When I run MAPS "run_pipeline_example.sh", it always throws error when processing chr13. I double checked my bed file and I didn't find anything wrong with chr13. Here is the error message.
Traceback (most recent call last):
File "/mnt/tscc/huh025/MAPS/MAPS/bin/MAPS/MAPS.py", line 236, in
main()
File "/mnt/tscc/huh025/MAPS/MAPS/bin/MAPS/MAPS.py", line 233, in main
init(p)
File "/mnt/tscc/huh025/MAPS/MAPS/bin/MAPS/MAPS.py", line 120, in init
ps_short = pd.read_csv(parse_fname(CHR, 'short', params),header=None,sep='\t')
File "/mnt/silencer2/home/huh025/anaconda2/envs/py3/lib/python3.7/site-packages/pandas/io/parsers.py", line 685, in parser_f
return _read(filepath_or_buffer, kwds)
File "/mnt/silencer2/home/huh025/anaconda2/envs/py3/lib/python3.7/site-packages/pandas/io/parsers.py", line 457, in _read
parser = TextFileReader(fp_or_buf, kwds)
File "/mnt/silencer2/home/huh025/anaconda2/envs/py3/lib/python3.7/site-packages/pandas/io/parsers.py", line 895, in init
self._make_engine(self.engine)
File "/mnt/silencer2/home/huh025/anaconda2/envs/py3/lib/python3.7/site-packages/pandas/io/parsers.py", line 1135, in _make_engine
self._engine = CParserWrapper(self.f, self.options)
File "/mnt/silencer2/home/huh025/anaconda2/envs/py3/lib/python3.7/site-packages/pandas/io/parsers.py", line 1917, 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
-- handling MACS2 peaks -- handling short.bed
Hi,
When I run MAPS "run_pipeline_example.sh", it always throws error when processing chr13. I double checked my bed file and I didn't find anything wrong with chr13. Here is the error message.
Traceback (most recent call last): File "/mnt/tscc/huh025/MAPS/MAPS/bin/MAPS/MAPS.py", line 236, in
main()
File "/mnt/tscc/huh025/MAPS/MAPS/bin/MAPS/MAPS.py", line 233, in main
init(p)
File "/mnt/tscc/huh025/MAPS/MAPS/bin/MAPS/MAPS.py", line 120, in init
ps_short = pd.read_csv(parse_fname(CHR, 'short', params),header=None,sep='\t')
File "/mnt/silencer2/home/huh025/anaconda2/envs/py3/lib/python3.7/site-packages/pandas/io/parsers.py", line 685, in parser_f
return _read(filepath_or_buffer, kwds)
File "/mnt/silencer2/home/huh025/anaconda2/envs/py3/lib/python3.7/site-packages/pandas/io/parsers.py", line 457, in _read
parser = TextFileReader(fp_or_buf, kwds)
File "/mnt/silencer2/home/huh025/anaconda2/envs/py3/lib/python3.7/site-packages/pandas/io/parsers.py", line 895, in init
self._make_engine(self.engine)
File "/mnt/silencer2/home/huh025/anaconda2/envs/py3/lib/python3.7/site-packages/pandas/io/parsers.py", line 1135, in _make_engine
self._engine = CParserWrapper(self.f, self.options)
File "/mnt/silencer2/home/huh025/anaconda2/envs/py3/lib/python3.7/site-packages/pandas/io/parsers.py", line 1917, 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