# align.seqs question

**URL:** <https://forum.mothur.org/t/align-seqs-question/2149>\
**Category:** Commands in mothur\
**Created:** [November 30, 2014, 3:10am UTC](https://forum.mothur.org/t/align-seqs-question/2149 "2014-11-30T03:10:02Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![suttee2011](https://avatars.discourse-cdn.com/v4/letter/s/898d66/32.png) [@suttee2011](https://forum.mothur.org/u/suttee2011)\
**Post date:** [November 30, 2014, 3:10am UTC](https://forum.mothur.org/t/align-seqs-question/2149/1 "2014-11-30T03:10:02Z")

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Hi,  
When I use “align.seqs(fasta=raw.shhh.trim.unique.fasta, reference=silva.bacteria.fasta, processors=8,flip=t)” and " summary.seqs(fasta=raw.shhh.trim.unique.align, name=raw.shhh.trim.unique.names)", the mothur told me"IGJ6AI201CLN84 is not in your name or count file,please correct."How can I handle it?  
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:** [December 1, 2014, 3:41pm UTC](https://forum.mothur.org/t/align-seqs-question/2149/2 "2014-12-01T15:41:47Z")

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I think you perhaps want to run…

summary.seqs(fasta=raw.shhh.trim.unique.align, name=raw.shhh.trim.names)

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**Author:** ![suttee2011](https://avatars.discourse-cdn.com/v4/letter/s/898d66/32.png) [@suttee2011](https://forum.mothur.org/u/suttee2011)\
**Post date:** [December 1, 2014, 4:09pm UTC](https://forum.mothur.org/t/align-seqs-question/2149/3 "2014-12-01T16:09:26Z")

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> [@pschloss](#):
>
> I think you perhaps want to run…
> 
> summary.seqs(fasta=raw.shhh.trim.unique.align, name=raw.shhh.trim.names)

I try it again,but this time when I use “trim.seqs(fasta=raw.shhh.fasta, name=raw.shhh.names, oligos=raw.oligos, pdiffs=2, bdiffs=1, maxhomop=8, minlength=200, flip=T, processors=8)” and then “summary.seqs(fasta=raw.shhh.trim.fasta, name=raw.shhh.trim.names)”, mothur also told me the same mistake.More, when I use “processors=8” , my CPU only use 1 processor.I wonder if I use motnur in a wrong way?

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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:** [December 4, 2014, 9:17pm UTC](https://forum.mothur.org/t/align-seqs-question/2149/4 "2014-12-04T21:17:01Z")

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This error most often occurs when you mistakenly given mothur the wrong filename. One way to avoid this is to use the “current” option.

mothur \> trim.seqs(fasta=GQY1XT001.shhh.fasta, name=GQY1XT001.shhh.names, oligos=GQY1XT001.oligos, pdiffs=2, bdiffs=1, maxhomop=8, minlength=200, flip=T, processors=2)  
mothur \> summary.seqs(fasta=current, name=current)

If you think you are giving mothur the correct names, you can send me your log file, fasta and name file at [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com). I am happy to take a look.

-Sarah