Issues when running split.groups

Commands in mothur
1

Hi there,

I recently encountered a problem while running split.groups. Here is the command I used:


mothur > split.groups(fasta=A11178.extendedFrags.trim.fasta, group=A11178.extendedFrags.groups)
and here is the error message I got after 5 hours of analysis:

[ERROR]: You are missing (
Invalid.

I don’t get what I’m missing here. Can you please help?

Thanks!

Claire

2

Did you get any output? If you hit the enter key at the prompt you will typically get that error.

3

just one file out of the ~200 I was expecting:

A11178.extendedFrags.trim.Km4?.fasta

not sure why a question mark was added at the end of the sample name.

the analysis was running overnight, so I doubt that enter was pressed, except for right after the command was entered.

4

Is “Km4?” one of your group names? Do your files have any special formatting? We have seen reports of problems reading files when you have a Unicode(UTF-8, with BOM) or Unicode(UTF-8, no BOM). Opening the file in Textwrangler and saving as Unicode(UTF-8) resolved those issues. If you don’t think this is the source of the issue, can you send your logfile and input files to mothur.bugs@gmail.com?

5

Hello
I am new to mothur but after seeing lot of mothur sample data and batch I learned the analysis.
Before deunique.seqs everything was working fine
but when I used split.groups some errors were flashing. Here i was used the output of deunique.seqs and I created group file from fasta output of deunique.seqs command.Can you tell me which input file to be used here and why group file and the fasta file aren’t matching?

6

Could you post the exact commands you ran, as well as the version of mothur you are using?