# problem with trim.seqs command
**URL:** https://forum.mothur.org/t/problem-with-trim-seqs-command/1208
**Category:** Commands in mothur
**Created:** [February 1, 2013, 12:30pm UTC](https://forum.mothur.org/t/problem-with-trim-seqs-command/1208 "2013-02-01T12:30:30Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@manuelaira](https://forum.mothur.org/u/manuelaira)
#### Post date: [February 1, 2013, 12:30pm UTC](https://forum.mothur.org/t/problem-with-trim-seqs-command/1208/1 "2013-02-01T12:30:30Z")
Hi There,
i just had a doubt regarding the trim.seqs command. When I try to use to start analyzing my data. When I type this:
trim.seqs(fasta=sample.fna, oligos=sample.oligos, qfile=sample.qual, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, processors=2)
I get the following error: You have 223893 sequences in your fasta file, but 633071 sequences in your quality file.
My first option was to use sffinfo with the original sff file, which I have, but after sffinfo(sff=HZSC42M02.sff, flow=T), I get the following error:
[WARNING]: Your sff file may be corrupted! Sequence:
Clip Qual Left = 5, but we only read 1 bases.
Clip Qual Right = 1280, but we only read 1 bases.
What can be happening here?
Thank you very much for your help
Manuel Aira
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [February 1, 2013, 1:01pm UTC](https://forum.mothur.org/t/problem-with-trim-seqs-command/1208/2 "2013-02-01T13:01:10Z")
Sounds like there’s a problem with your sff file - can you get a “fresh” copy from your sequence provider?
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### Author:  [@manuelaira](https://forum.mothur.org/u/manuelaira)
#### Post date: [February 1, 2013, 1:48pm UTC](https://forum.mothur.org/t/problem-with-trim-seqs-command/1208/3 "2013-02-01T13:48:59Z")
I am sorry but I cannot understand what means “fresh”
The provider upload the files ( .sff, .fna and .qual) to our ftp 2 times, and I got the same errors all the time.
Thank you very much for your help and fast response
Regards,
Manuel Aira
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [February 1, 2013, 7:57pm UTC](https://forum.mothur.org/t/problem-with-trim-seqs-command/1208/4 "2013-02-01T19:57:33Z")
Not sure what to tell you. Sounds like their version of the sff file is corrupted too.
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### Author:  [@manuelaira](https://forum.mothur.org/u/manuelaira)
#### Post date: [February 4, 2013, 8:56am UTC](https://forum.mothur.org/t/problem-with-trim-seqs-command/1208/5 "2013-02-04T08:56:32Z")
Thank you very much for your help. I will talk with the sequence provider in order to know if there was any problem during the 454 run.
Regards,
Manuel Aira