Can Qiime assign taxonomy to proteins?

I am trying to run Qiime2 to taxonomically annotate proteins. So far, I have run this command to import a FASTA as a Qiime object:

qiime tools import --type "FeatureData[ProteinSequence]" --input-path protein_fasta_qiime2_test/non_chimeric_prot_corr_q2_import_test.fasta --output-path sequences.qza

and have tried running this command to classify the sequences

qiime feature-classifier classify-hybrid-vsearch-sklearn

but it doesn't accept "FeatureData[ProteinSequence]" as a valid input format. How can I classify protein sequences taxonomically with Qiime2? Also, would it be preferable (faster or more accurate) to common methods with BLAST or DIAMOND?

Welcome @iquasere !

QIIME 2 cannot currently assign taxonomy to proteins. It is a work in progress to add this functionality (contributions are very welcome! :wink: ), see here for more details and relevant discussion:

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