Hey, I am trying to make a phylogenetic tree, but when I use roary as the first step the NHX file is returning 0 bytes. I am not sure if this is supposed to happen or what to do to fix it.
This sounds like a data or parameter problem. If you want to share your history, we will take a look and try to advise. This would flush out any actual bugs as well.
If you are not sure how to share your history, search this forum for the instructions with “sharing your history”