The *more comprehensive results* bit here is confusing to me, and note that ``subsampled_failures.fasta`` is created (see ``step1_otus/``). Also, *additional filtering* sounds to me like things are being discarded from the analysis but that's not what's happening. I think this section should be modified as follows:

``
Then the failures.fasta file is randomly subsampled to ``PERCENT_SUBSAMPLE`` of the sequences creating a ``subsampled_failures.fna``. These sequences are clustered de novo, and each cluster centroid is then chosen as a "new reference sequence" for use in a subsequent closed-reference OTU picking step. Modifying ``PERCENT_SUBSAMPLE`` can have a big effect on run time for this workflow, but will not affect the final OTUs.