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).