When using the linked Pr2 V5 database with DECIPHER IDtaxa, I have found that there are no ranks associated with the taxonomic assignments given by the classifier. This has resulted in my inability to form a taxonomy table based on the assignments given by the classifier. When I run the code below, I get a taxonomy table that is entirely NA values. I'm not sure how to solve this, and if there is a fix that someone knows to include ranks in the classifier, I would be highly appreciative.

#assign taxonomy using IDtaxa and Pr2 DB
dna.20 <- DNAStringSet(getSequences(seqtab.2020)) 
file_trained = "/Users/rettigm/Downloads/pr2_version_5.0.0_SSU.decipher.trained.rds"
trainingSet <- readRDS(file_trained)
ids.20 <- IdTaxa(dna.20, trainingSet, strand = "top", processors = NULL, verbose = TRUE)
ranks.pr2 <- c("kingdom", "division", "phylum", "class", "order", "family", "genus", "species")

taxid.20 <- t(sapply(ids.20, function(x) {
        m <- match(ranks.pr2, x$rank)
        taxa.20 <- x$taxon[m]
        taxa.20[startsWith(taxa.20, "unclassified_")] <- NA
        taxa.20
}))
colnames(taxid.20) <- ranks.pr2; rownames(taxid.20) <- getSequences(seqtab.2020)

sessionInfo( ): R version 4.4.0 (2024-04-24) Platform: x86_64-apple-darwin20 Running under: macOS Ventura 13.2.1

This is the output of each row of the classifier, which has no rank associated with it, an issue I do not experience with the SILVA database. I am suspecting that this is the source of issue I'm having attempting to build the taxonomy table.

This is the issue I'm having with the taxonomy table, I suspect the lack of rank in the assignment prevents the taxonomy from mapping properly into the taxonomy table.