Hey there @jhines1! It was a problem with file line-endings --- your fasta file had a mix of LF and CRLF, which vsearch wasn't cleaning out, so when q2-vsearch was parsing the intermediate files created by vsearch there were all kinds of crazy going on in the file. I converted the file to use only unix-style line-endings and have returned it to you in a DM. Happy QIIMEing! 
:qiime2:
1 Like