Error of scv.tl.recover_dynamics() for sbutype cluster

[Xin-jxy]

Hello,

Thanks for this practical analyse tool theislab team!!

I have some issues due to command scv.tl.recover_dynamics() for the subtype cluster.

My question is : there is this error appears when I tried to apply the command with subtype cluster with this new dataset '''adata=adata[adata.obs['louvain'].isin(['4', '15'])]''', but it was ok when I apply it to the whole dataset. For the information, I was running this command with the terminal of MacOs even thought I write my script in Pycharm. And I verified there is "velocity_genes" appears after the precedent step.

The version of tools : Python-->3.8 scVelo-->0.2.3

The error appears:

Stack trace

recovering dynamics (using 1/4 cores)
  0%|          | 0/243 [00:00<?, ?gene/s]
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
    exitcode = _main(fd, parent_sentinel)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/spawn.py", line 125, in _main
    prepare(preparation_data)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/spawn.py", line 236, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
    main_content = runpy.run_path(main_path,
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/runpy.py", line 265, in run_path
    return _run_module_code(code, init_globals, run_name,
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/runpy.py", line 97, in _run_module_code
    _run_code(code, mod_globals, init_globals,
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/Users/xinyue/scRNA-seq_python/test.py", line 72, in <module>
    print(buildAnndataFromStarCurr(sys.argv[1]))
  File "/Users/xinyue/scRNA-seq_python/test.py", line 33, in buildAnndataFromStarCurr
    scv.tl.recover_dynamics(adata_a)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/site-packages/scvelo/tools/dynamical_model.py", line 488, in recover_dynamics
    res = _parallelize(
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/site-packages/scvelo/tools/dynamical_model.py", line 1266, in wrapper
    queue = Manager().Queue()
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/context.py", line 57, in Manager
    m.start()
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/managers.py", line 579, in start
    self._process.start()
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/process.py", line 121, in start
    self._popen = self._Popen(self)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/context.py", line 284, in _Popen
    return Popen(process_obj)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
    super().__init__(process_obj)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
    self._launch(process_obj)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
    _check_not_importing_main()
  File "/usr/local/Caskroom/miniconda/base/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 "test.py", line 72, in <module>
    print(buildAnndataFromStarCurr(sys.argv[1]))
  File "test.py", line 33, in buildAnndataFromStarCurr
    scv.tl.recover_dynamics(adata_a)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/site-packages/scvelo/tools/dynamical_model.py", line 488, in recover_dynamics
    res = _parallelize(
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/site-packages/scvelo/tools/dynamical_model.py", line 1266, in wrapper
    queue = Manager().Queue()
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/context.py", line 57, in Manager
    m.start()
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/managers.py", line 583, in start
    self._address = reader.recv()
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/connection.py", line 250, in recv
    buf = self._recv_bytes()
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/connection.py", line 414, in _recv_bytes
    buf = self._recv(4)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/multiprocessing/connection.py", line 383, in _recv
    raise EOFError
EOFError

Thank you very much for your help

XIN

[WeilerP]

@Xin-jxy, which kind of MacOs are you using? Is it by any chance a M1? Found this question on stackoverflow which looks similar to your problem? Haven't really looked into this, though.
Also, du you encounter the same issue when running the code e.g. in a Jupyter notebook?

[Xin-jxy]

@WeilerP Thank you for replying, I have MacOs version 11.2.3, so probably I have same problem, but I retried with a new script without based on Pycharm, and it works!!! I don't really understand why, on contrast, I've never tried in a Jupyter notebook.

XIN