Error running qiime feature-classifier classify-consensus-vsearch

QIIME2 Version:
VirtualBox, qiime2-2020.2

qiime feature-classifier classify-consensus-vsearch --p-top-hits-only --i-reference-reads mCOI-id99-sequences.qza --i-reference-taxonomy mCOI-id99-taxa-Majority.qza --i-query …/…/…/sequences.qza --o-classification vsearch_id99_consensus_taxonomy.qza --verbose

Error Message:
Plugin error from feature-classifier:

‘Identifier 315 was reported in taxonomic search results, but was not present in the reference taxonomy.’

I have already checked to see if all IDs for reference sequences and taxonomy match via Excel. I have also run classify-consensus-blast: “qiime feature-classifier classify-consensus-blast --i-reference-reads mCOI-id99-sequences.qza --i-reference-taxonomy mCOI-id99-taxa-Majority.qza --p-maxaccepts 1 --p-perc-identity 0.99 --p-query-cov 0.9 --p-strand both --i-query …/…/…/sequences.qza --o-classification id99-majority-blast-taxonomy.qza” which has no error using the same reference sequences and taxonomy.

I am curious what this KeyError may be arising from.


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:

Good luck!

Hello @Nicholas_Bokulich!

I used Notepad++ to change the line endings of my files from Windows (CR LF) to Unix (LF) before importing into Qiime2 and it fixed the issue!

Thank you for the help!

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