The tool always seemed to fail at 99% for both the BL and EL Layers
With the error "Reading off the end of the data. Tried to read 6 bits when only 1 available"
and fails at "BL ANALYSIS: 99.0% EL ANALYSIS: 98.8% BL_EL_RPU WRITING: 99.0%"
The issue was not the path like the other user were having.
The error was definitely occurring due to issues with my input files
When examining the BL and EL layers in a Hex editor the last line always was not complete.
BL Layer

EL Layer

When I fill the empty bytes with 00 on the last lines
BL Layer

EL Layer

Everything worked perfectly

