# Problems after trim.seqs

**URL:** <https://forum.mothur.org/t/problems-after-trim-seqs/961>\
**Category:** Commands in mothur\
**Created:** [July 4, 2012, 7:33am UTC](https://forum.mothur.org/t/problems-after-trim-seqs/961 "2012-07-04T07:33:33Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Jasmin](https://avatars.discourse-cdn.com/v4/letter/j/9de053/32.png) [@Jasmin](https://forum.mothur.org/u/Jasmin)\
**Post date:** [July 4, 2012, 7:33am UTC](https://forum.mothur.org/t/problems-after-trim-seqs/961/1 "2012-07-04T07:33:33Z")

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Hello,

I am a new user of mothur. After I tried the shhh.flows approach I wanted to try the command trim.seqs and compare the results. The computation of trim.seqs seems to work but I can not use the command summary.seqs on the fasta-file afterwards.

Filename.trim.fasta is not a valid parameter.  
The valid parameters are: fasta, names, processors, inputdir, and outputdir.  
Using filename.trim.fasta as inputfile for the fasta parameter.  
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is filename.flow.shhh.trim.names which seems to match filename.trim.fasta  
[Error]: did not complete summary.seqs

What did I do wrong? Colleagues of mine who could not use shhh.flows approach for their data had not this error when they tried the trim.seqs approach. Do you know how I can fix this problem?

Thank you in advance for your help!

Kind regards,  
Jasmin

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**Author:** ![Jasmin](https://avatars.discourse-cdn.com/v4/letter/j/9de053/32.png) [@Jasmin](https://forum.mothur.org/u/Jasmin)\
**Post date:** [July 4, 2012, 8:17am UTC](https://forum.mothur.org/t/problems-after-trim-seqs/961/2 "2012-07-04T08:17:46Z")

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and there is an aditional problem with the unique.seqs command.

I try to use my files from the shhh.flows approach. the error I get is:

names is not a valid parameter.  
The valid parameters are: fasta, name, processors, inputdir, and outputdir.  
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is filename.flow.shhh.trim.names which seems to match filename.flow.shhh.trim.fasta  
[Error]: did not complete unique.seqs

Do you know, what kind of mistake I did and how to fix it?

Thank you in advance!

All the best!  
Jasmin

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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:** [July 5, 2012, 1:03pm UTC](https://forum.mothur.org/t/problems-after-trim-seqs/961/3 "2012-07-05T13:03:54Z")

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Could you post the commands you are running?

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<div class="post-metadata">

**Author:** ![Jasmin](https://avatars.discourse-cdn.com/v4/letter/j/9de053/32.png) [@Jasmin](https://forum.mothur.org/u/Jasmin)\
**Post date:** [July 5, 2012, 2:11pm UTC](https://forum.mothur.org/t/problems-after-trim-seqs/961/4 "2012-07-05T14:11:35Z")

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Sure, here they are:

from the Schloss SOP I run the

trim.seqs(fasta=filename.fasta, oligos=filename.oligos, qfile=filename.qual, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=25, qwindowsize=50, processors=2)

there is a Warning: This command can take a namefile and you did not provide one. The current namefile is filename.flow.shhh.trim.names which seems to fit filename.fasta

but it computes  
afterwards I try the command sumamry.seqs(filename.trim.fasta)  
than the Error occurs, that I described in the prevouis post.

for the second error the command is:

unique.seqs(fasta=filename.flow.shhh.trim.fasta, name=filename.flow.shhh.trim.names)

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<div class="post-metadata">

**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:** [July 5, 2012, 3:08pm UTC](https://forum.mothur.org/t/problems-after-trim-seqs/961/5 "2012-07-05T15:08:43Z")

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For the command: sumamry.seqs(filename.trim.fasta) you want: summary.seqs(fasta=filename.trim.fasta).

For the “names is not a valid parameter.” error, I suspect you typed: unique.seqs(fasta=filename.flow.shhh.trim.fasta, names=filename.flow.shhh.trim.names) instead of unique.seqs(fasta=filename.flow.shhh.trim.fasta, name=filename.flow.shhh.trim.names).