Availabilty of mapping NCBI TaxID to Species name

[franzosa]

It sounds like you might be using MetaPhlAn 4 with HUMAnN 3.6? If so, please see this discussion:

Metaphlan4 species not included in Humann3.5 output?

Hi! I noticed that in the Humann3.5 pathway abundance output, only a subset of the Metaphlan4 species are present as contributors to pathway abundance (i.e. SGB species and some others are missing in the pathway file). Is this supposed to be the case? If so, is the Humann3.5 output not representative of all the species present based on the Metaphlan4 genomes? Thank you, Brandi