Given a taxonomic file that contains spaces, e.g.
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus]; s__
APP properly generates a raw OTU table

However, after rarefaction, the spaces in the taxonomic strings are removed
k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__[Ruminococcus];s__

This removal of spaces is apparently due to the QIIME script that takes care of the rarefaction and is very problematic for programs that rely on these taxonomic strings to remain unchanged.