Hi @mradz,
One solution to the problem is outlined here. A slightly different solution is outlined below:
phy <- qza_to_phyloseq( features="feature-table.qza", tree="tree-mproot.qza", taxonomy="taxonomy.qza",metadata="mapping.txt" )
tax <- as.data.frame(as(tax_table(phy), "matrix"))
ntax <- tax %>% separate("Kingdom",
c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"), sep=";")
tax_table(phy) <- tax_table(as.matrix(ntax))
Or, you can try using one of the newly formatted SILVA(v138) references for your taxonomy. These import w/o issue using qiime2r (I use it quite often).
-Mike