# trim.flows unable to open my flow file and oligo file

**URL:** https://forum.mothur.org/t/trim-flows-unable-to-open-my-flow-file-and-oligo-file/1979
**Category:** Commands in mothur
**Created:** [August 13, 2014, 2:11pm UTC](https://forum.mothur.org/t/trim-flows-unable-to-open-my-flow-file-and-oligo-file/1979 "2014-08-13T14:11:02Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![sricd4](https://avatars.discourse-cdn.com/v4/letter/s/46a35a/32.png) [@sricd4](https://forum.mothur.org/u/sricd4)
#### Post date: [August 13, 2014, 2:11pm UTC](https://forum.mothur.org/t/trim-flows-unable-to-open-my-flow-file-and-oligo-file/1979/1 "2014-08-13T14:11:02Z")

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Hi,  
I am trying to open the Lam\_bacteria\_SFF.flow file generated using sffinfo command,but it is not accepting the file,could you please help me to execute my files.  
Thanks,  
srisailam.  
mothur \> trim.flows(flow=Lam\_bacteria\_SFF.flow, oligos= Lam\_bacteria1.oligos,minflows=200, maxflows=500, pdiffs=2, bdiffs=1, processors=2)

Unable to open Lam\_bacteria\_SFF.flow  
Unable to open Lam\_bacteria1.oligos

Using 2 processors.  
[ERROR]: did not complete trim.flows.

mothur \> trim.flows(flow=Lam\_bacteria\_SFF.flow, oligos= Lam\_bacteria1.oligos,minflows=200, maxflows=500, pdiffs=2, bdiffs=1, processors=4)

Unable to open Lam\_bacteria\_SFF.flow  
Unable to open Lam\_bacteria1.oligos

Using 4 processors.  
[ERROR]: did not complete trim.flows.

mothur \> trim.flows(flow=Lam\_bacteria\_SFF.flow, oligos= Lam\_bacteria1.oligos,minflows=200, maxflows=500, pdiffs=2, bdiffs=1, processors=4)

Unable to open Lam\_bacteria\_SFF.flow  
Unable to open Lam\_bacteria1.oligos

Using 4 processors.  
[ERROR]: did not complete trim.flows.

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<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: [August 13, 2014, 2:35pm UTC](https://forum.mothur.org/t/trim-flows-unable-to-open-my-flow-file-and-oligo-file/1979/2 "2014-08-13T14:35:00Z")

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You’re likely in the wrong folder. From within mothur can you type:

system(ls) [for mac/linux]

or

system(dir) [for windows]

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<div class="post-metadata">

### Author: ![sricd4](https://avatars.discourse-cdn.com/v4/letter/s/46a35a/32.png) [@sricd4](https://forum.mothur.org/u/sricd4)
#### Post date: [August 13, 2014, 3:54pm UTC](https://forum.mothur.org/t/trim-flows-unable-to-open-my-flow-file-and-oligo-file/1979/3 "2014-08-13T15:54:25Z")

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Hi,  
Thank you of your help.when I typed the command it shows like this.  
regards,  
srisailam.  
mothur \> system(ls)

Lam\_bact\_codes.oligos  
Lam\_bacteria.oligos.txt  
Lam\_bacteria1.oligos.txt  
Lam\_bacteria\_SFF.fasta  
Lam\_bacteria\_SFF.flow  
Lam\_bacteria\_SFF.qual  
Lam\_bacteria\_SFF.sff  
Lam\_bacteria\_SFF.summary  
Lam\_oligos.txt  
commandScreen.output  
mothur.1407945143.logfile

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<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: [August 15, 2014, 12:43am UTC](https://forum.mothur.org/t/trim-flows-unable-to-open-my-flow-file-and-oligo-file/1979/4 "2014-08-15T00:43:54Z")

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Looks like you might have skipped the sffinfo step