missing file?

Hi folks,

I’m in the 454 SOP, and I noticed a number of commands that call for the file GQY1XT001.fasta. This doesn’t seem to be in the zipped SOP folder. When this appeared early on, in the command summary.seqs(fasta=GQY1XT001.fasta)>, I figured you were just showing us the command.

But, it appears later, in the section “Using quality scores,” here: trim.seqs(fasta=GQY1XT001.fasta, oligos=GQY1XT001.oligos, qfile=GQY1XT001.qual, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, processors=2)> and in the subsequent command, so I think I may be missing the file. Or no?


You would have to download the full sff file and run sff.info on the file. The files we posted for the tutorial are a subset of the larger sff file with the goal of pursuing the flow-based approach on a small demonstration dataset.

Hope this helps,

It does, thanks. In the meantime, another question on the 454 SOP.

I’m up to the point where you want to calculate the number of otu’s in the mock set. You provide this command:

system(cut -f 2 *error.summary | sort | uniq > mock.accnos)

Problem is, I’m using a pc, so I don’t have unix commands. So, I followed your further instructions, to take only the 2nd column in the “error.summary” file, sort, remove duplicates and remove “reference.” Saved. But, when I run the following command:

mothur > get.seqs(accnos=mock.accnos, fasta=HMP_MOCK.v35.filter.fasta)

I get:

Your file does not contain any sequence from the .accnos file.
Selected 0 sequences from your fasta file.

Output File Names:

Should I have left something else in the mock.accnos file?


Hmmm. Can you triple check that your accnos file is a text file? Assuming it is, could you then post the first 5 lines of your mock.accnos and the first five lines of HMP_MOCK.v35.filter.fasta?


I did that triple check, and, in fact, I had saved it in unicode. Subsequently got it to work. Thanks, again!