Error in flowgrams command

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?

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

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

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

Pat

Thanks for your suggestion