benchmarking issue

[AO33]

I am running a benchmark analysis using 'pheval-utils benchmark --run-yaml ...' command and I recieve the following error

[2025-12-05 18:00:19] [INFO] [benchmark.py:29] - Analysing results in .../pstore_0.1.25_phenio100_merged_preliminary/pheval_gene_results
[2025-12-05 18:00:19] [INFO] [rank_stats.py:166] - Generating ranking statistics for phenio100...
[2025-12-05 18:22:18] [INFO] [binary_classification_curves.py:125] - Calculating ROC and Precision-Recall metrics
Traceback (most recent call last):
File ".../bin/pheval-utils", line 7, in
sys.exit(pheval_utils())
File ".../python3.11/site-packages/polars/lazyframe/frame.py", line 2422, in collect
return wrap_df(ldf.collect(engine, callback))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: file name contained an unexpected NUL byte: ... (set POLARS_VERBOSE=1 to see full path)

All pheval results files within this directory are able to be read into memory though without issue using polars (I can do this manually within a jupyter notebook just fine)... So maybe something to do with how pheval benchmarking is dealing with the filepaths? Not entirely sure here because this issue doesn't show up for some of the other runs that I have done

[yaseminbridges]

Thanks - is that the full traceback, or was anything above/below omitted? The extra frames are often useful because they show which part of the lazy computation Polars was evaluating when it hit the NUL-byte error. If you can share the complete traceback, that will help narrow down what’s introducing the problematic path.

For context, the benchmark pipeline uses scan_parquet(..., include_file_paths="file_path"), so Polars includes the original file paths as a column. My guess is that the NUL byte is coming from one of those paths rather than from the Parquet files themselves, since you can read each file manually without issues. It might be worth checking the captured file paths in the results directory to see if any contain unexpected characters.

[AO33]

This was a weird one. I think the issue was caused by a phenopacket(s) with zero phenotypes. Since removing those phenopackets and rerunning the data I haven't encountered this error again.

But here is the rest of the full trace (it was able to get past the first bit of the benchmarking, so it ran for a while before erroring)

[2025-12-05 18:22:18] [INFO] [binary_classification_curves.py:125] - Calculating ROC and Precision-Recall metrics
Traceback (most recent call last):
File ".../envs/phevalExps/bin/pheval-utils", line 7, in
sys.exit(pheval_utils())
^^^^^^^^^^^^^^
File ".../envs/phevalExps/lib/python3.11/site-packages/click/core.py", line 1161, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".../envs/phevalExps/lib/python3.11/site-packages/click/core.py", line 1082, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File ".../envs/phevalExps/lib/python3.11/site-packages/click/core.py", line 1697, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".../envs/phevalExps/lib/python3.11/site-packages/click/core.py", line 1443, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".../envs/phevalExps/lib/python3.11/site-packages/click/core.py", line 788, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".../envs/phevalExps/lib/python3.11/site-packages/pheval/cli_pheval_utils.py", line 348, in benchmark
benchmark_runs(
File ".../envs/phevalExps/lib/python3.11/site-packages/pheval/analyse/benchmark.py", line 134, in benchmark_runs
benchmark(
File ".../envs/phevalExps/lib/python3.11/site-packages/pheval/analyse/benchmark.py", line 104, in benchmark
stats, curve_results, true_positive_cases = process_stats(config.runs, benchmark_type)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File .../envs/phevalExps/lib/python3.11/site-packages/pheval/analyse/benchmark.py", line 81, in process_stats
pl.concat(stats, how="vertical").collect(),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".../python3.11/site-packages/polars/_utils/deprecation.py", line 97, in wrapper
return function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File ".../python3.11/site-packages/polars/lazyframe/opt_flags.py", line 328, in wrapper
return function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File ".../python3.11/site-packages/polars/lazyframe/frame.py", line 2422, in collect
return wrap_df(ldf.collect(engine, callback))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: file name contained an unexpected NUL byte: ... (set POLARS_VERBOSE=1 to see full path)