I’m trying to use results from Mothur into Picrust.
I run my sample roughly as defined in the MiSeq SOP:
I use the Silva database as in the SOP and go all the way until the phylotype clustering.
Then I wanted to convert the shared file obtained after make.shared into a biom compatible with Picrus (Greengenes).
I tried to perform what is described in this link http://www.mothur.org/wiki/Make.biom
But I get an error:
make.biom(shared=finalreads.tx.shared, label=1, reftaxonomy=gg_13_5_99.gg.tax, constaxonomy=finalreads.tx.1.cons.taxonomy,picrust=99_otu_map.txt)
[ERROR]: Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides; is not in taxonomy tree, please correct.
I must be doing something wrong but I’m not sure what.
Any help is greatly appreciated (even if just a link to any documentation I may be missing).