no name file generated from initial trim.seqs in Schloss SOP

Commands in mothur
1

Hi,

I’ve been following the Schloss SOP and get stuck when I come to the first unique.seqs step as I don’t have a name file to include. Don’t have access to the sff files so jumped straight to trim.seqs. I’ve been using the following code and get the following output.

trim.seqs(fasta=Myfile.fna, oligos=Myfile.txt, qfile=Myfile.qual, maxambig=0, maxhomop=8, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, processors=16)

Output File Names:
Myfile.trim.fasta
Myfile.scrap.fasta
Myfile.trim.qual
Myfile.scrap.qual
Myfile.groups

Is the name file only generated when using the shhh.flows procedure?

Also, I’ve found that further in the analyses I have issues with names and group files not matching up, don’t know if this is related.

Any help greatly appreciated

Bruce

2

Is the name file only generated when using the shhh.flows procedure?

Right - and you’ll get it when you run unique.seqs in the next step of the SOP. Unfortunately the file names given in the SOP are for our standard way of doing things, which is with shhh.flows. It shouldn’t be too hard to plug in the latest versions of the fasta, group, and names files through out. Alternatively, wherever we give one of those file names, if you just use “current” (without the quotes), you should be fine.

Pat