Problems after trim.seqs

Hello,

I am a new user of mothur. After I tried the shhh.flows approach I wanted to try the command trim.seqs and compare the results. The computation of trim.seqs seems to work but I can not use the command summary.seqs on the fasta-file afterwards.

Filename.trim.fasta is not a valid parameter.
The valid parameters are: fasta, names, processors, inputdir, and outputdir.
Using filename.trim.fasta as inputfile for the fasta parameter.
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is filename.flow.shhh.trim.names which seems to match filename.trim.fasta
[Error]: did not complete summary.seqs

What did I do wrong? Colleagues of mine who could not use shhh.flows approach for their data had not this error when they tried the trim.seqs approach. Do you know how I can fix this problem?

Thank you in advance for your help!

Kind regards,
Jasmin

and there is an aditional problem with the unique.seqs command.

I try to use my files from the shhh.flows approach. the error I get is:

names is not a valid parameter.
The valid parameters are: fasta, name, processors, inputdir, and outputdir.
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is filename.flow.shhh.trim.names which seems to match filename.flow.shhh.trim.fasta
[Error]: did not complete unique.seqs

Do you know, what kind of mistake I did and how to fix it?

Thank you in advance!

All the best!
Jasmin

Could you post the commands you are running?

Sure, here they are:

from the Schloss SOP I run the

trim.seqs(fasta=filename.fasta, oligos=filename.oligos, qfile=filename.qual, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=25, qwindowsize=50, processors=2)

there is a Warning: This command can take a namefile and you did not provide one. The current namefile is filename.flow.shhh.trim.names which seems to fit filename.fasta

but it computes
afterwards I try the command sumamry.seqs(filename.trim.fasta)
than the Error occurs, that I described in the prevouis post.

for the second error the command is:

unique.seqs(fasta=filename.flow.shhh.trim.fasta, name=filename.flow.shhh.trim.names)

For the command: sumamry.seqs(filename.trim.fasta) you want: summary.seqs(fasta=filename.trim.fasta).

For the “names is not a valid parameter.” error, I suspect you typed: unique.seqs(fasta=filename.flow.shhh.trim.fasta, names=filename.flow.shhh.trim.names) instead of unique.seqs(fasta=filename.flow.shhh.trim.fasta, name=filename.flow.shhh.trim.names).