# "Summary.seqs" went wrong after "trim.seqs"

**URL:** <https://forum.mothur.org/t/summary-seqs-went-wrong-after-trim-seqs/1163>\
**Category:** Commands in mothur\
**Created:** [December 30, 2012, 4:46am UTC](https://forum.mothur.org/t/summary-seqs-went-wrong-after-trim-seqs/1163 "2012-12-30T04:46:01Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Arthur](https://avatars.discourse-cdn.com/v4/letter/a/958977/32.png) [@Arthur](https://forum.mothur.org/u/Arthur)\
**Post date:** [December 30, 2012, 4:46am UTC](https://forum.mothur.org/t/summary-seqs-went-wrong-after-trim-seqs/1163/1 "2012-12-30T04:46:01Z")

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hi  
When I am trying summary.seqs(fasta=ba2.shhh.trim.fasta, name=ba1.shhh.trim.names) after trim.seqs(fasta=ba2.shhh.fasta, name=ba1.shhh.names, oligos=ba2.oligos, pdiffs=2, bdiffs=1, maxhomop=8, minlength=200, flip=T, processors=4), mothur output [ERROR] followed by a large part of blanks, and then “\>HNWL0GD01BNIBJ is not in your name or count file, please correct.” I guess HNWL0GD01BNIBJ was in ba2.shhh.scrap.names, but I can not find it there. Even though mothur can still go with summary.seqs() in this step, things will get worse in the future steps like align.seqs.

mothur \> summary.seqs()  
Using ba2.shhh.trim.unique.align as input file for the fasta parameter.

Using 4 processors.  
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is ba2.shhh.names which seems to match ba2.shhh.trim.unique.align.

Start End NBases Ambigs Polymer NumSeqs  
Minimum: 0 0 0 0 1 1  
2.5%-tile: 1044 1051 2 0 1 1783  
25%-tile: 1044 1103 10 0 2 17823  
Median: 1044 1106 22 0 2 35645  
75%-tile: 42779 43116 25 0 2 53467  
97.5%-tile: 43115 43116 61 0 4 69506  
Maximum: 43116 43117 280 0 7 71288  
Mean: 12878.2 12981.8 23.5171 0 2.20825

# of Seqs: 71288

So NBase seems too small. Is there anything wrong?

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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:** [January 4, 2013, 1:35pm UTC](https://forum.mothur.org/t/summary-seqs-went-wrong-after-trim-seqs/1163/2 "2013-01-04T13:35:12Z")

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The ‘\>’ character before the sequence name makes me suspect a input file format issue. Could you send your input files and logfile to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com)?