets annoying when it runs for 14hrs and stops without a resume option. Hope you understand!