Error in flowgrams command

mothur bugs
1

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?
2

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

3

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

4

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

Pat

5

Thanks for your suggestion