Hi @Mike26, can you try filtering (filter_otus_from_otu_table.py) using your uncollapsed table - that is, the table before running qiime taxa collapse? You can follow the suggestions here to produce a QIIME 1-ready BIOM table that should work for filter_otus_from_otu_table.py. @jairideout might still have some additional comments, but please give this a shot in the meantime. Thanks!
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