Sudden problem running script - likely problem updating AMRfinder database?
Hi,
So script worked perfectly a few weeks ago, but now it wont run, see error messages below:
Traceback (most recent call last):
File "/home/ngs/diphtoscan/__main__.py", line 321, in <module>
update_database(args,MLST_db,TOX_db)
File "/home/ngs/diphtoscan/module/updating_database.py", line 57, in update_database
complete_missing_classification(arguments.path + '/data/resistance/' + date + '/fam.tab')
File "/home/ngs/diphtoscan/module/updating_database.py", line 30, in complete_missing_classification
df = pd.read_csv(path, sep="\t", escapechar="\\", engine="python")
File "/home/ngs/.local/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/ngs/.local/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 626, in _read
return parser.read(nrows)
File "/home/ngs/.local/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1923, in read
) = self._engine.read( # type: ignore[attr-defined]
File "/home/ngs/.local/lib/python3.10/site-packages/pandas/io/parsers/python_parser.py", line 288, in read
alldata = self._rows_to_cols(content)
File "/home/ngs/.local/lib/python3.10/site-packages/pandas/io/parsers/python_parser.py", line 1063, in _rows_to_cols
self._alert_malformed(msg, row_num + 1)
File "/home/ngs/.local/lib/python3.10/site-packages/pandas/io/parsers/python_parser.py", line 781, in _alert_malformed
raise ParserError(msg)
pandas.errors.ParserError: Expected 18 fields in line 119, saw 35