# missing file?

**URL:** https://forum.mothur.org/t/missing-file/1656
**Category:** Commands in mothur
**Created:** [January 21, 2014, 10:02pm UTC](https://forum.mothur.org/t/missing-file/1656 "2014-01-21T22:02:19Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![lycophidion](https://avatars.discourse-cdn.com/v4/letter/l/df705f/32.png) [@lycophidion](https://forum.mothur.org/u/lycophidion)
#### Post date: [January 21, 2014, 10:02pm UTC](https://forum.mothur.org/t/missing-file/1656/1 "2014-01-21T22:02:19Z")

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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?

Thanks,  
Mike

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### Author: ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [January 22, 2014, 12:56pm UTC](https://forum.mothur.org/t/missing-file/1656/2 "2014-01-22T12:56:54Z")

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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,  
Pat

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### Author: ![lycophidion](https://avatars.discourse-cdn.com/v4/letter/l/df705f/32.png) [@lycophidion](https://forum.mothur.org/u/lycophidion)
#### Post date: [January 23, 2014, 3:40am UTC](https://forum.mothur.org/t/missing-file/1656/3 "2014-01-23T03:40:05Z")

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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:  
HMP\_MOCK.v35.filter.pick.fasta

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

Thanks!

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### Author: ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [January 24, 2014, 1:07pm UTC](https://forum.mothur.org/t/missing-file/1656/4 "2014-01-24T13:07:30Z")

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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?

Thanks  
Pat

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### Author: ![lycophidion](https://avatars.discourse-cdn.com/v4/letter/l/df705f/32.png) [@lycophidion](https://forum.mothur.org/u/lycophidion)
#### Post date: [February 6, 2014, 3:06am UTC](https://forum.mothur.org/t/missing-file/1656/5 "2014-02-06T03:06:48Z")

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