The agent logs can be found in:
Windows- %USERPROFILE%\AppData\Roaming\EPI2MEAgent\logs\main.log
Ubuntu- ~/.config/EPI2MEAgent/logs/main.log
OSX- ~/Library/Logs/EPI2MEAgent/main.log
The logs are also accessible from the Epi2me Agent interface, from the Epi2me Agent drop down menu on your computer (normally top left of screen) you can select the "open Epi2me Agent logs folder" option.