Python Bonobo RuntimeError: This context cannot be stopped as it never started (extract)

Pretty often, when I run Bonobo's ETL graph with PyCharm debugger, I get an exception stated in the title: (RuntimeError: This context cannot be stopped as it never started (extract)

What is strange about the issue, is that it seems to be non-deterministic. Sometimes it throws, sometimes it doesn't (around 50/50 likelihood). When running my code straight from the command line, everything is ok. (At least I haven't encountered the exception yet.)

Is this a code issue or do I do something wrong?

Attached below are snippets showing how I use Bonobo.

bonobo version  
bonobo v.0.6.1 (in /Users/walkingdude/.pyenv/versions/3.6.2/envs/rb-3.6.2/lib/python3.6/site-packages)

python --version
python 3.6.2

My code:

    def load_transcripts(self, data_file_names):
        self.logger.info("Will use Bonobo now, to prepare flat data collection.")
        bonobo.run(
            self.get_graph(data_file_names),
            services=get_services()
        )
        flat_collect_df = pd.DataFrame(flat_dict_list)
        record_count = flat_collect_df.shape[0]
        self.logger.info("Bonobo extracted {} messages out of {} input files."
                         .format(record_count, len(data_file_names)))
        flat_collect_df = self.enrich_contact_and_user(flat_collect_df, self.connector)
        self.load_chat_data(flat_collect_df, self.connector)

    def get_graph(self, input_files):
        graph = bonobo.Graph()
        graph.add_chain(
            extract(input_files),
            get_conversations,
            get_conversation_parts_with_data,
            filter_parts_without_messages,
            prepare_flat_message_records,
            self.load_to_list,
        )
        return graph

def get_services():
    return {}

    def flat_list(self, context):
        yield flat_dict_list

    @use_context_processor(flat_list)
    def load_to_list(self, flat_list, row):
        flat_df_lock.acquire()
        flat_list.append(row)
        flat_df_lock.release()

Stack trace:

Traceback (most recent call last):
  File "/Applications/PyCharm CE.app/Contents/helpers/pydev/pydevd.py", line 1668, in <module>
    main()
  File "/Applications/PyCharm CE.app/Contents/helpers/pydev/pydevd.py", line 1662, in main
    globals = debugger.run(setup['file'], None, None, is_module)
  File "/Applications/PyCharm CE.app/Contents/helpers/pydev/pydevd.py", line 1072, in run
    pydev_imports.execfile(file, globals, locals)  # execute the script
  File "/Applications/PyCharm CE.app/Contents/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "/Users/walkingdude/PycharmProjects/rbscience/rapportboost/etl/commands/loadHomebaseIntercomTranscripts.py", line 295, in <module>
    local_run()
  File "/Users/walkingdude/PycharmProjects/rbscience/rapportboost/etl/commands/loadHomebaseIntercomTranscripts.py", line 284, in local_run
    homebase_loader.run()
  File "/Users/walkingdude/PycharmProjects/rbscience/rapportboost/etl/commands/loadHomebaseIntercomTranscripts.py", line 50, in run
    self.load_transcripts(data_file_names)
  File "/Users/walkingdude/PycharmProjects/rbscience/rapportboost/etl/commands/loadHomebaseIntercomTranscripts.py", line 59, in load_transcripts
    services=get_services()
  File "/Users/walkingdude/.pyenv/versions/rb-3.6.2/lib/python3.6/site-packages/bonobo/_api.py", line 67, in run
    return strategy.execute(graph, plugins=plugins, services=services)
  File "/Users/walkingdude/.pyenv/versions/rb-3.6.2/lib/python3.6/site-packages/bonobo/execution/strategies/executor.py", line 45, in execute
    context.stop()
  File "/Users/walkingdude/.pyenv/versions/rb-3.6.2/lib/python3.6/site-packages/bonobo/execution/contexts/graph.py", line 102, in stop
    node_context.stop()
  File "/Users/walkingdude/.pyenv/versions/rb-3.6.2/lib/python3.6/site-packages/bonobo/execution/contexts/node.py", line 169, in stop
    super().stop()
  File "/Users/walkingdude/.pyenv/versions/rb-3.6.2/lib/python3.6/site-packages/bonobo/execution/contexts/base.py", line 96, in stop
    raise RuntimeError('This context cannot be stopped as it never started ({}).'.format(get_name(self)))
RuntimeError: This context cannot be stopped as it never started (extract).