nickjcroucher
commented
1 year ago It seems this might be a problem with the latest version of numpy interfacing with numba: https://github.com/numba/numba/issues/8615#issuecomment-1434358853.
Would you mind trying downgrading numpy to 1.23.0, as suggested in that link, in case that fixes the problem?
leabednarczuk
Hello
I installed Github with conda as explained in the documentation. Then I created my alignment with SKA and I obtained my .aln output. The issues occur when I try to run this line : $ run_gubbins.py test.aln
Here what the terminal display:
Traceback (most recent call last): File "/home/bednarczuk/anaconda3/bin/run_gubbins.py", line 33, in
sys.exit(load_entry_point('gubbins==3.2.1', 'console_scripts', 'run_gubbins.py')())
File "/home/bednarczuk/anaconda3/bin/run_gubbins.py", line 25, in importlib_load_entry_point
return next(matches).load()
File "/home/bednarczuk/anaconda3/lib/python3.10/importlib/metadata/init.py", line 171, in load
module = import_module(match.group('module'))
File "/home/bednarczuk/anaconda3/lib/python3.10/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1050, in _gcd_import
File "", line 1027, in _find_and_load
File "", line 992, in _find_and_load_unlocked
File "", line 241, in _call_with_frames_removed
File "", line 1050, in _gcd_import
File "", line 1027, in _find_and_load
File "", line 1006, in _find_and_load_unlocked
File "", line 688, in _load_unlocked
File "", line 883, in exec_module
File "", line 241, in _call_with_frames_removed
File "/home/bednarczuk/anaconda3/lib/python3.10/site-packages/gubbins/init.py", line 16, in
from gubbins import common
File "/home/bednarczuk/anaconda3/lib/python3.10/site-packages/gubbins/common.py", line 42, in
from gubbins.pyjar import jar, get_base_patterns
File "/home/bednarczuk/anaconda3/lib/python3.10/site-packages/gubbins/pyjar.py", line 18, in
import numba
File "/home/bednarczuk/anaconda3/lib/python3.10/site-packages/numba/init.py", line 42, in
from numba.np.ufunc import (vectorize, guvectorize, threading_layer,
File "/home/bednarczuk/anaconda3/lib/python3.10/site-packages/numba/np/ufunc/init.py", line 3, in
from numba.np.ufunc.decorators import Vectorize, GUVectorize, vectorize, guvectorize
File "/home/bednarczuk/anaconda3/lib/python3.10/site-packages/numba/np/ufunc/decorators.py", line 3, in
from numba.np.ufunc import _internal
SystemError: initialization of _internal failed without raising an exception
It looks like the problem is the Numba package so I tried to re install it but I still get this error message.
Thank you in advance for your precious help !