Thanks for the great code..However, the run_squad.py for BERT Large seems to not have the vocab_file and bert_config_file (or other) options/arguments. Did you push the latest version?
Also, it is looking for a pytorch model file (a bin file). Does it need to be there?

I also had to add this line to the file to make BERT base to run on Squad 1.1:
parser.add_argument('--do_lower_case', action="store_true", default=True, help="Lowercase the input")