qiime feature-classifier classify-consensus-vsearch error

[Nicholas_Bokulich]

Hello again @Asha1 and welcome to the forum @mica.tosi !

I apologize both for the delay, I was out of the office.

@mica.tosi

I’m new to the forum, so I hope to be following the rules. I was about to post a new topic about a similar error, but since this was recently posted, I figured it’s easy to ask here.

Yes thanks indeed for asking in this topic! It seems you have identical issues so asking here will save us all time. And thanks for troubleshooting this a little bit and providing details on your process.

This issue is almost always caused by formatting issues, occasionally very cryptic issues. So we usually only see this crop up when someone is generating their own reference database since the kinks have mostly been worked out for commonly used databases — or when the reference sequences and taxonomy really do not match (honest mistakes happen!)

So with that in mind please see this:

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…

My hunch is that you both could have this same issue with invisible line breaks causing formatting issues. Want to take a look and report back?