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Bioconductor / Biostrings

Efficient manipulation of biological strings
https://bioconductor.org/packages/Biostrings
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Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 50 (char '2') not in lookup table #68

Closed safiqu closed 2 years ago

safiqu commented 2 years ago

I am trying to use customised data base.

Code 👍 "tax <- addSpecies(seqtab.nochim, refFasta = "/srv/SP_Pro_acnes.fa")"

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

My species fasta file looks like this:

ID001 Cutibacterium acnesA1 GTTGCACACCAGGGGGTCAACTTGGCGTCCTCAGTTCAAAATTGATTCAAACTAACAGTTCCATGTCGGGAAACAGCACCAGGAAGCTCGTGACAT ID002 Cutibacterium acnesA10 GTTGCACACCAGGGGGTCAACTTGGCGTCCTCAGTTCAAAATTGATTCAAACTAACAGTTCCATGCCGGGAAACAGCACCAGGAAGCTCGTGACA

I did not get it what I need to improve in dada2 pipeline or fasta files

hpages commented 2 years ago

This is a question for the dada2 authors/maintainers and you should ask it on the Bioconductor support site. Make sure to: (1) tag your question properly, (2) provide a reproducible example (the above code is not), and (3) format your code properly (by putting it between ``` lines).

Thanks, H.