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balabanmetin / apples

distance based phylogenetic placement
GNU General Public License v3.0
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NameError: name 'treecore' is not defined #8

Closed hmatsu1226 closed 4 years ago

hmatsu1226 commented 4 years ago

I had following error message in running apples, and the calculation did not appear to be progressing. I use python 3.8.1 on macOS Catalina. I hope you will be able to provide the information.

% run_apples.py -d data/small_dist.mat -t data/small_backbone.nwk multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/Users/matsumoto/.pyenv/versions/3.8.1/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/Users/matsumoto/.pyenv/versions/3.8.1/lib/python3.8/multiprocessing/pool.py", line 51, in starmapstar return list(itertools.starmap(args[0], args[1])) File "/Users/matsumoto/.pyenv/versions/3.8.1/bin/run_apples.py", line 26, in runquery for l in treecore.tree.traverse_postorder(internal=False): NameError: name 'treecore' is not defined """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/Users/matsumoto/.pyenv/versions/3.8.1/bin/run_apples.py", line 159, in results = pool.starmap(runquery, queries) File "/Users/matsumoto/.pyenv/versions/3.8.1/lib/python3.8/multiprocessing/pool.py", line 372, in starmap return self._map_async(func, iterable, starmapstar, chunksize).get() File "/Users/matsumoto/.pyenv/versions/3.8.1/lib/python3.8/multiprocessing/pool.py", line 768, in get raise self._value NameError: name 'treecore' is not defined

balabanmetin commented 4 years ago

Python 3.8 broke APPLES. I made necessary changes and it should work now. Please upgrade your APPLES version to 1.3.0 by running the following command:

pip3 install --upgrade apples

or cloning the newest version from github.

hmatsu1226 commented 4 years ago

Thank you for your quick response.