Assign taxonomy is not working

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safiq713 • 0

@d764bdb7

Last seen 2.0 years ago

Germany

I want to assign taxonomy to my data. Ref data I have downloaded from SILVA data and it is fasta format. I dont get why this is not working any suggestion will be big help

Code

Assign taxonomy

taxa <- addSpecies(seqtab.nochim, refFasta = "arb-silva.de_2022-04-08_id1144657_tax_silva.fasta")

Refe data looks like this: ">ADJL01000005.3856.5362 Bacteria;Actinobacteriota;Actinobacteria;Propionibacteriales;Propionibacteriaceae;Cutibacterium;Propionibacterium acnes J165 UUUUCAUUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGGAAAGGCCC UGCUUUUGUGGGGUGCUCGAGUGGCGAACGGGUGAGUAACACGUGAGUAACCUGCCCUUGACUUUGGGAUAACUUCAGGA"

Error: "

" Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 50 (char '2') not in lookup table"

Assigntaxonomy dada2 • 1.1k views

ADD COMMENT • link updated 2.0 years ago by shepherl 3.8k • written 2.0 years ago by safiq713 • 0

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What package is that function from?

ADD REPLY • link 2.0 years ago shepherl 3.8k

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dada2 pipeline

ADD REPLY • link 2.0 years ago safiq713 • 0

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Next time, please tag with the package name. There is a mechanism in the support site to notify package maintainers but only if it is tagged with the package name. Cheers

ADD REPLY • link 2.0 years ago shepherl 3.8k

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