# New groupfile needed after unique.seqs?
**URL:** https://forum.mothur.org/t/new-groupfile-needed-after-unique-seqs/1278
**Category:** Commands in mothur
**Created:** [March 27, 2013, 4:13pm UTC](https://forum.mothur.org/t/new-groupfile-needed-after-unique-seqs/1278 "2013-03-27T16:13:32Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@geboro](https://forum.mothur.org/u/geboro)
#### Post date: [March 27, 2013, 4:13pm UTC](https://forum.mothur.org/t/new-groupfile-needed-after-unique-seqs/1278/1 "2013-03-27T16:13:32Z")
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:
make.shared(list=SEQS\_aligned.unique.filter.unique.phylip.fn.list,group=SEQSaligned.group,label=0.030)
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…
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [March 27, 2013, 5:33pm UTC](https://forum.mothur.org/t/new-groupfile-needed-after-unique-seqs/1278/2 "2013-03-27T17:33:37Z")
Did you forget to include the names file when you ran the cluster command?
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### Author:  [@geboro](https://forum.mothur.org/u/geboro)
#### Post date: [March 28, 2013, 8:37am UTC](https://forum.mothur.org/t/new-groupfile-needed-after-unique-seqs/1278/3 "2013-03-28T08:37:18Z")
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.
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [March 28, 2013, 10:30am UTC](https://forum.mothur.org/t/new-groupfile-needed-after-unique-seqs/1278/4 "2013-03-28T10:30:20Z")
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.
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### Author:  [@geboro](https://forum.mothur.org/u/geboro)
#### Post date: [April 8, 2013, 7:22am UTC](https://forum.mothur.org/t/new-groupfile-needed-after-unique-seqs/1278/5 "2013-04-08T07:22:14Z")
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);
unique.seqs(fasta=S3\_aligned.unique.filter.fasta,name=S3\_aligned.names);
dist.seqs(fasta=S3\_aligned.unique.filter.unique.fasta,processors=6,output=lt,cutoff=0.030);
hcluster(phylip=S3\_aligned.unique.filter.unique.phylip.dist,method=furthest,cutoff=0.030,hard=t,name=S3\_aligned.unique.filter.names);
make.shared(list=S3\_aligned.unique.filter.unique.phylip.fn.list,group=S3.group,label=0.030)”
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [April 8, 2013, 11:34am UTC](https://forum.mothur.org/t/new-groupfile-needed-after-unique-seqs/1278/6 "2013-04-08T11:34:32Z")
How did you create the group file? Could you run the following commands so we can see where the discrepancy starts?
split.groups(fasta=S3\_aligned.fasta, group=S3.group)
unique.seqs(fasta=current)
split.groups(fasta=current, name=current, group=current)
filter.seqs(fasta=current,vertical=T,processors=6)
split.groups(fasta=current, name=current, group=current)
unique.seqs(fasta=current, name=current)
split.groups(fasta=current, name=current, group=current)
dist.seqs(fasta=current,processors=6,output=lt,cutoff=0.030)
split.groups(fasta=current, name=current, group=current)
hcluster(phylip=current,method=furthest,cutoff=0.030,hard=t,name=current)
list.seqs(list=current)
Also, you might be interested in Pat’s example analysis’, [http://www.mothur.org/wiki/Schloss\_SOP](http://www.mothur.org/wiki/Schloss_SOP) or [http://www.mothur.org/wiki/MiSeq\_SOP](http://www.mothur.org/wiki/MiSeq_SOP).