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biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
31 stars 6 forks source link

IndexError: list index out of range #42

Closed mnrusimh closed 7 years ago

mnrusimh commented 7 years ago

I installed epic ver. 0.1.18 and no issues were reported. However, when I try running it on any dataset including the example dataset shipped with the software, I am getting the following error.

mnrusimh@bioserv:/nfs/analysis/epic$ epic --treatment test.bed --control control.bed

epic --treatment test.bed --control control.bed

epic --treatment test.bed --control control.bed # epic_version: 0.1.18, pandas_version: 0.12.0 (File: epic, Log level: INFO, Time: Tue, 04 Oct 2016 09:45:41 )

Traceback (most recent call last): File "/home/mnrusimh/Applications/epic/bin/epic", line 5, in pkg_resources.run_script('bioepic==0.1.18', 'epic') File "/nfs/bio/sw/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 505, in run_script self.require(requires)[0].run_script(script_name, ns) File "/nfs/bio/sw/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 1245, in run_script execfile(script_filename, namespace, namespace) File "/home/mnrusimh/Applications/epic/lib/python2.7/site-packages/bioepic-0.1.18-py2.7.egg/EGG-INFO/scripts/epic", line 193, in estimated_readlength = find_readlength(args) File "/home/mnrusimh/Applications/epic/lib/python2.7/site-packages/bioepic-0.1.18-py2.7.egg/epic/utils/find_readlength.py", line 36, in find_readlength names=["Start", "End"]) File "/nfs/bio/sw/lib/python2.7/site-packages/pandas-0.12.0-py2.7-linux-x86_64.egg/pandas/io/parsers.py", line 400, in parser_f return _read(filepath_or_buffer, kwds) File "/nfs/bio/sw/lib/python2.7/site-packages/pandas-0.12.0-py2.7-linux-x86_64.egg/pandas/io/parsers.py", line 205, in _read return parser.read() File "/nfs/bio/sw/lib/python2.7/site-packages/pandas-0.12.0-py2.7-linux-x86_64.egg/pandas/io/parsers.py", line 608, in read ret = self._engine.read(nrows) File "/nfs/bio/sw/lib/python2.7/site-packages/pandas-0.12.0-py2.7-linux-x86_64.egg/pandas/io/parsers.py", line 1028, in read data = self._reader.read(nrows) File "parser.pyx", line 706, in pandas.parser.TextReader.read (pandas/parser.c:6745) File "parser.pyx", line 728, in pandas.parser.TextReader._read_low_memory (pandas/parser.c:6964) File "parser.pyx", line 804, in pandas.parser.TextReader._read_rows (pandas/parser.c:7780) File "parser.pyx", line 865, in pandas.parser.TextReader._convert_column_data (pandas/parser.c:8512) File "parser.pyx", line 1105, in pandas.parser.TextReader._get_column_name (pandas/parser.c:11684) IndexError: list index out of range

endrebak commented 7 years ago

Your pandas version is ancient. I guess I should throw an error if it is too old. Thanks for reporting.

Fix it by running

pip install pandas==0.18.1

On Tuesday, October 4, 2016, Ram Podicheti notifications@github.com wrote:

I installed epic ver. 0.1.18 and no issues were reported. However, when I try running it on any dataset including the example dataset shipped with the software, I am getting the following error.

mnrusimh@bioserv:/nfs/analysis/epic$ epic --treatment test.bed --control control.bed

epic --treatment test.bed --control control.bed

epic --treatment test.bed --control control.bed # epic_version: 0.1.18,

pandas_version: 0.12.0 (File: epic, Log level: INFO, Time: Tue, 04 Oct 2016 09:45:41 ) Traceback (most recent call last): File "/home/mnrusimh/Applications/epic/bin/epic", line 5, in pkg_resources.run_script('bioepic==0.1.18', 'epic') File "/nfs/bio/sw/lib/python2.7/site-packages/distribute-0.6. 34-py2.7.egg/pkg_resources.py", line 505, in run_script self.require(requires)[0].run_script(script_name, ns) File "/nfs/bio/sw/lib/python2.7/site-packages/distribute-0.6. 34-py2.7.egg/pkg_resources.py", line 1245, in run_script execfile(script_filename, namespace, namespace) File "/home/mnrusimh/Applications/epic/lib/python2.7/site- packages/bioepic-0.1.18-py2.7.egg/EGG-INFO/scripts/epic", line 193, in estimated_readlength = find_readlength(args) File "/home/mnrusimh/Applications/epic/lib/python2.7/site- packages/bioepic-0.1.18-py2.7.egg/epic/utils/find_readlength.py", line 36, in find_readlength names=["Start", "End"]) File "/nfs/bio/sw/lib/python2.7/site-packages/pandas-0.12.0- py2.7-linux-x86_64.egg/pandas/io/parsers.py", line 400, in parser_f return _read(filepath_or_buffer, kwds) File "/nfs/bio/sw/lib/python2.7/site-packages/pandas-0.12.0- py2.7-linux-x86_64.egg/pandas/io/parsers.py", line 205, in _read return parser.read() File "/nfs/bio/sw/lib/python2.7/site-packages/pandas-0.12.0- py2.7-linux-x86_64.egg/pandas/io/parsers.py", line 608, in read ret = self._engine.read(nrows) File "/nfs/bio/sw/lib/python2.7/site-packages/pandas-0.12.0- py2.7-linux-x86_64.egg/pandas/io/parsers.py", line 1028, in read data = self._reader.read(nrows) File "parser.pyx", line 706, in pandas.parser.TextReader.read (pandas/parser.c:6745) File "parser.pyx", line 728, in pandas.parser.TextReader._read_low_memory (pandas/parser.c:6964) File "parser.pyx", line 804, in pandas.parser.TextReader._read_rows (pandas/parser.c:7780) File "parser.pyx", line 865, in pandas.parser.TextReader._convert_column_data (pandas/parser.c:8512) File "parser.pyx", line 1105, in pandas.parser.TextReader._get_column_name (pandas/parser.c:11684) IndexError: list index out of range

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