PulpSolverError after ~30 minutes on full dataset (4371 trees), works on small subset

[tomulanovski]

Hi,
I'm encountering a PulpSolverError when running PolyPhest on a full dataset of 4371 trees. The script runs for approximately 30 minutes before failing with this error. When I test on a small subset of the data, it completes successfully.
The command i ran:
python $POLYPHEST --gene_tree_file $GENE_TREES --consensus_multiset_file $MULTISET --filter_strategy percentile --output_dir $OUTPUT_DIR --percentile 50 --use_near_isomorphic True --isomorphic_threshold 0.2

Error message:
Traceback (most recent call last):
File "Polyphest/Polyphest.py", line 215, in
main(
File "Polyphest/Polyphest.py", line 99, in main
result = infer_network(
File "Polyphest/Polyphest.py", line 24, in infer_network
mul_tree, clusters = multree_builder.generate_multree(
File "Polyphest/polyphest/multree_builder.py", line 533, in generate_multree
selected_backbone_clusters = select_backbone_clusters(filtered_core_clusters, filtered_ambiguous_clusters,
File "Polyphest/polyphest/multree_builder.py", line 248, in select_backbone_clusters
problem.solve(pulp.PULP_CBC_CMD(msg=True))
File ".local/lib/python3.9/site-packages/pulp/pulp.py", line 1883, in solve
status = solver.actualSolve(self, **kwargs)
File ".local/lib/python3.9/site-packages/pulp/apis/coin_api.py", line 112, in actualSolve
return self.solve_CBC(lp, **kwargs)
File ".local/lib/python3.9/site-packages/pulp/apis/coin_api.py", line 181, in solve_CBC
raise PulpSolverError(
pulp.apis.core.PulpSolverError: Pulp: Error while trying to execute, use msg=True for more details/.local/lib/python3.9/site-packages/pulp/solverdir/cbc/linux/64/cbc

What I've tried so far:

Verified that the cbc solver is installed and executable
Ran with msg=True for more verbose output — the same error still occurs
Increased the memory allocation — no change
Reduced the dataset — on a small subset of trees, the script completes successfully

Environment:

Python 3.9
PuLP 2.x (the version installed in the environment)
Running on a computing cluster

Thank you in advance!