NameError: name 'vertex_counter' is not defined about talon HOT 6 CLOSED

It looks like you are having the same issue as in #136, vaguely. I noticed that you're both using Python >= 3.10. Digging into this, it looks like the behaviour of sharing these "counter" variables between multiprocessing threads has changed (see https://stackoverflow.com/questions/70552775/multiprocess-inherently-shared-memory-in-no-longer-working-on-python-3-10-comin). Maybe you could try downgrading your Python version. I will likely try to update the requirements in the setup.py file to solve this in the future, once I've done some testing on my end.

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Hi there, can you please let me know what version of TALON you're running?

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talon 5.0 pypi_0 pypi

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It seems to initiate properly but then fails:

[ 2023-10-11 13:41:18 ] Started TALON run
[ 2023-10-11 13:42:27 ] Merged input SAM/BAM files
[ 2023-10-11 13:43:03 ] Split reads into 305 intervals
[ 2023-10-11 13:43:05 ] Launching parallel annotation jobs
[ 2023-10-11 13:43:05 ] Annotating reads in interval GL000009.2:116008-116358...
[ 2023-10-11 13:43:05 ] Annotating reads in interval GL383522.1:57520-77044...
[ 2023-10-11 13:43:05 ] Annotating reads in interval GL383582.2:2045-71551...
[ 2023-10-11 13:43:05 ] Annotating reads in interval GL000194.1:44042-106555...

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Thanks so much for the reply. Ill try it now.

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Just to follow up, I tested this behavior and found that I was able to reproduce your issue with Python >= 3.8, as the Stackoverflow thread I found suggested. I have now included <3.8 as a Python dependency in the installation requirements in the latest release. Please try installing with this version and see if this fixes your issue!

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