# sequence name mismatch error in trim.seqs
**URL:** https://forum.mothur.org/t/sequence-name-mismatch-error-in-trim-seqs/490
**Category:** Commands in mothur
**Created:** [March 18, 2011, 3:25am UTC](https://forum.mothur.org/t/sequence-name-mismatch-error-in-trim-seqs/490 "2011-03-18T03:25:45Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@lschaef](https://forum.mothur.org/u/lschaef)
#### Post date: [March 18, 2011, 3:25am UTC](https://forum.mothur.org/t/sequence-name-mismatch-error-in-trim-seqs/490/1 "2011-03-18T03:25:45Z")
I’m getting a mismatch error when I try to do trim.seqs using the .fasta and .qual files I received from our sequencing center. When I run summary.seqs on the .fasta file, everything works fine. When I run trim.seqs, I get the error below, then mothur hangs and I end up having to close the terminal window.
mothur \> trim.seqs(fasta=GM2GI8201.sff.fa, oligos=Britton2TagsLumped.oligos, qfile=GM2GI8201.sff.fa.qual, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, processors=2)
sequence name mismatch between fasta: GM2GI8201CC5ON and qual file: 5
sequence name mismatch between fasta: GM2GI8201EKZTJ and qual file: 7
sequence name mismatch between fasta: GM2GI8201CJX7V and qual file: 0
sequence name mismatch between fasta: GM2GI8201E0TS3 and qual file: 6
sequence name mismatch between fasta: GM2GI8201DN5QE and qual file: 0
sequence name mismatch between fasta: GM2GI8201DS8XI and qual file: 7
sequence name mismatch between fasta: GM2GI8201CFDPW and qual file: 5
I should mention that I used these same files to process my data using RDP’s pyro pipeline, and didn’t have an issue. I saw that someone previously reported a mismatch error with trim.seqs and it turned out that the sequences giving the error had a length of zero. However, this isn’t the case for me; although some of these are short, a few are decent lengths, and BLASTing them shows that they are indeed 16S. Any thoughts or help much appreciated.
Thanks,
Laura
---
### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [March 18, 2011, 3:10pm UTC](https://forum.mothur.org/t/sequence-name-mismatch-error-in-trim-seqs/490/2 "2011-03-18T15:10:08Z")
Hey Laura,
Could you re-download mothur (v.1.17.3) and give that a whirl? I think this might be related to a bug we found during the workshop. Let me know how it goes…
Pat
---
### Author:  [@lschaef](https://forum.mothur.org/u/lschaef)
#### Post date: [March 22, 2011, 5:17pm UTC](https://forum.mothur.org/t/sequence-name-mismatch-error-in-trim-seqs/490/3 "2011-03-22T17:17:00Z")
Thanks Pat. I downloaded the new version and voila - it works.
---
### Author:  [@Rohan](https://forum.mothur.org/u/Rohan)
#### Post date: [August 4, 2011, 7:15pm UTC](https://forum.mothur.org/t/sequence-name-mismatch-error-in-trim-seqs/490/4 "2011-08-04T19:15:51Z")
Hi Pat,
I think this has popped up again in mothur v.1.21.0.
It seemed to be working fine in mothur v.1.20.3.
Rohan
---
### Author:  [@Rohan](https://forum.mothur.org/u/Rohan)
#### Post date: [August 6, 2011, 7:15pm UTC](https://forum.mothur.org/t/sequence-name-mismatch-error-in-trim-seqs/490/5 "2011-08-06T19:15:59Z")
Ok so I was a bit wrong about what I said.
For some reason it doesn’t work in either version of mothur on my install on Ubuntu 10.04. I used readline and the 64bit flags on compilation. It works fine unless I specify more than one processor then it spits out a bunch of mismatch errors. I’m fasta and qual file generated in mothur from Sanger-style fastq files.
For whatever reason it all works well when I try it on OSX.
Rohan