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You probably want to run ExpandObjects and Basement separately from EnergyPlus. The best place to probably look at this is the RunEPlus.bat file or the EPL-run.bat file. These are located in the root folder of where ever you installed EnergyPlus on Windows.
The basement program needs specific files to exist in the folder and generates files in that folder. EnergyPlus then uses those files. ExpandObjects does some of the work for you and creates the BasementGHTIn.idf file.
https://bigladdersoftware.com/epx/docs/24-2/auxiliary-programs/use-of-the-ground-temperatures-with-slabs.html#introduction-003
You can also use subprocess to run those but would have to recreate the file manipulation part.