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ImagoXV / NanoASV

NanoASV official repo
GNU General Public License v3.0
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Need to update bwa to bwa-mem2 #34

Closed ImagoXV closed 7 months ago

ImagoXV commented 7 months ago

I used bwa for simplicity sake, but now I need to change it for bwa-mem2 which is supposed to be more memory efficient and faster

ImagoXV commented 7 months ago

First docker build did not run well. Silva indexing killed. Memory ?

Edit : Yes it's memory related. bwa was indexing without a problem, but bwa-mem2 (which is supposed to better handle memory is out of bound. I Can't manage to check memory allocation for the docker build process.

ImagoXV commented 7 months ago

https://github.com/bwa-mem2/bwa-mem2/issues/255

ImagoXV commented 7 months ago

Yeah bwa-mem2 memory usage is 72Gb for Silva indexing.

Cannot do the indexing on a regular laptop. We'll stay with bwa for now.