check_output can fail with ValueError

gistfile1.txt

Traceback (most recent call last):
  File "/home/ganwell/.pyenv/versions/3.5.1/bin/structureshrink", line 9, in <module>
    load_entry_point('structureshrink==0.0.1', 'console_scripts', 'structureshrink')()
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/site-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/site-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/site-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/site-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/site-packages/structureshrink/__main__.py", line 250, in shrinker
    shrinker.shrink()
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/site-packages/structureshrink/shrinker.py", line 163, in shrink
    lambda ls: self.classify(ngram.join(ls)) == label
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/site-packages/structureshrink/shrinker.py", line 291, in _lsmin
    ls = _expmin(ls, criterion)
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/site-packages/structureshrink/shrinker.py", line 330, in _expmin
    if criterion(s):
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/site-packages/structureshrink/shrinker.py", line 163, in <lambda>
    lambda ls: self.classify(ngram.join(ls)) == label
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/site-packages/structureshrink/shrinker.py", line 87, in classify
    result = self.__classify(preprocessed)
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/site-packages/structureshrink/__main__.py", line 132, in classify_data
    test, timeout=timeout, stdin=subprocess.DEVNULL)
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/subprocess.py", line 629, in check_output
    **kwargs).stdout
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/subprocess.py", line 701, in run
    stdout, stderr = process.communicate()
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/subprocess.py", line 1068, in communicate
    stdout, stderr = self._communicate(input, endtime, timeout)
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/subprocess.py", line 1693, in _communicate
    selector.register(self.stdout, selectors.EVENT_READ)
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/selectors.py", line 342, in register
    key = super().register(fileobj, events, data)
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/selectors.py", line 228, in register
    key = SelectorKey(fileobj, self._fileobj_lookup(fileobj), events, data)
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/selectors.py", line 215, in _fileobj_lookup
    return _fileobj_to_fd(fileobj)
  File "/home/ganwell/.pyenv/versions/3.5.1/lib/python3.5/selectors.py", line 39, in _fileobj_to_fd
    "{!r}".format(fileobj)) from None
ValueError: Invalid file object: <_io.BufferedReader name=5>