I ran into a bug with the get.otus command, but I have to admit that I still use v.1.36.1.
Please let me know if you have fixed the bug in the current version (v1.38.0), thus if it is worth asking our IT department to get a new version installed before I go further with my analyses.
According, to the mothur wiki, it is possible to use a shared file in the get.otus command, but when I run the following, I get an error message:
mothur > get.otus(groups=CtrS1-CtrS2-NTC, shared=LDS15.16S.an.rare_rem.shared, label=0.03)
shared is not a valid parameter.
The valid parameters are: group, list, accnos, groups, label, seed, inputdir, and outputdir.
You have no current group file and the group parameter is required.
You have no current list file and the list parameter is required.
[ERROR]: did not complete get.otus.
Kind regards, Anke.