So I saw that my problem is that my library list is not setup, and for some reason, the user we are using, does not have a Job Description. So to over come this I added the following code before calling the program.run()
CommandCall command = new CommandCall(system);
command.run("ADDLIBLE LIB(LIBNAME)");
command.run("ADDLIBLE LIB(LIBNAME2)");
This simply add this LIBNAME, and LIBNAME2 to the user's library list.