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September 20, 2021 07:55
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Build a SILVA tree using FastTree
@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?
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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.