Error running qiime feature-classifier classify-consensus-vsearch

[Nicholas_Bokulich]

Welcome to the forum @phila!

This is a cryptic error; when it occurs it indicates some sort of formatting error, usually in custom reference databases. See this topic, I have a hunch this is the cause:

Feature classifiier consensus vsearch - key error

Thanks for sharing! This one stumped me for a while because your files look fine to the naked eye, have the same number of entries, etc, and I don't have your query sequences to replicate the exact error you have. But I believe I discovered the problem: Your fasta file (but not your taxonomy file) contains invisible special characters (^M) at the end of the accession #s (this is a windows newline character). vsearch seems to be interpreting this newline character as part of the accession # a…

Good luck!