Hi @sejsong,
Unfortunately the QIIME 2 plugin for deblur only works with fastqs at the moment, although this is our fault, there’s no reason it couldn’t work with fasta. We’ve got an open issue to correct that. You could always try using deblur directly.
At the moment, the best you’ll be able to do with QIIME 2 (without the fastq files) is to perform an QIIME 1-like OTU picking.
Sorry I don’t have a better solution 