# trim.flows command does not accept oligos file

**URL:** https://forum.mothur.org/t/trim-flows-command-does-not-accept-oligos-file/2356
**Category:** Commands in mothur
**Created:** [May 22, 2015, 8:19am UTC](https://forum.mothur.org/t/trim-flows-command-does-not-accept-oligos-file/2356 "2015-05-22T08:19:18Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![Jan88](https://avatars.discourse-cdn.com/v4/letter/j/f05b48/32.png) [@Jan88](https://forum.mothur.org/u/Jan88)
#### Post date: [May 22, 2015, 8:19am UTC](https://forum.mothur.org/t/trim-flows-command-does-not-accept-oligos-file/2356/1 "2015-05-22T08:19:18Z")

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Hi,

I am stuck in the 454 SOP to analyse my 454 data. My previous post disappeared somehow from this forum but I really hope someone could see what I am doing wrong.

```nohighlight

```

mothur \> sffinfo(sff=HD13.sff, flow=T)

Extracting info from HD13.sff …  
10000  
18736  
It took 17 secs to extract 18736.  
Output File Names:  
HD13.fasta  
HD13.qual  
HD13.flow

  
mothur \> trim.flows(flow=HD13.flow, oligos= primerseq.oligos, order=B)

bash: syntax error near unexpected token `flow=HD13.flow,’

```nohighlight

```

My oligos file looks like this:

- forward ATTAGATACCCNGGTAG vF  
reverse ACGGGCGGTGWGTRC vR

No barcodes are needed since I have already demultiplexed data. The pool.trim.flow file has as its first line “450”. Let me know If you need more information.

Any help is welcome 🙂  
Jan

---

<div class="post-metadata">

### 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: [May 25, 2015, 2:44pm UTC](https://forum.mothur.org/t/trim-flows-command-does-not-accept-oligos-file/2356/2 "2015-05-25T14:44:02Z")

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You have a space between the equals sign and the oligos file name. Remove that extra space and you should be good to go.

Pat