trim.seqs problem?

I’m trying to run trim.seqs on ~440K titanium reads as follows:
mothur > trim.seqs(fasta=S1_S2.fna, qfile=S1_S2.fna.qual, qaverage=25, qthreshold=25, qtrim=T, processors=4)

It’s been running for about 80 minutes and has only generated temp files for the first four sequences despite maxing out the four assigned processors.

Is it working, or have I done something wrong?


In version 1.15.0, we made some changes to the internal workings of the trim.seqs command and unfortunately added and indexing error when qtrim=T, :oops: . This caused all sequences to be scrapped. The fix will be part of 1.16.0.