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.