I found an interesting glitch with the get.lineage command. I’m using the current version of Mothur (v15). When I run the get.lineage command on only a fasta file, I get the correct results. However, when I combine the command with the “name” function, for example: get.lineage(taxonomy=, taxon=, name=, fasta=), my “.pick.fasta” file contains samples that aren’t of the requested taxon. The “.pick.names” file seems fine. I noticed the problem when I tried re-running classify.seqs on my “.pick.fasta” file and received and error about the “.pick.names” file not containing a certain sequence. When I looked closer, I realized my fasta file contained multiple sequences from the wrong taxon. It seems like mothur did filter out a lot of the sequences since my input and output files are different sizes, but it added a few wrong sequences into the fasta file and not the names file so I don’t know exactly where the glitch is.
This isn’t a major problem since running the commands separately give accurate files, but if someone tries to combine the functions into one command line it can cause a hassle. I just wanted to bring it to attention. I can send my input files if you want/need to look at the bug closer. Just let me know. Thanks!