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Published 20 hours ago • verified publisher icon arq5x

Error while loading VCF

Open kpalanikannan opened this issue 7 years ago • 1 comments

Hi,

Can any one help to track the issue with the error below?

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Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init fields[5] = l.get(fields[5].lower(), fields[5]) self._prepare_samples() IndexError File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples : list index out of range self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_load_chunk.load(parser, args) args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init gemini_loader = GeminiLoader(args) gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn fields[5] = l.get(fields[5].lower(), fields[5]) IndexError : fields[5] = l.get(fields[5].lower(), fields[5]) list index out of rangeIndexError: list index out of range

self._prepare_samples()

File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_load_chunk.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init self._prepare_samples() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples self.ped_hash = load_ped_file(self.args.ped_file) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 36, in load_ped_file fields = _fix_ped_affected(fields) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 48, in _fix_ped_affected fields[5] = l.get(fields[5].lower(), fields[5]) IndexError: list index out of range Traceback (most recent call last): File "/home/palani.k/bin/gemini", line 7, in gemini_main.main() File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 204, in load_fn gemini_load.load(parser, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 49, in load load_multicore(args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 93, in load_multicore chunks = load_chunks_multicore(grabix_file, args) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 264, in load_chunks_multicore wait_until_finished(procs) File "/MGMSTAR1/SHARED/ANALYSIS/RESOURCES/Tools/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 359, in wait_until_finished raise ValueError("Processing failed on GEMINI chunk load") ValueError: Processing failed on GEMINI chunk load

kpalanikannan avatar Jul 04 '17 11:07 kpalanikannan

hi, does your ped file have 6 columns for all rows?

brentp avatar Jul 04 '17 13:07 brentp