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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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funannotate clean takes a lot of time #965

Open Nitin123-4 opened 9 months ago

Nitin123-4 commented 9 months ago

Hi team, I can see funannotate clean takes a lot of time, no cpu option to make it faster? Thanks.

hyphaltip commented 9 months ago

it uses multi-threaded minimap2 - you can also try AAFTF which has a AAFTF rmdup step that Jon and I also wrote and ported from funannotate, it is nearly the same the clean step and may run a little faster. the step is a function of how many contigs you have, a very large fragmented genome will end up taking a while because there is a lot of comparisons to make.

hyphaltip commented 8 months ago

please let us know whether you tried additional approaches but the clean step does a lot of comparisons if there are many individual contigs - it uses multiple threads I believe but helpful if you can provide a sample of what you commands you tried.