Did you copy all 20 WAD files, starting alphabetically with ATTACK.WAD, into the source_wads/ subdirectory before running WadSmoosh?
oh, i need the wads? not just master.wad?
When you buy the Master Levels you get 20 WAD files, it's not an all-in-one thing. Master.wad must have been generated by some other tool, WadSmoosh doesn't support that.