trim.seqs-problem with qfile

I have data from 454 pyrosequencing. I used for denoising my data: mothur > shhh.flows(flow=sample.flow, order=B, LookUp_Titanium.pat). Outputs were used in next step with the command “trim.seqs” and parameter “qaverage”: mothur > trim.seqs(fasta=sample.shhh.fasta, qfile=sample.shhh.qual, qaverage=25). Program wrote “Error in reading your qfile, at position -1. Blank name” and mothur falled down. Could somebody help me with this problem? Many thanks.

If you’re doing shhh.flows, you don’t need to run trim.seqs with quality score values. The shhh.flows qscore values are pretty meaningless. Checkout the pipeline at


Many thanks.