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Save BenKaehler/d9291d59bce5cd3d2a90c73b822b3a21 to your computer and use it in GitHub Desktop.
Hi @chiehchangchen, that step works for me, sorry. I checked with QIIME 2 2023.7.0.
This script does not create or load a taxonomic classifier, so I would guess that you have accidentally downloaded the wrong file or have a classifier lying around from something else you're working on.
@BenKaehler , thanks for your great instructions. I've followed your instruction and build he SILVA138.1 tree and the masked aligned fata file successfully. However, I failed to build SEPP reference.
I've tried both SILVA138.1 tree and your SILVA138 tree with corresponding masked-aln fasta files as https://github.com/smirarab/sepp-refs/blob/master/silva/README.md described. I got error "ERROR: Bad base (.) at site 2347 of sequence 1" when I want to resolve polytomies. Since I am a newbie, do you have any idea to solve the problem?
It would be helpful to build SILVA SEPP reference !
However, I got error at step "Convert the SILVA sequences from RNA to DNA and import them into a QIIME Artifact, "
I think the qiime2 pretrained classifier changed and it cause the error. Would you update the note to solve the error for new qiime2 classifier ?
File "/home/ccadmin/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/core/transform.py", line 58, in make_transformation
raise Exception("No transformation from %r to %r" %
Exception: No transformation from <class 'q2_feature_classifier._taxonomic_classifier.TaxonomicClassiferTemporaryPickleDirFmt'> to <class 'q2_types.feature_data._transformer.DNAIterator'>