# Error in flowgrams command

**URL:** <https://forum.mothur.org/t/error-in-flowgrams-command/2995>\
**Category:** mothur bugs\
**Created:** [September 26, 2016, 4:32pm UTC](https://forum.mothur.org/t/error-in-flowgrams-command/2995 "2016-09-26T16:32:34Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![mariscuba](https://avatars.discourse-cdn.com/v4/letter/m/48db29/32.png) [@mariscuba](https://forum.mothur.org/u/mariscuba)\
**Post date:** [September 26, 2016, 4:32pm UTC](https://forum.mothur.org/t/error-in-flowgrams-command/2995/1 "2016-09-26T16:32:34Z")

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Hi,  
I’m a new mothur user and I have some problem using the shhh.flows command in R. It appears this:

mothur \> shhh.flows(file=…/…/.flow.files, processors=1)

Using 1 processors.

> > > > > Processing …/…/.trim.flow (file 1 of 1) \<\<\<\<\<  
> > > > > Reading flowgrams…  
> > > > > Identifying unique flowgrams…  
> > > > > Calculating distances between flowgrams…  
> > > > > 0 0 0  
> > > > > 0 0 0

Total time: 0 0

Clustering flowgrams…  
[ERROR]: …/…/.trim.shhh.dist is blank. Please correct.  
\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*# **#** # **#** # **#** # **#** # **#** #  
Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||||

* * *

Warning messages:  
1: running command 'C:\WINDOWS\system32\cmd.exe /c C:/Users/…/…/mothur.exe “#shhh.flows(file=…/…/.flow.files.flow.files, processors=1)” ’ had status 5  
2: In shell(flow.command) :  
'C:\WINDOWS\system32\cmd.exe /c C:/Users/…/…/mothur.exe “#shhh.flows(file=…/…/.flow.files.flow.files, processors=1)” ’ execution failed with error code 5

  
Could you help me to solve it, thanks?

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**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:** [September 30, 2016, 3:53pm UTC](https://forum.mothur.org/t/error-in-flowgrams-command/2995/2 "2016-09-30T15:53:34Z")

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Can you post the actual commands you are running? Also, how are you running trim.flows? Do you have an error for that command?

Pat

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**Author:** ![mariscuba](https://avatars.discourse-cdn.com/v4/letter/m/48db29/32.png) [@mariscuba](https://forum.mothur.org/u/mariscuba)\
**Post date:** [October 15, 2016, 5:37pm UTC](https://forum.mothur.org/t/error-in-flowgrams-command/2995/3 "2016-10-15T17:37:00Z")

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Sorry for the late, I didn’t see the answer. :?

I solved with that problems, however I have a inquisitiveness. I am working with the COI barcodes and I need to fix your pipeline for my purposes.  
Do you think that the “align.seqs” command is peculiar for COI or can I avoid it? I mean, once have the first “.trim.fasta”, could I go directly to the clustering steps?

Many thanks

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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:** [October 17, 2016, 12:55pm UTC](https://forum.mothur.org/t/error-in-flowgrams-command/2995/4 "2016-10-17T12:55:51Z")

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I strongly encourage people to align their sequences since it will detect non-specific amplification

Pat

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**Author:** ![mariscuba](https://avatars.discourse-cdn.com/v4/letter/m/48db29/32.png) [@mariscuba](https://forum.mothur.org/u/mariscuba)\
**Post date:** [October 20, 2016, 3:54pm UTC](https://forum.mothur.org/t/error-in-flowgrams-command/2995/5 "2016-10-20T15:54:32Z")

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Thanks for your suggestion