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    The most important thing is missing: the errors and their stacktraces. Commented Jan 23, 2018 at 20:37
  • @CristiFati - They are not PyCharm errors. If you do not work with ArcPy you will not understand the errors so they're a bit irrelevant to my post, but I understand why you asked for them. They are errors sent by the software program because an arcpy tool failed. For instance, one of them is "Error 000732: Input Features: Dataset #1; #2 does not exist or is not supported" (they do exist and they are supported). Despite the errors being ArcPy errors, it is a problem with the IDE because I can run this script elsewhere and it works as expected. I can even run it in PyCharm if not in debug mode. Commented Jan 23, 2018 at 20:53
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    Hmm, it might have smth to do with the way that Pycharm calls its debugger (pydevd.py) which might conflict with the other tool. Try running it with/without debug get the 1st lines from the Pycharm console (that is the cmdline) and do some comparisons. Commented Jan 23, 2018 at 20:58
  • @CristiFati - Possibly, though aside from the pyded.py being called with some extra flags (--multiproc --qt-support = auto --client 127.0.0.1 --port 5727) I'm not seeing much difference. The problem seems to stem from the breakpoints; it runs successfully in "Run" mode and "Debug" mode as long as when in debug mode there are zero breakpoints (which kinda defeats the purpose of debug). Commented Jan 23, 2018 at 21:08
  • Cross-posted as gis.stackexchange.com/q/268973/115 Commented Jan 24, 2018 at 4:27