Thanks Alain & Matthew, I added the name of the main class to the arguments list and this worked. My new submit file is as follows: Universe = java Executable = gab142_2.jar jar_files = gab142_2.jar Arguments = ggraph.geom.Gabriel -i io3.txt Output = gab142.out Error = gab142.error transfer_input_files = io3.txt should_transfer_files = YES when_to_transfer_output = ON_EXIT Queue