taxonomy files problems - urgent

Hi all,
it’s some days I’m having problems with the controls of “classify.seqs” and “classify.otus”. My inputs were:
[b]classify.seqs(fasta=/…/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick97.fasta, count=/…/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.count_table, reference=/…fasta, taxonomy=/…taxonomy, cutoff=97)

classify.otu(list=/…, count=/…/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.count_table, taxonomy=/…wang.taxonomy, label=unique)[/b]

Some weeks ago, they both worked very well and I obtained the respective out-files. During these days, I managed them to remove rare OTUs from my data-sets and the results is:
XXXXX is in your taxonomy file and is not in your template file. Please correct.
It took 0 seconds get probabilities.

For each single sequences and, of course, I didn’t obtain any outs. The references in the taxonomy are present and correct. Some weeks ago, everything was ok, now nope. Is something changed with the new upload of mothur?

Thank you for the suggestions.

I uploaded version 1.39.3 which corrects a bug in classify.seqs. You can download it here: