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Mouse-Imaging-Centre / pydpiper

Python code for flexible pipeline control
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pydpiper/2.0.12 twolevel_model_building.py fails to start with --run-maget #401

Open gdevenyi opened 5 years ago

gdevenyi commented 5 years ago

Looks like maybe a problem with --outputdir

Fixed if I remove --outputdir

Traceback (most recent call last):
  File "/opt/quarantine/pydpiper/2.0.12/install/bin/twolevel_model_building.py", line 4, in <module>
    __import__('pkg_resources').run_script('pydpiper==2.0.12', 'twolevel_model_building.py')
  File "/opt/quarantine/anaconda/5.1.0-python3/install/lib/python3.6/site-packages/pkg_resources/__init__.py", line 750, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/opt/quarantine/anaconda/5.1.0-python3/install/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1527, in run_script
    exec(code, namespace, namespace)
  File "/opt/quarantine/pydpiper/2.0.12/install/lib/python3.6/site-packages/pydpiper-2.0.12-py3.6.egg/EGG-INFO/scripts/twolevel_model_building.py", line 298, in <module>
    main(sys.argv)
  File "/opt/quarantine/pydpiper/2.0.12/install/lib/python3.6/site-packages/pydpiper-2.0.12-py3.6.egg/EGG-INFO/scripts/twolevel_model_building.py", line 295, in main
    execute(two_level_pipeline(options).stages, options)
  File "/opt/quarantine/pydpiper/2.0.12/install/lib/python3.6/site-packages/pydpiper-2.0.12-py3.6.egg/pydpiper/execution/application.py", line 154, in execute
    ensure_output_paths_in_dir(stages, options.application.output_directory)
  File "/opt/quarantine/pydpiper/2.0.12/install/lib/python3.6/site-packages/pydpiper-2.0.12-py3.6.egg/pydpiper/execution/application.py", line 85, in ensure_output_paths_in_dir
    % (item[0], item[1], d) for item in not_in_dir])
<CLIP spamming of tons and tons of lines>
gdevenyi commented 5 years ago

Probably related to #400

bcdarwin commented 5 years ago

I assume the error at the bottom of this traceback is some error about output files not in output dir?

gdevenyi commented 5 years ago

It spams so many lines that I stopped it before it could finish