Issue with running oncodriveFML

[estefanidis]

Hello,

I am encountering this error when running oncodriveFML:

% oncodrivefml -i TCGA_mutations_archetype_1.4ofml.tsv -e updated_exome_panel.bed --signature-correction wx -c /Users/vanstefanidis/Documents/PanCanv2/pan_cancer_immune_archetypes/TCGA_stuff/Ferriol_OncodriveFML/oncodrivefml_v2.conf -o /Users/vanstefanidis/Documents/PanCanv2/pan_cancer_immune_archetypes/TCGA_stuff/Ferriol_OncodriveFML
2024-11-20 15:08:32 oncodrivefml INFO -- Using HG19 as reference genome
2024-11-20 15:08:32 oncodrivefml INFO -- Running analysis
Parsing elements 'updated_exome_panel.bed': 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▉| 290532/290533 [00:01<00:00, 161291.97it/s]
2024-11-20 15:08:37 oncodrivefml INFO -- Mapping mutations
* [0 muts]
2024-11-20 15:08:37 oncodrivefml INFO -- Computing signatures
2024-11-20 15:08:39 oncodrivefml INFO -- Computing OncodriveFML
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/multiprocessing/pool.py", line 125, in worker
   result = (True, func(*args, **kwds))
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/site-packages/oncodrivefml/utils.py", line 27, in executor_run
   return executor.run()
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/site-packages/oncodrivefml/executors/element.py", line 132, in run
   self.scores = Scores(self.name, self.segments, self.score_config)
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/site-packages/oncodrivefml/scores.py", line 270, in __init__
   self._load_scores()
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/site-packages/oncodrivefml/scores.py", line 306, in _load_scores
   with scores_reader as reader:
AttributeError: __enter__
"""

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

Traceback (most recent call last):
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/bin/oncodrivefml", line 8, in <module>
   sys.exit(cmdline())
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/site-packages/click/core.py", line 1128, in __call__
   return self.main(*args, **kwargs)
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/site-packages/click/core.py", line 1053, in main
   rv = self.invoke(ctx)
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/site-packages/click/core.py", line 1395, in invoke
   return ctx.invoke(self.callback, **ctx.params)
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/site-packages/click/core.py", line 754, in invoke
   return __callback(*args, **kwargs)
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/site-packages/oncodrivefml/main.py", line 127, in cmdline
   main(mutations_file, elements_file, output_folder, config_file, samples_blacklist, override_config, force)
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/site-packages/oncodrivefml/main.py", line 58, in main
   analysis.run()
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/site-packages/oncodrivefml/oncodrivefml.py", line 233, in run
   for executor in loop_logging(map_func(executor_run, element_executors), size=len(element_executors), step=6*self.cores):
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/site-packages/oncodrivefml/utils.py", line 61, in loop_logging
   for i, value in enumerate(iterable):
 File "/Users/vanstefanidis/anaconda3/envs/new_oncodrivefml/lib/python3.10/multiprocessing/pool.py", line 873, in next
   raise value
AttributeError: __enter__

Any ideas what the problem is?

I am running it on Mac, using python 3.10 and I am encountering the same issue with the example data.

Many thanks!

[FerriolCalvet]

@estefanidis noticed that this is the problem that was reported in #1 so my guess is that we would need to wait for that to be addressed before having this solved.

Closing this issue since the other one already comes with suggestions of potential solutions.