Issues when running split.groups

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 (

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



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

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


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.

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

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?

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