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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?
The text was updated successfully, but these errors were encountered:
I noticed that on my HPC the
diamond
step oforthofinder
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 orthofinderWorkingDirectory
providing more--threads
to it and then (2) killing the originaldiamond
processes. Then, everything gets through very quickly andorthofinder
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 inGENESPACE
nor inorthofinder
— should I go down toorthofinder
issues then?The text was updated successfully, but these errors were encountered: