Hello, I created a genome scale model using carveme and then tried to run the MassChargeCuration function of MCC. It looks to have worked because I can generate a visual report, but at every gather id for metabolite step I also get this error message:
Gathering ids for metabolites: 93%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 947/1020 [20:36<01:12, 1.01it/s]ERROR:root:Error searching for identifier in biocyc: Traceback (most recent call last): File "MCC/DataCollection/DataCollection.py", line 243, in get_ids if (not (found := self.interfaces[db_identifier].search_identifier(names, DB_ids)) is None) and (len(found) > 0): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "MCC/DataCollection/Requests/BioCyc.py", line 86, in search_identifier df = pd.read_csv(StringIO(response.text), sep = "\t") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "pandas/io/parsers/readers.py", line 1026, in read_csv return _read(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "pandas/io/parsers/readers.py", line 626, in _read return parser.read(nrows) ^^^^^^^^^^^^^^^^^^ File "micom/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1923, in read ) = self._engine.read( # type: ignore[attr-defined] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "micom/lib/python3.11/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read chunks = self._reader.read_low_memory(nrows) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "parsers.pyx", line 838, in pandas._libs.parsers.TextReader.read_low_memory File "parsers.pyx", line 905, in pandas._libs.parsers.TextReader._read_rows File "parsers.pyx", line 874, in pandas._libs.parsers.TextReader._tokenize_rows File "parsers.pyx", line 891, in pandas._libs.parsers.TextReader._check_tokenize_status File "parsers.pyx", line 2061, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields in line 128, saw 2
Not sure if this is actually resulting in a bug or not.
Hello, I created a genome scale model using carveme and then tried to run the MassChargeCuration function of MCC. It looks to have worked because I can generate a visual report, but at every gather id for metabolite step I also get this error message:
Gathering ids for metabolites: 93%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ | 947/1020 [20:36<01:12, 1.01it/s]ERROR:root:Error searching for identifier in biocyc: Traceback (most recent call last): File "MCC/DataCollection/DataCollection.py", line 243, in get_ids if (not (found := self.interfaces[db_identifier].search_identifier(names, DB_ids)) is None) and (len(found) > 0): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "MCC/DataCollection/Requests/BioCyc.py", line 86, in search_identifier df = pd.read_csv(StringIO(response.text), sep = "\t") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "pandas/io/parsers/readers.py", line 1026, in read_csv return _read(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "pandas/io/parsers/readers.py", line 626, in _read return parser.read(nrows) ^^^^^^^^^^^^^^^^^^ File "micom/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1923, in read ) = self._engine.read( # type: ignore[attr-defined] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "micom/lib/python3.11/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read chunks = self._reader.read_low_memory(nrows) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "parsers.pyx", line 838, in pandas._libs.parsers.TextReader.read_low_memory File "parsers.pyx", line 905, in pandas._libs.parsers.TextReader._read_rows File "parsers.pyx", line 874, in pandas._libs.parsers.TextReader._tokenize_rows File "parsers.pyx", line 891, in pandas._libs.parsers.TextReader._check_tokenize_status File "parsers.pyx", line 2061, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields in line 128, saw 2Not sure if this is actually resulting in a bug or not.