nodes.dmp has empty rank for taxa of rank "subclass"
the workaround attributes the rank "subclass" when the rank is empty

removed mesh-tree from roots config files
mesh-download.snakefile download current MeSH tree
scripts/roots2mesh-tree.py translates a root file into a list of MeSH paths
mesh-microbio.snakefile creates the MeSH path list for microorganisms roots

cut-root.py computes the path from the taxid
cut-root.py thus takes an additional argument, the NCBI nodes.dmp file
More robust if a root taxid changes path