Evaluation error - TMscore not found

[mndavies286]

Hi

I'm running the MINE tutorial and I'm having an issue with the final command

GPU=0 bash scripts/k_fold_eval.sh summaries 111 mean 0

I assume I've failed to generate data at the previous stage but could you suggest where I'm going wrong?

100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:04<00:00,  2.42it/s]
  0%|                                                                                                                                                                                                                          | 0/299 [00:00<?, ?it/s]/bin/sh: 1: /home/matthewdavies/MEAN/evaluation/TMscore: not found
  0%|                                                                                                                                                                                                                          | 0/299 [00:01<?, ?it/s]
/bin/sh: 1: /home/matthewdavies/MEAN/evaluation/TMscore: not found
/bin/sh: 1: /home/matthewdavies/MEAN/evaluation/TMscore: not found
/bin/sh: 1: /home/matthewdavies/MEAN/evaluation/TMscore: not found
/bin/sh: 1: /home/matthewdavies/MEAN/evaluation/TMscore: not found
/bin/sh: 1: /home/matthewdavies/MEAN/evaluation/TMscore: not found
/bin/sh: 1: /home/matthewdavies/MEAN/evaluation/TMscore: not found
/bin/sh: 1: /home/matthewdavies/MEAN/evaluation/TMscore: not found
concurrent.futures.process._RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/opt/conda/lib/python3.7/concurrent/futures/process.py", line 239, in _process_worker
    r = call_item.fn(*call_item.args, **call_item.kwargs)
  File "/opt/conda/lib/python3.7/concurrent/futures/process.py", line 198, in _process_chunk
    return [fn(*args) for args in chunk]
  File "/opt/conda/lib/python3.7/concurrent/futures/process.py", line 198, in <listcomp>
    return [fn(*args) for args in chunk]
  File "generate.py", line 74, in eval_one
    summary['TMscore'] = tm_score(cplx.get_heavy_chain(), new_cplx.get_heavy_chain())
  File "/home/matthewdavies/MEAN/evaluation/tm_score.py", line 31, in tm_score
    score = float(res.group(1))
AttributeError: 'NoneType' object has no attribute 'group'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "generate.py", line 257, in <module>
    main(args)
  File "generate.py", line 214, in main
    average_test(args, model, test_set, test_loader, device)
  File "generate.py", line 174, in average_test
    summaries = process_map(partial(eval_one, out_dir=out_dir, cdr=cdr_type), inputs, max_workers=args.num_workers, chunksize=10)
  File "/opt/conda/lib/python3.7/site-packages/tqdm/contrib/concurrent.py", line 130, in process_map
    return _executor_map(ProcessPoolExecutor, fn, *iterables, **tqdm_kwargs)
  File "/opt/conda/lib/python3.7/site-packages/tqdm/contrib/concurrent.py", line 76, in _executor_map
    return list(tqdm_class(ex.map(fn, *iterables, **map_args), **kwargs))
  File "/opt/conda/lib/python3.7/site-packages/tqdm/std.py", line 1195, in __iter__
    for obj in iterable:
  File "/opt/conda/lib/python3.7/concurrent/futures/process.py", line 483, in _chain_from_iterable_of_lists
    for element in iterable:
  File "/opt/conda/lib/python3.7/concurrent/futures/_base.py", line 598, in result_iterator
    yield fs.pop().result()
  File "/opt/conda/lib/python3.7/concurrent/futures/_base.py", line 435, in result
    return self.__get_result()
  File "/opt/conda/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
AttributeError: 'NoneType' object has no attribute 'group'

[kxz18]

Hi~Did you first compile the TMscore.cpp into binary executable file? The compile command can be found in scripts/setup.sh (line 8)

[mndavies286]

I re-ran the setup and it seemed to work fine. Thanks for your help.