get.oturep error

Commands in mothur
1 
mothur > get.oturep(fasta=current, group=current, list=current, name=current)
Using msflag.stab.trim.contigs.good.unique.good.filter.precluster.pick.pick.fasta as input file for the fasta parameter.
Using msflag.stab.contigs.good.good.pick.pick.groups as input file for the group parameter.
Using msflag.stab.trim.contigs.good.unique.good.filter.precluster.pick.pick.an.list as input file for the list parameter.
Using msflag.stab.trim.contigs.good.unique.good.filter.precluster.pick.pick.names as input file for the name parameter.
Using msflag.stab.trim.contigs.good.unique.good.filter.precluster.pick.pick.fasta.25.dist as input file for the column parameter.
[ERROR]: Could not open msflag.stab.trim.contigs.good.unique.good.filter.precluster.pick.pick.fasta.25.dist

It seems to be running ok even though it threw this error. Why is it trying to open a distance file? should I just ignore?

2

The get.oturep command requires a distance matrix unless you are using the abundance method. It looks like mothur accidentally saved a temporary distance file from a previous command as the current file for the column parameter. It tried to open current file for you (the temporary file), but the previous command had already deleted it, hence the error message. You can either run:

mothur > get.oturep(fasta=current, group=current, list=current, name=current, method=abundance) - chooses the sequence with the highest abundance to be the representative sequence.

or

mothur > get.oturep(fasta=current, group=current, list=current, name=current, column=yourDistanceMatrix) - chooses the sequence with the smallest maximum distance to the other sequences to be the representative sequence.

3

ah, thanks