Name file error - possible bug?

When I merge the names files from two samples that I want to compare, I run into this error:

mothur > merge.files(input=P121.shhh.trim.names-T121.shhh.trim.names, output=PT121.shhh.trim.names)

Output File Name:

mothur > summary.seqs(fasta=PT121.shhh.trim.fasta, name=PT121.shhh.trim.names)
[ERROR]: HDXKKXU02ECBKF is not in your namefile, please correct.

I checked - the listed sequence is present in both the original and merged names files, as well as in the merged fasta and group files.
I am using the newest version - v.1.24.1. FWIW, I have used the merge.files command with no problems on v.1.23.1.

Any thoughts on how I can get around this? Thanks in advance!

Could you send your logfile and P121.shhh.trim.names, T121.shhh.trim.names, P121.shhh.trim.fasta and T121.shhh.trim.fasta to

This doesn’t appear to be a problem with the merge.files command. When I run summary.seqs(fasta=P121.shhh.trim.fasta, name=P121.shhh.trim.names), the same error occurs. How did you generate the fasta and names files?

Hi Sarah,

I have successfully used the summary.seqs command with those two files (using v.24.0). I just sent you the logfile. The fasta and names files were generated from sff files via the Schloss SOP (sffinfo, trim.flows, shhh.flows, trim.seqs).


Hi Archana,
Thanks for sending your files. I think I found the problem. When you ran

mothur > unique.seqs(fasta=P121.shhh.trim.fasta, name=P121.shhh.trim.names)
810 716

Output File Names:

The problem is occurring because when you run the unique.seqs command the new name file created has the same name as the old name file. This is confusing, so we will be adding a check of the namesfile name to the unique.seqs command. In the next release when a namefile is provided the new namefile is not created with the same name. For now you want to run merge.files(fasta= P121.shhh.trim.unique.fasta-T121.shhh.trim.unique.fasta) and merge.files(name=P121.shhh.trim.names-T121.shhh.trim.names)

Hi Sarah,

Ok, so I would just merge the files after the unique.seqs command. That makes sense.

Thanks so much for your help!