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?
QIIME 2 cannot currently assign taxonomy to proteins. It is a work in progress to add this functionality (contributions are very welcome!
), see here for more details and relevant discussion:
I was excited to see the 2021.2 version including q2-types that can read proteins/amino acid sequences. But I am getting errors importing an unaligned .fasta file, which contains typical fasta headers and amino acid sequence lines. I reference this announcement about protein types (
QIIME 2 2021.2 is now available).
Can I confirm the formats/q2-types listed in the announcement are immediately available? For instance, when running a qiime tools import command, it yields an error: No …
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