possible bug from the shhh.flows command?

mothur bugs
1

Hi Mothur users and developers,

I am using the 454 SOP from the Mothur wiki in order to clean and analyze soil microbiota data. When I ask for a summary right after the shhh.flows command, I get the following message:
">GO2E1OJ01
C29JQ is not in your name or count file, please correct.
[ERROR]: process 0 only processed 1 of 76197 sequences assigned to it, quitting.

[ERROR]: process 1 only processed 1 of 76197 sequences assigned to it, quitting.

[ERROR]: process 2 only processed 1 of 76197 sequences assigned to it, quitting.
"
When I open the names file (in my case, it is named “1.shhh.trim.names”) the first name I have is GO2E1OJ01C29JQ - I am not sure why Mothur can’t find it.

Here is a view of the first names that are in the names file:
GO2E1OJ01C29JQ GO2E1OJ01C29JQ
GO2E1OJ01CXH24 GO2E1OJ01CXH24
GO2E1OJ01BWKB9 GO2E1OJ01BWKB9
GO2E1OJ01BH0FK GO2E1OJ01BH0FK
GO2E1OJ01BAEKD GO2E1OJ01BAEKD
GO2E1OJ01CI04J GO2E1OJ01CI04J
GO2E1OJ01BPNW8 GO2E1OJ01BPNW8
GO2E1OJ01DS55E GO2E1OJ01DS55E
GO2E1OJ01ANM7U GO2E1OJ01ANM7U
GO2E1OJ01BWO5D GO2E1OJ01BWO5D
GO2E1OJ01CLOSL GO2E1OJ01CLOSL
GO2E1OJ01CXD1J GO2E1OJ01CXD1J


I was wondering if this is a problem that you have had before. If you came across a similar problem, please share your solution.

Thank you!

2

There is a ‘>’ character before your sequence name. I suspect mothur is not reading the fasta file properly. Did you alter the file somehow? Save it with hidden formatting? Something like (UTF - 16, no BOM) or (UTF - 8, with BOM)? Hidden characters can cause the read to get off track. If this isn’t the case and you want me to track down the issue for you, you can send your files to mothur.bugs@gmail.com.

3

Hi,

Thank you for the quick response. I did not modify any file, but I would be more than happy to have your assistance. Please let me know what files would be necessary to send to you. I see that somebody else has had a very similar problem: http://www.www.mothur.org/forum/viewtopic.php?f=3&t=1873&sid=4200d72550efde69a1fa6e328e255567
I was wondering what was the solution found for that other user.

Thank you!