KeyError: 'chrom' during final output merging step #112
Description
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