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Add an option to increase number of threads per diamond run #167

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taprs opened this issue Sep 17, 2024 · 0 comments
Open

Add an option to increase number of threads per diamond run #167

taprs opened this issue Sep 17, 2024 · 0 comments

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@taprs
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taprs commented Sep 17, 2024

I noticed that on my HPC the diamond step of orthofinder takes forever for the octoploid species with ~100k gene models being BLASTed against itself.

My workaround was (1) manually running the exact diamond command in the orthofinder WorkingDirectory providing more --threads to it and then (2) killing the original diamond processes. Then, everything gets through very quickly and orthofinder does not notice the interception :)

But I think there might be a nicer way to provide more threads per diamond run. I haven't found one neither in GENESPACE nor in orthofinder — should I go down to orthofinder issues then?

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