hicMergeLoops throws an error
portbo opened this issue · 1 comments
Conda version installed
hicInfo 3.7.dev, python = 3.8
Command:
hicMergeLoops -i inter_30_1kb_corrected.cool inter_30_5kb_corrected.cool nter_30_25kb_corrected.cool -o merged_results.bedgrap
h -r 25000
error:
DEBUG:h5py._conv:Creating converter from 7 to 5
DEBUG:h5py._conv:Creating converter from 5 to 7
DEBUG:h5py._conv:Creating converter from 7 to 5
DEBUG:h5py._conv:Creating converter from 5 to 7
Traceback (most recent call last):
File "/conda_data/envs/hicexplorer/bin/hicMergeLoops", line 7, in
main()
File "/.local/lib/python3.8/site-packages/hicexplorer/hicMergeLoops.py", line 157, in main
dataframe = readFile(file)
File "/home/.local/lib/python3.8/site-packages/hicexplorer/hicMergeLoops.py", line 142, in readFile
return pd.read_csv(pFile, sep='\t', header=None)
File "/conda_data/envs/hicexplorer/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
return _read(filepath_or_buffer, kwds)
File "/conda_data/envs/hicexplorer/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 577, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/conda_data/envs/hicexplorer/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1407, in init
self._engine = self._make_engine(f, self.engine)
File "/conda_data/envs/hicexplorer/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1679, in _make_engine
return mapping[engine](f, **self.options)
File "/conda_data/envs/hicexplorer/lib/python3.8/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 550, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 758, in pandas._libs.parsers.TextReader._get_header
File "pandas/_libs/parsers.pyx", line 850, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._check_tokenize_status
File "pandas/_libs/parsers.pyx", line 2021, in pandas._libs.parsers.raise_parser_error
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte
Oops, tried to merge cool files instead of bedgraph files. Sorted now.