# trim.seqs sequence mismatch

**URL:** <https://forum.mothur.org/t/trim-seqs-sequence-mismatch/1545>\
**Category:** Commands in mothur\
**Created:** [October 18, 2013, 8:00pm UTC](https://forum.mothur.org/t/trim-seqs-sequence-mismatch/1545 "2013-10-18T20:00:17Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![akoliver](https://avatars.discourse-cdn.com/v4/letter/a/e68b1a/32.png) [@akoliver](https://forum.mothur.org/u/akoliver)\
**Post date:** [October 18, 2013, 8:00pm UTC](https://forum.mothur.org/t/trim-seqs-sequence-mismatch/1545/1 "2013-10-18T20:00:17Z")

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I have run trim.seqs on two data sets for MiSeq and keep getting "sequence name mismatch btwn fatsa:\_\_\_\_\_\_ and qual file: \_\_\_\_\_\_\_\_\_… however I am still getting output files. Should I be concerned about the output files from this command?

Thanks!

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**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [October 21, 2013, 12:17pm UTC](https://forum.mothur.org/t/trim-seqs-sequence-mismatch/1545/2 "2013-10-21T12:17:30Z")

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The mismatch error message is telling you that mothur is using the quality values from the sequence in named in the quality file to trim the sequence named in the fasta file. You do not want to use those outputs. I have modified mothur so that it will abort the command in this case and remove the output files.

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**Author:** ![akoliver](https://avatars.discourse-cdn.com/v4/letter/a/e68b1a/32.png) [@akoliver](https://forum.mothur.org/u/akoliver)\
**Post date:** [October 22, 2013, 9:04pm UTC](https://forum.mothur.org/t/trim-seqs-sequence-mismatch/1545/3 "2013-10-22T21:04:28Z")

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Ah, I figured that might be the case, thank you!