remove.seqs with names file

mothur bugs
1

It seems like remove.seqs should remove the entire row (ie. all identical sequences) from the .names file, but it only seems to remove the specified accession number, leaving the remaining identical accession numbers in the .names file. For example,

pico Ag105_StdOut.filter.filter.filter.names
…
F567RGU01A38JT F567RGU01A38JT,F567RGU01A3FZG
…

mothur> remove.seqs(accnos=Ag105_Pyro.chimeras, name=Ag105_Pyro.filter.filter.filter.names)
pico Ag105_StdOut.filter.filter.filter.pick.names
…
F567RGU01A3FZG F567RGU01A3FZG
…

This causes problems later, such as:

get.oturep(column=Ag105_final_stdout.dist, name=Ag105_final_stdout.names, list=Ag105_final_stdout.fn.list, fasta=Ag105_final_stdout.fasta, label=0.10)
********************###########
Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||||

0.10 53
F567RGU01A3FZG is missing from your fasta or name file. Please correct.

2

Maybe the problem here is actually with the get.oturep function, which should have the flexibility to work with a mismatch between the number of records in a *.unique.fasta file and the number of rows in the corresponding *.names file.