Difficulty with closed reference OTU clustering

Hi Justine,
I encountered another error in clustering feature table. I downloaded pretrained gg-13-8-99-515-806-nb-classifier.qza from qiime2.org

qiime vsearch cluster-features-closed-reference
–i-table table.qza
–i-sequences rep-seqs.qza
–i-reference-sequences gg-13-8-99-515-806-nb-classifier.qza
–p-perc-identity 0.99
–o-clustered-table table-cr-99.qza
–o-clustered-sequences rep-seqs-cr-99.qza
–o-unmatched-sequences unmatched-cr-99.qza

The error is as follows:
There was a problem with the command:
(1/1) invalid value for ‘–i-reference-sequence’ : Expected an artifact of at least type FeatureData[Sequence]. An artifact of type TaxonomicClassifier was provided.

Any help please?

Hi @baronhabtom - the cluster-features-closed-reference command does not use a pretrained feature classifier - these are two different techniques.

You can download the GG reference sequences and import them, or download a SILVA db release, already imported into QIIME 2.

Hope that helps! :qiime2:

2 Likes

Hi Matthew,
Thank you
It worked.