OrthoFinder
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Published
20 hours ago •
davidemms
davidemms
ExampleData-related Issues
Using OrthoFinder tutorials (found here: https://davidemms.github.io/orthofinder_tutorials/downloading-and-running-orthofinder.html), I ran into some issues trying to run the provided code. I am using Bioconda on Mac. This line of code - orthofinder -f ExampleData/ - resulted in the issues copied below.
(base) Students-MacBook-Pro:~ student$ cd Desktop
(base) Students-MacBook-Pro:Desktop student$ cd orthofinder_tutorial/OrthoFinder
(base) Students-MacBook-Pro:OrthoFinder student$ ls
ExampleData License.md bin orthofinder version_2.4.0
ExampleData.zip README.md config.json tools
**(base) Students-MacBook-Pro:OrthoFinder student$ orthofinder -f ExampleData**
OrthoFinder version 2.4.0 Copyright (C) 2014 David Emms
2020-09-09 10:54:46 : Starting OrthoFinder
8 thread(s) for highly parallel tasks (BLAST searches etc.)
1 thread(s) for OrthoFinder algorithm
Checking required programs are installed
----------------------------------------
Test can run "mcl -h" - ok
Test can run "fastme -i /Users/student/Desktop/orthofinder_tutorial/OrthoFinder/ExampleData/OrthoFinder/Results_Sep09/WorkingDirectory/SimpleTest.phy -o /Users/student/Desktop/orthofinder_tutorial/OrthoFinder/ExampleData/OrthoFinder/Results_Sep09/WorkingDirectory/SimpleTest.tre" - ok
Dividing up work for BLAST for parallel processing
--------------------------------------------------
2020-09-09 10:54:46 : Creating diamond database 1 of 4
2020-09-09 10:54:46 : Creating diamond database 2 of 4
2020-09-09 10:54:46 : Creating diamond database 3 of 4
2020-09-09 10:54:46 : Creating diamond database 4 of 4
Running diamond all-versus-all
------------------------------
Using 8 thread(s)
2020-09-09 10:54:46 : This may take some time....
Traceback (most recent call last):
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1678, in main
ptm_initialised = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
exitcode = _main(fd, parent_sentinel)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 125, in _main
prepare(preparation_data)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 236, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 265, in run_path
return _run_module_code(code, init_globals, run_name,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/student/miniconda3/bin/orthofinder", line 7, in <module>
main(args)
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1771, in main
ptm = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
Traceback (most recent call last):
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1678, in main
ptm_initialised = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
Traceback (most recent call last):
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1678, in main
ptm_initialised = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
exitcode = _main(fd, parent_sentinel)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 125, in _main
prepare(preparation_data)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 236, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 265, in run_path
return _run_module_code(code, init_globals, run_name,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/student/miniconda3/bin/orthofinder", line 7, in <module>
main(args)
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1771, in main
ptm = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
self._popen = self._Popen(self)
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
_check_not_importing_main()
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
exitcode = _main(fd, parent_sentinel)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 125, in _main
prepare(preparation_data)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 236, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
Traceback (most recent call last):
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1678, in main
main_content = runpy.run_path(main_path,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 265, in run_path
return _run_module_code(code, init_globals, run_name,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/student/miniconda3/bin/orthofinder", line 7, in <module>
main(args)
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1771, in main
ptm_initialised = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
ptm = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multip super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
rocessing/context.py", line 283, in _Popen
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
exitcode = _main(fd, parent_sentinel)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 125, in _main
prepare(preparation_data)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 236, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 265, in run_path
return _run_module_code(code, init_globals, run_name,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/student/miniconda3/bin/orthofinder", line 7, in <module>
main(args)
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1771, in main
ptm = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
Traceback (most recent call last):
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1678, in main
ptm_initialised = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
exitcode = _main(fd, parent_sentinel)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 125, in _main
prepare(preparation_data)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 236, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 265, in run_path
return _run_module_code(code, init_globals, run_name,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/student/miniconda3/bin/orthofinder", line 7, in <module>
main(args)
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1771, in main
ptm = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
Traceback (most recent call last):
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1678, in main
ptm_initialised = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
Traceback (most recent call last):
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1678, in main
