I got the 201901 phylogenetic tree from metaphlan/utils/mpa_v30_CHOCOPhlAn_201901_species_tree.nwk, then I use calculate_unifrac.R to run my merged tables, then warnings showed:
"WARNING: 9 species not present in the tree were removed from the input profile.
Olsenella_profusa
Collinsella_stercoris
Gemella_bergeri
Granulicatella_elegans
Ruminococcus_champanellensis
Bulleidia_extructa
Sutterella_parvirubra
Cloacibacillus_evryensis
Giardia_intestinalis
"
I used the chocophlan 201901b as the reference database, does the tree file from github not match with 201901b?