create database

Commands in mothur
1

Dear All, I am trying to “create database”.
In the command:
mothur > get.oturep(list=final.an.list, label=0.03, fasta=final.fasta, column=final.dist, name=final.names)
mothur > classify.otu(list=final.an.list, name=final.names, taxonomy=final.taxonomy, label=0.03)
mothur > create.database(list=final.an.list, label=0.03, repfasta=final.an.0.03.rep.fasta, repname=final.an.0.03.rep.names, constaxonomy=final.an.0.03.cons.taxonomy)

here these “final” give me some troubles. what is the final.names file? Is it = stability.trim.contigs.good.names? or something else?
I can understand final.an.list = stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.list
and
final.fasta = stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta
and
final.dist = stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.dist
What about the final taxonomy file? Is stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy? or stability.an.cons.taxonomy?
Thank you!

2

There is not an exact way to know what the “final” files relate to without seeing your log file. In Pat’s pipeline he renames the fasta, list, column and other files to avoid confusion with mothur’s long filenames. You can rename your files at any time or not at all.

What about the final taxonomy file? Is stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy? or stability.an.cons.taxonomy?

If you are looking at the classify.otu command, mothur is looking for the *.wang.pick.taxonomy file to be the final.taxonomy. The classify.otu command uses the taxonomy file created by classify.seqs to look up the classifications for each sequence in a given OTU and then find a consensus taxonomy for the OTU.