Hi,
When I use “align.seqs(fasta=raw.shhh.trim.unique.fasta, reference=silva.bacteria.fasta, processors=8,flip=t)” and " summary.seqs(fasta=raw.shhh.trim.unique.align, name=raw.shhh.trim.unique.names)", the mothur told me"IGJ6AI201CLN84 is not in your name or count file,please correct."How can I handle it?
Thanks! 
I think you perhaps want to run…
summary.seqs(fasta=raw.shhh.trim.unique.align, name=raw.shhh.trim.names)
I try it again,but this time when I use “trim.seqs(fasta=raw.shhh.fasta, name=raw.shhh.names, oligos=raw.oligos, pdiffs=2, bdiffs=1, maxhomop=8, minlength=200, flip=T, processors=8)” and then “summary.seqs(fasta=raw.shhh.trim.fasta, name=raw.shhh.trim.names)”, mothur also told me the same mistake.More, when I use “processors=8” , my CPU only use 1 processor.I wonder if I use motnur in a wrong way?
This error most often occurs when you mistakenly given mothur the wrong filename. One way to avoid this is to use the “current” option.
mothur > trim.seqs(fasta=GQY1XT001.shhh.fasta, name=GQY1XT001.shhh.names, oligos=GQY1XT001.oligos, pdiffs=2, bdiffs=1, maxhomop=8, minlength=200, flip=T, processors=2)
mothur > summary.seqs(fasta=current, name=current)
If you think you are giving mothur the correct names, you can send me your log file, fasta and name file at mothur.bugs@gmail.com. I am happy to take a look.
-Sarah