I get this message while using the new training set (PDS) :
Reading in the trainset14_032015.pds.tax taxonomy… DONE.
‘GL982576_U010303693’ is in your template file and is not in your taxonomy file. Please correct.
Did you get this message too ?
Ok, GL982576_U010303693 appears two times in the files .tax and .fasta of the training set (version 14 of the 16S rDNA reference (PDS)). I’ve deleted one of them in both files and now it works. Might be useful to correct the file on the Mothur website.
Sorry about that, it seems that the original files from the RDP had the duplication. If you try again, everything should work now. Thanks for the heads up!