NameError: name 'vertex_counter' is not defined

[Kiliankleemann]

Tried to run TALON with the following command:
mkdir TALON_output
talon --f config.csv
--db hg38.db
--build hg38_rmsk_ucsd
--threads 4
--o TALON_output/

but I got this error:
Traceback (most recent call last):
File "/Users/kiliankleemann/anaconda3/lib/python3.11/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "/Users/kiliankleemann/anaconda3/lib/python3.11/multiprocessing/pool.py", line 51, in starmapstar
return list(itertools.starmap(args[0], args[1]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kiliankleemann/anaconda3/lib/python3.11/site-packages/talon/talon.py", line 2333, in parallel_talon
annotation_info = annotate_read(record, cursor, run_info,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kiliankleemann/anaconda3/lib/python3.11/site-packages/talon/talon.py", line 2514, in annotate_read
annotation_info = identify_monoexon_transcript(chrom, positions, strand,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kiliankleemann/anaconda3/lib/python3.11/site-packages/talon/talon.py", line 1817, in identify_monoexon_transcript
vertex_IDs, v_novelty, diff_5p, diff_3p = match_monoexon_vertices(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kiliankleemann/anaconda3/lib/python3.11/site-packages/talon/talon.py", line 193, in match_monoexon_vertices
vertex_match = create_vertex(chromosome, position, location_dict, run_info)[
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kiliankleemann/anaconda3/lib/python3.11/site-packages/talon/talon.py", line 416, in create_vertex
new_ID = vertex_counter.increment()
^^^^^^^^^^^^^^
NameError: name 'vertex_counter' is not defined

[fairliereese]

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

[Kiliankleemann]

talon 5.0 pypi_0 pypi

[Kiliankleemann]

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...

[fairliereese]

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.

[Kiliankleemann]

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

[fairliereese]

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!