Epinano delta: pandas.errors.EmptyDataError: No columns to parse from file

[kwonej0617]

Hi. Thank you for developing a useful tool. I have run Epinano delta with public data (HEK293T) and I got the following error. Could you please help me fix it?

Traceback (most recent call last):
  File "/usr/local/bin/EpiNano/misc/Epinano_make_delta.py", line 46, in <module>
    with open (mod,'r') as fh:
FileNotFoundError: [Errno 2] No such file or directory: 'data/output/Epinano/HEK293T-rep1/wt.plus_strand.per.site.5mer.csv'
Traceback (most recent call last):
  File "/usr/local/bin/EpiNano/Epinano_Predict.py", line 97, in <module>
    predict_df = pd.read_csv (args['predict'],compression='gzip') if args['predict'].endswith ('.gz') else pd.read_csv (args['predict'])
  File "/usr/local/lib/python3.6/site-packages/pandas/io/parsers.py", line 702, in parser_f
    return _read(filepath_or_buffer, kwds)
  File "/usr/local/lib/python3.6/site-packages/pandas/io/parsers.py", line 429, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/usr/local/lib/python3.6/site-packages/pandas/io/parsers.py", line 895, in __init__
    self._make_engine(self.engine)
  File "/usr/local/lib/python3.6/site-packages/pandas/io/parsers.py", line 1122, in _make_engine
    self._engine = CParserWrapper(self.f, **self.options)
  File "/usr/local/lib/python3.6/site-packages/pandas/io/parsers.py", line 1853, in __init__
    self._reader = parsers.TextReader(src, **kwds)
  File "pandas/_libs/parsers.pyx", line 545, in pandas._libs.parsers.TextReader.__cinit__
pandas.errors.EmptyDataError: No columns to parse from file

The file that causes FileNotFoundError: [Errno 2] above, data/output/Epinano/HEK293T-rep1/wt.plus_strand.per.site.5mer.csv exists in the path. So I am not sure why I got the error.

(base) [ejkwon@hpcc04 ]$ ls data/output/Epinano/HEK293T-rep1/wt.plus_strand.per.site.5mer.csv
data/output/Epinano/HEK293T-rep1/wt.plus_strand.per.site.5mer.csv

Also, here is the command line I run.

#make delta features
singularity exec /share/pkg/containers/epinano/epinano_1.2.1.sif python3 /usr/local/bin/EpiNano/misc/Epinano_make_delta.py Epinano/HEK293T-rep/wt.plus_strand.per.site.5mer.csv Epinano/HEK293T-rep/ko.plus_strand.per.site.5mer.csv 5 5 > wt_ko_delta.5mer.csv

Could you please help me fix the error? Thank you so much for your help.