Hi Aeriel,
I worked on the q2-fragment-insertion plugin, which wraps SEPP and I want to encourage you to use it since it handles those types of complications plus its using the latest version of the code which reduces the memory footprint a lot.
To save you some computation, you can manually edit your newick tree file. All you need to do is jump to the very end of the one line and add a branch length to the k__bacteria, i.e. ":0.0965499)'k__Bacteria');" need to become ":0.0965499)'k__Bacteria':0.0);"