If the species tree contains non-unique names, the mkdb command ends up in an infinite loop and memory blows up. The NCBI taxonomy has a few cases where the name is not unique, so this can indeed happen.
I suggest to check that all names are unique once the species tree has been loaded and error out in case there are duplicates.
If the species tree contains non-unique names, the mkdb command ends up in an infinite loop and memory blows up. The NCBI taxonomy has a few cases where the name is not unique, so this can indeed happen.
I suggest to check that all names are unique once the species tree has been loaded and error out in case there are duplicates.