KeyError: 'chrom' during final output merging step

[bea1896]

I encountered an error while running Circle-Map during the final output merging step. The pipeline completes all previous stages without issues, but it consistently crashes when writing the final output. I would appreciate clarification about what this error indicates, what the underlying cause might be, and how it can be resolved or worked around.

The full traceback and environment details are included below.

2025-12-05 14:16:41: Writting final output to disk Traceback (most recent call last): File "/home/davide/circlemap-env/bin/Circle-Map", line 7, in sys.exit(main()) File "/home/davide/circlemap-env/lib64/python3.9/site-packages/circlemap/circle_map.py", line 1165, in main run = circle_map() File "/home/davide/circlemap-env/lib64/python3.9/site-packages/circlemap/circle_map.py", line 187, in init output = merge_final_output(self.args.sbam, self.args.output, begin, self.args.split, File "/home/davide/circlemap-env/lib64/python3.9/site-packages/circlemap/utils.py", line 1266, in merge_final_output second_merging_round = unparsed_pd.sort_values(['chrom', 'start', 'end']).reset_index() File "/home/davide/circlemap-env/lib64/python3.9/site-packages/pandas/core/frame.py", line 7194, in sort_values keys = [self._get_label_or_level_values(x, axis=axis) for x in by] File "/home/davide/circlemap-env/lib64/python3.9/site-packages/pandas/core/frame.py", line 7194, in keys = [self._get_label_or_level_values(x, axis=axis) for x in by] File "/home/davide/circlemap-env/lib64/python3.9/site-packages/pandas/core/generic.py", line 1914, in _get_label_or_level_values raise KeyError(key) KeyError: 'chrom'

biopython 1.77 Circle-Map 1.1.5 edlib 1.3.9.post1 llvmlite 0.43.0 numba 0.60.0 numpy 2.0.2 pandas 2.3.3 pip 25.3 pybedtools 0.12.0 pysam 0.23.3 python-dateutil 2.9.0.post0 pytz 2025.2 scipy 1.13.1 setuptools 53.0.0 six 1.17.0 tqdm 4.67.1 tzdata 2025.2

[iprada]

Hi,

I do suspect this is a pandas version error. I unfortunately have no idea how to fix it and I have been away from the code for too long. I wonder what happens if you use the versions indicated in the setup.py (https://github.com/iprada/Circle-Map/blob/master/setup.py). I never saw this problem myself.

I am sorry I cannot be very helpful here.

best,

Inigo