Uchime using 2 processors

Commands in mothur
1

I’m using Uchime for chimera calling. The server I am working on has 8 processors but when Uchime starts I get the following message:

Checking sequences from data/mothur/process/stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta ...
Reducing processors to 2.

Is this intrinsic to Uchime? Even for 2 samples it is taking a long time to complete (over 2hrs). I want it to use all processors available to run faster. Is this possible?

2

Uchime distributes the processors, giving one for each sample). But, only uses 1 processor per sample - I suppose it is linked to the method used for identifying chimeras.

2 Likes
3

uchime is very slow. Can you switch to vsearch?

4

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