Hi QIIME 2 community,
I am running into an issue while attempting to assign taxonomy to 16S data using VSEARCH with the Silva 2024 classifier. Here’s the error message I receive:
(1/1) Invalid value for '--i-reference-taxonomy': Expected an artifact of at least type FeatureData[Taxonomy]. An artifact of type TaxonomicClassifier was provided.
Below is the command I used for VSEARCH taxonomic classification:
VSEARCH Taxonomic Classification with Silva 2024 Classifier
rule vsearch_silva_2024:
input:
classifier2="nanopore/silva_classifier_2024.qza",
rep_seqs="nanopore/7_denovo_rep_seqs.qza",
reference="nanopore/99_otus.qza",
output:
qza_vsearch_silva_2024="nanopore/2024_silva_taxonomy_vsearch.qza",
search_res="nanopore/2024_silva_taxonomy_vsearch_search_results.qza",
threads: 36,
shell:
"""
qiime feature-classifier classify-consensus-vsearch
--i-query {input.rep_seqs}
--i-reference-reads {input.reference}
--i-reference-taxonomy {input.classifier2}
--p-perc-identity 0.9
--p-query-cov 0.8
--p-maxaccepts 100
--p-maxrejects 100
--p-maxhits 3
--p-min-consensus 0.7
--p-strand 'both'
--p-unassignable-label 'Unassigned'
--p-threads {threads}
--o-classification {output.qza_vsearch_silva_2024}
--o-search-results {output.search_res}
--verbose
"""
Problem Summary
It seems that I may have used a TaxonomicClassifier artifact instead of the expected FeatureData[Taxonomy] file for --i-reference-taxonomy. I understand that VSEARCH requires a FeatureData[Taxonomy] file, not a trained classifier.
Could anyone guide me on how to obtain or create a FeatureData[Taxonomy] file that’s compatible with this setup? Any advice on locating the correct file in the Silva and greenegen database or converting my current classifier would be greatly appreciated.
I am testing SILVA and greenegen to see which database gives more reliable results.
Thank you!