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Published 20 hours ago • verified publisher icon nextgenusfs

funannotate clean takes a lot of time

Open Nitin123-4 opened this issue 9 months ago • 2 comments

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

Nitin123-4 avatar Sep 26 '23 06:09 Nitin123-4

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 avatar Sep 26 '23 16:09 hyphaltip

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.

hyphaltip avatar Oct 24 '23 18:10 hyphaltip