# Issues with trim.seqs qtrim parameter

**URL:** https://forum.mothur.org/t/issues-with-trim-seqs-qtrim-parameter/442
**Category:** Commands in mothur
**Created:** [January 10, 2011, 3:02am UTC](https://forum.mothur.org/t/issues-with-trim-seqs-qtrim-parameter/442 "2011-01-10T03:02:44Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![ewilbanks](https://avatars.discourse-cdn.com/v4/letter/e/c67d28/32.png) [@ewilbanks](https://forum.mothur.org/u/ewilbanks)
#### Post date: [January 10, 2011, 3:02am UTC](https://forum.mothur.org/t/issues-with-trim-seqs-qtrim-parameter/442/1 "2011-01-10T03:02:44Z")

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Hi!

I seem to be having a problem using the qtrim parameter in the trim.seqs command. When I run it without the qtrim parameter – allowing it to scrap all files that don’t meet the qthreshold – I get plenty of reads in my .trim.fasta file. However, if I try to force triming using qtrim=true, my .trim.fasta file is empty! Am I doing something wrong here?

Thanks!  
Lizzy

```nohighlight
mothur > trim.seqs(fasta=raw_pinkB.fasta, qfile=raw_pinkB.qual, qthreshold=5)
mothur > summary.seqs(fasta=raw_pinkB.trim.fasta)

                Start End NBases Ambigs Polymer
Minimum: 0 0 0 0 1
2.5%-tile: 1 58 58 0 3
25%-tile: 1 271 271 0 4
Median: 1 383 383 0 5
75%-tile: 1 458 458 0 6
97.5%-tile: 1 517 517 0 8
Maximum: 1 614 614 0 31
# of Seqs: 257983

Output File Name:
raw_pinkB.trim.fasta.summary

mothur > trim.seqs(fasta=raw_pinkB.fasta, qfile=raw_pinkB.qual, qthreshold=5,qtrim=true)
mothur > summary.seqs(fasta=raw_pinkB.trim.fasta)

[ERROR]: raw_pinkB.trim.fasta is blank. Please correct.
Error in reading your fastafile, at position -1. Blank name.
Segmentation fault

```

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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: [January 10, 2011, 1:56pm UTC](https://forum.mothur.org/t/issues-with-trim-seqs-qtrim-parameter/442/2 "2011-01-10T13:56:16Z")

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Could you send your inputfiles and logfile to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com)?

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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 14, 2011, 1:57pm UTC](https://forum.mothur.org/t/issues-with-trim-seqs-qtrim-parameter/442/3 "2011-01-14T13:57:29Z")

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Thanks for bringing this bug to our attention. In version 1.15.0, we made some changes to the internal workings of the trim.seqs command and unfortunately added and indexing error, :oops: . The fix will be part of 1.16.0.