What is wrong with my phylogenetic tree pipeline based on the core genome such that they are branching off too many times?

Question

I am trying to build a phylogenetic tree based off the core genome of one strain of a bacterial species.

Currently, my pipeline is as follows:

1. Prokka (annotate and get the .gff files)
2. Roary (use .gff files to create core genome alignment file)
3. Convert the .aln file produced by Roary to a .phy file using Trimal
4. RAxML to create the tree (-f a -x 12345 -N 100 -o reference_genome

I have used Prokka to also generate the .gff file of my reference genome which I wanted to use as an output. However, this is the tree I get: Tree produced with FigTree

I am expecting less branches, and that there would be clearer groups.