Running mothur 1.27.0 on Ubuntu 11.04.
Iâ€™ve run into a problem with unifrac.unweighted not recognizing the groups I want it to compare. My â€œfinal.xxxxâ€ files are all equivalent to the â€œfinal.xxxxâ€ files produced by the Schloss SOP wiki page. At the point this script starts, I have 4 sets of 50 groups, so the group names are 9410.1, 9410.2, 9410.3, 9410.4, 9412.1, 9412.2, etc, where the â€œ.xâ€ at the end of the group name indicates which set the group belongs to. I want to use the unifrac commands to compare all four 9410.x groups to each other.
My script looks like this:
Dist.seqs(fasta=final.fasta, cutoff=0.15, processors=2)
Make.shared(list=final.an.list, group=final.groups, label=0.03)
Unifrac.unweighted(tree=final.an.0.03.subsample.thetayc.0.03.tre, groups=9410.1-9410.2-9410.3, random=t)
Everything appears fine until the unifrac command when I get an error saying â€œ9410.1 is not a valid group, and will be disregarded.â€ The error is repeated for all groups and the command defaults to doing a global comparison.
9410.4 is too small and removed by sub.sample, so I removed it from the unifrac command thinking it might be causing a problem. Didnâ€™t help. I used get.group() and all 3 of the groups that the unifrac command calls invalid show up. All groups also show up in the .tre file as well. Any thoughts?