Exclude-seqs error with imported FASTA file

[Nicholas_Bokulich]

Hey @Mehrbod_Estaki,
Nice cryptic issue. The problem is that your fasta file has CRLF (windows-style) line endings, most importantly at the ends of the fasta header lines. VSEARCH is interpreting these to be part of the sample ids, and so the vsearch alignment report gets FUBAR... sample ids and alignment stats get broken onto separate lines. This appears to be a wider problem with vsearch:

Best approach for analyzing Sanger sequences from ITS2 region

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:

You can fix by using mac2unix or tr -d "\r" < file or some other method to convert CRLF to CR line endings.

In a future release of QIIME 2 these invisible line endings will be detected on import, since they are likely to wreak havoc with other methods, not just anything based on vsearch.

Thanks for reporting!