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
ptm_initialised = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
exitcode = _main(fd, parent_sentinel)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 125, in _main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
prepare(preparation_data)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 236, in prepare
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
_fixup_main_from_path(data['init_main_from_path'])
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 265, in run_path
return _run_module_code(code, init_globals, run_name,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 97, in _run_module_code
exitcode = _main(fd, parent_sentinel)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 125, in _main
prepare(preparation_data)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 236, in prepare
_run_code(code, mod_globals, init_globals,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/student/miniconda3/bin/orthofinder", line 7, in <module>
_fixup_main_from_path(data['init_main_from_path'])
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 265, in run_path
main(args)
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1771, in main
return _run_module_code(code, init_globals, run_name,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/student/miniconda3/bin/orthofinder", line 7, in <module>
main(args)
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1771, in main
ptm = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
Traceback (most recent call last):
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1678, in main
Traceback (most recent call last):
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1678, in main
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
ptm_initialised = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
ptm = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
return Popen(process_obj)
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
ptm_initialised = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
exitcode = _main(fd, parent_sentinel)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 125, in _main
prepare(preparation_data)
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 236, in prepare
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
_fixup_main_from_path(data['init_main_from_path'])
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
raise RuntimeError('''
main_content = runpy.run_path(main_path,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 265, in run_path
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
exitcode = _main(fd, parent_sentinel)
return _run_module_code(code, init_globals, run_name,
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 125, in _main
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 97, in _run_module_code
prepare(preparation_data)
_run_code(code, mod_globals, init_globals,
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 236, in prepare
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
_fixup_main_from_path(data['init_main_from_path'])
File "/Users/student/miniconda3/bin/orthofinder", line 7, in <module>
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
main(args)
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1771, in main
main_content = runpy.run_path(main_path,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 265, in run_path
return _run_module_code(code, init_globals, run_name,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/student/miniconda3/bin/orthofinder", line 7, in <module>
main(args)
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1771, in main
ptm = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
ptm = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
return Popen(process_obj)
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
2020-09-09 10:54:47 : Done all-versus-all sequence search
Running OrthoFinder algorithm
-----------------------------
2020-09-09 10:54:47 : Initial processing of each species
Traceback (most recent call last):
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1678, in main
ptm_initialised = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
exitcode = _main(fd, parent_sentinel)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 125, in _main
prepare(preparation_data)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 236, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 265, in run_path
return _run_module_code(code, init_globals, run_name,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "/Users/student/miniconda3/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/student/miniconda3/bin/orthofinder", line 7, in <module>
main(args)
File "/Users/student/miniconda3/bin/scripts_of/__main__.py", line 1771, in main
ptm = parallel_task_manager.ParallelTaskManager_singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 321, in __init__
ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton()
File "/Users/student/miniconda3/bin/scripts_of/parallel_task_manager.py", line 316, in __init__
self.manager_process.start()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
return Popen(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/student/miniconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
ERROR: An error occurred, ***please review the error messages*** they may contain useful information about the problem.
Hi
Thanks for the report. I wonder if this is perhaps I python 3.8 related issue. Bioconda just upgraded to using python v 3.8 in the last week. Could you try setting up a biconda environment using python 3.7 instead, I think that should work.
I will also try and investigate why the version change might be causing a problem, but that might take a little longer.
All the best David
I had this problem too - MacBook Pro M1, MacOS 12.6, latest Anaconda & orthofinder install. I have Python 3.9 Based on suggestion above I did:
conda create -n test -c conda-forge -c bioconda python=3.7 orthofinder
Following this, I did:
conda activate test # possibly redundant? dunno..
Then I was able to run orthofinder -f ExampleData with no problems, suggesting that something in a later version of Python is the problem.
