Hi, I tried to filter the taxonomy using grep -v -i “Plantae|Feature” taxonomy.tsv | cut -f 1 > plantae.tsv. and I was left with one column so when I proceed to phyloseq to make a phyloseq object I get the rank names represented by one taxa
rank_names(phy)
[1] "ta1"tax_table() Taxonomy Table: [ 137012 taxa by 1 taxonomic ranks ]
thanks for your assistance in advance