New groupfile needed after unique.seqs?

Hi all,

I’m pretty far down the pipeline analysis and all I need is to make a shared file showing shared sequences between samples. I started with a FASTA file of clean sequences since quality control was done somewhere else, and I had a group file for that. now I’m running:


and get a zillion lines with error

“[ERROR]: TULA_9402 is in your groupfile and not your listfile. Please correct.”

does this mean I need to make a new groupfile for the representative set of sequences at label 0.030? I wonder how is the “unique” abundance information reincorporated into that then…

Did you forget to include the names file when you ran the cluster command?

I didn’t.

I used the unique.filter.names file produced by the second run of unique.seq after filtering. I supposed this contained the abundance information after unique.seq, so I didn’t used the first .names file produced by the first run of unique.seq.

Usually the error you are getting is caused by forgetting to include the name file on a command. If you post the commands you ran, I may be able to spot it.

Keep getting the same error. This is the command line I’m running (with newlines after the “;” for easier reading)

mothur “#unique.seqs(fasta=S3_aligned.fasta); filter.seqs(fasta=S3_aligned.unique.fasta,vertical=T,processors=6);

How did you create the group file? Could you run the following commands so we can see where the discrepancy starts?

split.groups(fasta=current, name=current, group=current)
split.groups(fasta=current, name=current, group=current)
unique.seqs(fasta=current, name=current)
split.groups(fasta=current, name=current, group=current)
split.groups(fasta=current, name=current, group=current)

Also, you might be interested in Pat’s example analysis’, or