theopoliss
commented
8 months ago It looks like there is a difference between the number of columns in the actual data of one of your GWAS summary statistic files versus the number of columns in the expected format. There may be extra columns or separators in line 2771 of one of your files that do not match the header line.
Dear all,
I am an absolute beginner in python as well as conducting analyses with SUPERGNOVA and have heavy problems to solve the following error.
SUPERGNOVA % python3 supergnova.py ./data/sumstats/Inter.txt ./data/sumstats/AccPA.txt \ --N1 102837 \ --N2 91084 \ --bfile data/bfiles/eur_chr@_SNPmaf5 \ --partition data/partition/eur_chr@.bed \ --out results.txt
Preparing files for analysis... Traceback (most recent call last): File "/Users//SUPERGNOVA/supergnova.py", line 93, in
pipeline(parser.parse_args())
File "/Users/ /SUPERGNOVA/supergnova.py", line 54, in pipeline
gwas_snps, bed, N1, N2 = prep(args.bfile, args.partition, args.sumstats1, args.sumstats2, args.N1, args.N2)
File "/Users//SUPERGNOVA/prep.py", line 65, in prep
dfs = [pd.read_csv(file, delim_whitespace=True)
File "/Users//SUPERGNOVA/prep.py", line 65, in
dfs = [pd.read_csv(file, delim_whitespace=True)
File "/Users//anaconda3/lib/python3.10/site-packages/pandas/util/_decorators.py", line 211, in wrapper
return func(args, kwargs)
File "/Users//anaconda3/lib/python3.10/site-packages/pandas/util/_decorators.py", line 331, in wrapper
return func(args, kwargs)
File "/Users//anaconda3/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv
return _read(filepath_or_buffer, kwds)
File "/Users//anaconda3/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 611, in _read
return parser.read(nrows)
File "/Users//anaconda3/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1778, in read
) = self._engine.read( # type: ignore[attr-defined]
File "/Users//anaconda3/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 230, in read
chunks = self._reader.read_low_memory(nrows)
File "pandas/_libs/parsers.pyx", line 808, in pandas._libs.parsers.TextReader.read_low_memory
File "pandas/_libs/parsers.pyx", line 866, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 852, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 1973, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 21 fields in line 2771, saw 28
Has someone any idea to solve this error? Thanks in advance for your help.