AttributeError: module '__main__' has no attribute '__spec__'

[paujedynak]

Hi, I was trying to run comb-p pipeline on Windows, Python 3.8.1. Input file: sorted .bed with p values in the 4th column, obtained for 450k Illumina experiment: 1 69591 69592 0.982159693721179 1 790667 790668 0.869352157002484 1 800083 800084 0.976817881693934 1 805541 805542 0.217375018346954 1 812539 812540 0.31980048550337 1 834183 834184 0.435330819704651

After running a command: python comb-p pipeline -c 4 --seed 0.001 --dist 500 -p mp --region-filter-p 0.05 --region-filter-n 2 full_path\bed_file.bed

I obtain the following output:

setting --acf-dist to 0.33 * --dist == 170 calculated stepsize as: 170 Traceback (most recent call last): File "comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.3', 'comb-p') File "C:\Users\pauli\miniconda3\envs\pau1\lib\site-packages\pkg_resources_init_.py", line 667, in run_script self.require(requires)[0].run_script(script_name, ns) File "C:\Users\pauli\miniconda3\envs\pau1\lib\site-packages\pkg_resources_init_.py", line 1464, in run_script exec(code, namespace, namespace) File "c:\users\pauli\miniconda3\envs\pau1\lib\site-packages\cpv-0.50.3-py3.8.egg\EGG-INFO\scripts\comb-p", line 39, in main() File "c:\users\pauli\miniconda3\envs\pau1\lib\site-packages\cpv-0.50.3-py3.8.egg\EGG-INFO\scripts\comb-p", line 36, in main module.main() File "C:\Users\pauli\miniconda3\envs\pau1\lib\site-packages\cpv-0.50.3-py3.8.egg\cpv\pipeline.py", line 70, in main return pipeline(col_num, args.step, File "C:\Users\pauli\miniconda3\envs\pau1\lib\site-packages\cpv-0.50.3-py3.8.egg\cpv\pipeline.py", line 101, in pipeline putative_acf_vals = acf.acf(bed_files, lags, col_num, simple=False, mlog=mlog) File "C:\Users\pauli\miniconda3\envs\pau1\lib\site-packages\cpv-0.50.3-py3.8.egg\cpv\acf.py", line 88, in acf imap = get_map() File "C:\Users\pauli\miniconda3\envs\pau1\lib\site-packages\cpv-0.50.3-py3.8.egg\cpv_common.py", line 169, in get_map p = Pool(min(4, cpu_count()), pool_sig) File "C:\Users\pauli\miniconda3\envs\pau1\lib\multiprocessing\context.py", line 119, in Pool return Pool(processes, initializer, initargs, maxtasksperchild, File "C:\Users\pauli\miniconda3\envs\pau1\lib\multiprocessing\pool.py", line 212, in init self._repopulate_pool() File "C:\Users\pauli\miniconda3\envs\pau1\lib\multiprocessing\pool.py", line 303, in _repopulate_pool return self._repopulate_pool_static(self._ctx, self.Process, File "C:\Users\pauli\miniconda3\envs\pau1\lib\multiprocessing\pool.py", line 326, in _repopulate_pool_static w.start() File "C:\Users\pauli\miniconda3\envs\pau1\lib\multiprocessing\process.py", line 121, in start self._popen = self._Popen(self) File "C:\Users\pauli\miniconda3\envs\pau1\lib\multiprocessing\context.py", line 326, in _Popen return Popen(process_obj) File "C:\Users\pauli\miniconda3\envs\pau1\lib\multiprocessing\popen_spawn_win32.py", line 45, in init prep_data = spawn.get_preparation_data(process_obj._name) File "C:\Users\pauli\miniconda3\envs\pau1\lib\multiprocessing\spawn.py", line 183, in get_preparation_data main_mod_name = getattr(main_module.spec, "name", None) AttributeError: module 'main' has no attribute 'spec'

I was wondering if this can be fixed somehow. Thank you! Pau

[brentp]

hi, I'm not able to help much on windows, but usually, you'd just run comb-p ... instead of python comb-p ... -- at least on linux.

[paujedynak]

Thanks for the prompt reply! It seems to me that the error AttributeError: module 'main' has no attribute 'spec' is typical for python, not OS dependent, isn't it? The software seems to work until some point, the last printed message is: setting --acf-dist to 0.33 * --dist == 170 calculated stepsize as: 170 and then it crashes.

And the python comb-p in my case is necessary, otherwise it does not work.

[ziphra]

Hello, I had the same issue, but I am running on Mac. I solved this issue using python3.7 instead of 3.8.

[brentp]

If anyone has a proper solution to this, I'd be happy to incorporate it. I found some stackoverflow posts that suggest to add: __spec__ = None.