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Roth-Lab / pyclone-vi

Fast method for inferring cancer clonal population structure from SNV data.
GNU General Public License v3.0
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AttributeError: module 'numpy' has no attribute 'math'. Did you mean: 'emath'? #39

Open endertial opened 1 week ago

endertial commented 1 week ago

Dear aroth85,

Thank you for developing pyclone-vi,

I would like to use the software to caculate CCF from targeted DNA sequencing data. I have performed SNV/INDEL calling and CNV to obtain minor and major cn to run pyclone.

I managed to install pyclone successfully by following the step by step procedure via conda, but when I run:

pyclone-vi fit -i examples/tracerx.tsv -o tracerx.h5 -c 40 -d beta-binomial -r 10 (example run)

I encounter this error message, "AttributeError: module 'numpy' has no attribute 'math'. Did you mean: 'emath'?"

full log file here: stderror.txt

How can I deal with it?

Thanks, Best regards,

Alessio

elhurtado commented 1 week ago

This should be resolved in PyClone-VI v0.1.5: https://github.com/Roth-Lab/pyclone-vi/releases/tag/0.1.5, 7e34dc89b63c527d5e8bafc8d8936f7e37853855

endertial commented 6 days ago

I have tried with the 0.1.5 version but running the example workflow another error occurred: Traceback (most recent call last): File "/home/simone/miniconda3/envs/pyclone-vi/bin/pyclone-vi", line 33, in sys.exit(load_entry_point('pyclone-vi==0.1.5', 'console_scripts', 'pyclone-vi')()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/simone/miniconda3/envs/pyclone-vi/bin/pyclone-vi", line 25, in importlib_load_entry_point return next(matches).load() ^^^^^^^^^^^^^^^^^^^^ File "/home/simone/miniconda3/envs/pyclone-vi/lib/python3.12/importlib/metadata/init.py", line 205, in load module = import_module(match.group('module')) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/simone/miniconda3/envs/pyclone-vi/lib/python3.12/importlib/init.py", line 90, in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1387, in _gcd_import File "", line 1360, in _find_and_load File "", line 1331, in _find_and_load_unlocked File "", line 935, in _load_unlocked File "", line 995, in exec_module File "", line 488, in _call_with_frames_removed File "/home/simone/miniconda3/envs/pyclone-vi/lib/python3.12/site-packages/pyclone_vi-0.1.5-py3.12.egg/pyclone_vi/cli.py", line 3, in File "/home/simone/miniconda3/envs/pyclone-vi/lib/python3.12/site-packages/pyclone_vi-0.1.5-py3.12.egg/pyclone_vi/run.py", line 5, in File "/home/simone/miniconda3/envs/pyclone-vi/lib/python3.12/site-packages/pyclone_vi-0.1.5-py3.12.egg/pyclone_vi/data.py", line 7, in File "/home/simone/miniconda3/envs/pyclone-vi/lib/python3.12/site-packages/pyclone_vi-0.1.5-py3.12.egg/pyclone_vi/math_utils.py", line 9, in File "/home/simone/miniconda3/envs/pyclone-vi/lib/python3.12/site-packages/numba/core/decorators.py", line 225, in wrapper disp.enable_caching() File "/home/simone/miniconda3/envs/pyclone-vi/lib/python3.12/site-packages/numba/core/dispatcher.py", line 808, in enable_caching self._cache = FunctionCache(self.py_func) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/simone/miniconda3/envs/pyclone-vi/lib/python3.12/site-packages/numba/core/caching.py", line 601, in init self._impl = self._impl_class(py_func) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/simone/miniconda3/envs/pyclone-vi/lib/python3.12/site-packages/numba/core/caching.py", line 337, in init raise RuntimeError("cannot cache function %r: no locator available " RuntimeError: cannot cache function 'log_beta': no locator available for file '/home/simone/miniconda3/envs/pyclone-vi/lib/python3.12/site-packages/pyclone_vi-0.1.5-py3.12.egg/pyclone_vi/math_utils.py'

elhurtado commented 6 days ago

That error has to do with numba function caching. I've just pushed changes in v0.1.6 that removes numba caching