[BUG]ValueError: Number of passed names did not match number of header fields in the file A clear and concise description of what the bug is.
Damianyangyang opened this issue · 1 comments
Describe the bug
merge_metaphlan_tables.py *_abundance_metagenome.txt > output/merged_abundance_table.txt
Traceback (most recent call last):
File "/home/bioinfo/sunyy/.conda/envs/mpa4/bin/merge_metaphlan_tables.py", line 8, in
sys.exit(main())
File "/home/bioinfo/sunyy/.conda/envs/mpa4/lib/python3.7/site-packages/metaphlan/utils/merge_metaphlan_tables.py", line 73, in main
merge(args.aistms, open(args.o, 'w') if args.o else sys.stdout, args.gtdb_profiles)
File "/home/bioinfo/sunyy/.conda/envs/mpa4/lib/python3.7/site-packages/metaphlan/utils/merge_metaphlan_tables.py", line 35, in merge
iIn = pd.read_csv(f, sep='\t', skiprows=len(headers), names=names, usecols=[0,2] if not gtdb else range(2), index_col=0)
File "/home/bioinfo/sunyy/.local/lib/python3.7/site-packages/pandas/util/_decorators.py", line 311, in wrapper
return func(*args, **kwargs)
File "/home/bioinfo/sunyy/.local/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/bioinfo/sunyy/.local/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 482, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/home/bioinfo/sunyy/.local/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 811, in init
self._engine = self._make_engine(self.engine)
File "/home/bioinfo/sunyy/.local/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 1040, in _make_engine
return mapping[engine](self.f, **self.options) # type: ignore[call-arg]
File "/home/bioinfo/sunyy/.local/lib/python3.7/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 69, in init
self._reader = parsers.TextReader(self.handles.handle, **kwds)
File "pandas/_libs/parsers.pyx", line 542, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 770, in pandas._libs.parsers.TextReader._get_header
ValueError: Number of passed names did not match number of header fields in the file
Platform (please complete the following information):
- metaphlan4
Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.