FileNotFoundError: [Errno 2] No such file or directory: '/tmp/weirathe.ogeg0ayt/pathways.csv'

[nicolas-zimmermann]

Dear all, When I attempt to run the GSVA function GSVA.gsva(expression_df,geneset_df), I get the following error message

FileNotFoundError                         Traceback (most recent call last)
Cell In[5], line 1
----> 1 pathways_df = GSVA.gsva(expression_df,geneset_df)

File /usr/local/anaconda/anaconda3/envs/single_cell/lib/python3.11/site-packages/GSVA/__init__.py:103, in gsva(expression_df, geneset_df, method, kcdf, abs_ranking, min_sz, max_sz, parallel_sz, mx_diff, tau, ssgsea_norm, verbose, tempdir)
    101 sp = Popen(cmd,stdout=PIPE,stderr=destination)
    102 sp.communicate()
--> 103 output = pd.read_csv(os.path.join(tempdir,"pathways.csv"),index_col=0)
    104 output.index = output.index.astype(str)
    105 output.columns = output.columns.astype(str)

File /usr/local/anaconda/anaconda3/envs/single_cell/lib/python3.11/site-packages/pandas/util/_decorators.py:211, in deprecate_kwarg.<locals>._deprecate_kwarg.<locals>.wrapper(*args, **kwargs)
    209     else:
    210         kwargs[new_arg_name] = new_arg_value
--> 211 return func(*args, **kwargs)

File /usr/local/anaconda/anaconda3/envs/single_cell/lib/python3.11/site-packages/pandas/util/_decorators.py:331, in deprecate_nonkeyword_arguments.<locals>.decorate.<locals>.wrapper(*args, **kwargs)
    325 if len(args) > num_allow_args:
    326     warnings.warn(
    327         msg.format(arguments=_format_argument_list(allow_args)),
    328         FutureWarning,
    329         stacklevel=find_stack_level(),
    330     )
--> 331 return func(*args, **kwargs)

File /usr/local/anaconda/anaconda3/envs/single_cell/lib/python3.11/site-packages/pandas/io/parsers/readers.py:950, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, error_bad_lines, warn_bad_lines, on_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options)
    935 kwds_defaults = _refine_defaults_read(
    936     dialect,
    937     delimiter,
   (...)
    946     defaults={"delimiter": ","},
    947 )
    948 kwds.update(kwds_defaults)
--> 950 return _read(filepath_or_buffer, kwds)

File /usr/local/anaconda/anaconda3/envs/single_cell/lib/python3.11/site-packages/pandas/io/parsers/readers.py:605, in _read(filepath_or_buffer, kwds)
    602 _validate_names(kwds.get("names", None))
    604 # Create the parser.
--> 605 parser = TextFileReader(filepath_or_buffer, **kwds)
    607 if chunksize or iterator:
    608     return parser

File /usr/local/anaconda/anaconda3/envs/single_cell/lib/python3.11/site-packages/pandas/io/parsers/readers.py:1442, in TextFileReader.__init__(self, f, engine, **kwds)
   1439     self.options["has_index_names"] = kwds["has_index_names"]
   1441 self.handles: IOHandles | None = None
-> 1442 self._engine = self._make_engine(f, self.engine)

File /usr/local/anaconda/anaconda3/envs/single_cell/lib/python3.11/site-packages/pandas/io/parsers/readers.py:1735, in TextFileReader._make_engine(self, f, engine)
   1733     if "b" not in mode:
   1734         mode += "b"
-> 1735 self.handles = get_handle(
   1736     f,
   1737     mode,
   1738     encoding=self.options.get("encoding", None),
   1739     compression=self.options.get("compression", None),
   1740     memory_map=self.options.get("memory_map", False),
   1741     is_text=is_text,
   1742     errors=self.options.get("encoding_errors", "strict"),
   1743     storage_options=self.options.get("storage_options", None),
   1744 )
   1745 assert self.handles is not None
   1746 f = self.handles.handle

File /usr/local/anaconda/anaconda3/envs/single_cell/lib/python3.11/site-packages/pandas/io/common.py:856, in get_handle(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options)
    851 elif isinstance(handle, str):
    852     # Check whether the filename is to be opened in binary mode.
    853     # Binary mode does not support 'encoding' and 'newline'.
    854     if ioargs.encoding and "b" not in ioargs.mode:
    855         # Encoding
--> 856         handle = open(
    857             handle,
    858             ioargs.mode,
    859             encoding=ioargs.encoding,
    860             errors=errors,
    861             newline="",
    862         )
    863     else:
    864         # Binary mode
    865         handle = open(handle, ioargs.mode)

FileNotFoundError: [Errno 2] No such file or directory: '/tmp/weirathe.ogeg0ayt/pathways.csv'

I attempted removing the parallel_type variable in the file, as recommend in other issues thread but it doesn't seem to be working...

Any help or tips would be greatly appreciated

Best,