Hi!
I have put together a pipeline for preprocessing my sequences. I have several sff files that I would like to process in the same manner - each file includes several sequence tags by which I would like to be able to split the the results on at the end of the pipeline. So, I go through the denoising and chimera checking more or less as described in the Schloss SOP pipeline. Then I would like to use the split.groups command at the end to split the end result, but only get an error message.
Here is my pipeline:
set.dir(output=.)
sffinfo(sff=GQOGG8V06.sff, flow=T)
summary.seqs(fasta=GQOGG8V06.fasta)
Denoising
trim.flows(flow=GQOGG8V06.flow, oligos=…/infodata/noisetrimfile.tab, pdiffs=2, bdiffs=1, minflows=360, maxflows=720, processors=16)
shhh.flows(file=GQOGG8V06.flow.files, processors=16)
Trimming seqs that don’t match the primer, and
which are too short, and which have too low quality
trim.seqs(fasta=GQOGG8V06.shhh.fasta, name=GQOGG8V06.shhh.names, oligos=…/infodata/noisetrimfile.tab, pdiffs=0, bdiffs=0, maxhomop=8, minlength=200, processors=16)
summary.seqs(fasta=GQOGG8V06.shhh.trim.fasta)
unique.seqs(fasta=GQOGG8V06.shhh.trim.fasta)
summary.seqs(fasta=GQOGG8V06.shhh.trim.unique.fasta)
chimera.uchime(fasta=GQOGG8V06.shhh.trim.unique.fasta, name=GQOGG8V06.shhh.trim.names,reference=self)
remove.seqs(fasta=GQOGG8V06.shhh.trim.unique.fasta, accnos=GQOGG8V06.shhh.trim.unique.uchime.accnos, name=GQOGG8V06.shhh.trim.names, group=GQOGG8V06.shhh.groups)
summary.seqs(fasta=GQOGG8V06.shhh.trim.unique.pick.fasta)
chop.seqs(fasta=GQOGG8V06.shhh.trim.unique.pick.fasta, numbases=400, keep=front, short=T)
summary.seqs(fasta=GQOGG8V06.shhh.trim.unique.pick.chop.fasta)
split.groups(fasta=GQOGG8V06.shhh.trim.unique.pick.chop.fasta, group=GQOGG8V06.shhh.pick.groups)
Everything goes very nice until the last line where I get:
mothur > split.groups(fasta=GQOGG8V06.shhh.trim.unique.pick.chop.fasta, group=GQOGG8V06.shhh.pick.groups)
[ERROR]: Your fasta file contains 1139 valid sequences, and your groupfile contains 17094, please correct. Did you forget to include the name file?
mothur >
Now, I have been trying to figure out how to get the right groups file for this one, but I believe that I am missing something somewhere.
Thanks for your help!
Karin