[BUG] pyscenic grn

[ken-chen-18]

Hi,

I got this message in my slurm output file after running pyscenic grn, but I also got a NODE_FAIL message. I'm just wondering if, despite this message, the process was completed properly since it says finished.

Thanks, Ken

/global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]:

2023-09-19 15:08:15,847 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.

2023-09-19 15:09:00,280 - pyscenic.cli.pyscenic - INFO - Inferring regulatory networks. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: /global/home/users/kenchen/.conda/envs/regulon_3.9/lib/python3.9/site-packages/distributed/client.py:3160: UserWarning: Sending large graph of size 2.49 GiB. This may cause some slowdown. Consider scattering data ahead of time and using futures. warnings.warn( 2023-09-20 04:19:59,880 - distributed.nanny - WARNING - Worker process still alive after 3.199997711181641 seconds, killing 2023-09-20 04:19:59,911 - distributed.nanny - WARNING - Worker process still alive after 3.199999389648438 seconds, killing 2023-09-20 04:19:59,911 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing 2023-09-20 04:19:59,912 - distributed.nanny - WARNING - Worker process still alive after 3.199999694824219 seconds, killing 2023-09-20 04:19:59,912 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing 2023-09-20 04:19:59,913 - distributed.nanny - WARNING - Worker process still alive after 3.199999694824219 seconds, killing 2023-09-20 04:19:59,913 - distributed.nanny - WARNING - Worker process still alive after 3.199999694824219 seconds, killing 2023-09-20 04:19:59,913 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing 2023-09-20 04:19:59,914 - distributed.nanny - WARNING - Worker process still alive after 3.199999389648438 seconds, killing 2023-09-20 04:19:59,914 - distributed.nanny - WARNING - Worker process still alive after 3.199999389648438 seconds, killing 2023-09-20 04:19:59,915 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing 2023-09-20 04:19:59,915 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing 2023-09-20 04:19:59,915 - distributed.nanny - WARNING - Worker process still alive after 3.199999389648438 seconds, killing 2023-09-20 04:19:59,916 - distributed.nanny - WARNING - Worker process still alive after 3.199999389648438 seconds, killing 2023-09-20 04:19:59,916 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing 2023-09-20 04:19:59,916 - distributed.nanny - WARNING - Worker process still alive after 3.199999389648438 seconds, killing 2023-09-20 04:19:59,917 - distributed.nanny - WARNING - Worker process still alive after 3.199999694824219 seconds, killing 2023-09-20 04:19:59,917 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing 2023-09-20 04:19:59,917 - distributed.nanny - WARNING - Worker process still alive after 3.199999694824219 seconds, killing 2023-09-20 04:19:59,917 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing

2023-09-20 04:20:00,278 - pyscenic.cli.pyscenic - INFO - Writing results to file. preparing dask client parsing input creating dask graph 20 partitions computing dask graph not shutting down client, client was created externally finished

[YuliaInn]

I have a similar issue when running it on hpc with linux on intercative mode (220 gb memory, 2hrs time limit, 6 nodes), but after "consider scattering data ahead of time and using futures" it crashes because of timeout. I ran pyscenic grn command from jupyter on my local machine, it was faster and did not give me any warnings