{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/oncotator/issues/321","labels_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/321/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/321/comments","events_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/321/events","html_url":"https://github.com/broadinstitute/oncotator/issues/321","id":87430697,"number":321,"title":"Oncotator : IndexError exception in the middle of the script","user":{"login":"vigneshravi","id":8239398,"avatar_url":"https://avatars.githubusercontent.com/u/8239398?v=3","gravatar_id":"","url":"https://api.github.com/users/vigneshravi","html_url":"https://github.com/vigneshravi","followers_url":"https://api.github.com/users/vigneshravi/followers","following_url":"https://api.github.com/users/vigneshravi/following{/other_user}","gists_url":"https://api.github.com/users/vigneshravi/gists{/gist_id}","starred_url":"https://api.github.com/users/vigneshravi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vigneshravi/subscriptions","organizations_url":"https://api.github.com/users/vigneshravi/orgs","repos_url":"https://api.github.com/users/vigneshravi/repos","events_url":"https://api.github.com/users/vigneshravi/events{/privacy}","received_events_url":"https://api.github.com/users/vigneshravi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2015-06-11T17:56:51Z","updated_at":"2015-06-19T16:59:24Z","closed_at":null,"body":"I ran oncotator on a HC called VCF using the command\r\n\r\noncotator -i VCF -o VCF --db-dir /path_to/ngstools/oncotator_v1_ds_Jan262014/ Project_bwa_GatkHC.vcf Project_bwa_GatkHC_oncotator.vcf hg19\r\n\r\nThe script ran for about 214000 mutations and threw an exception. Pasting the error below. Can someone help me understand this error?\r\n\r\n2015-06-11 13:11:58,655 INFO [oncotator.output.OutputDataManager:194] Wrote 214000 mutations to tsv.\r\n\r\nTraceback (most recent call last):\r\n  File \"/home/Pythonmodules/bin/oncotator\", line 9, in <module>\r\n    load_entry_point('Oncotator==v1.5.1.0', 'console_scripts', 'oncotator')()\r\n  File \"/home/Pythonmodules/lib/python2.7/site-packages/Oncotator-v1.5.1.0-py2.7.egg/oncotator/Oncotator.py\", line 292, in main\r\n    annotator.annotate()\r\n  File \"/home/Pythonmodules/lib/python2.7/site-packages/Oncotator-v1.5.1.0-py2.7.egg/oncotator/Annotator.py\", line 403, in annotate\r\n    filename = self._outputRenderer.renderMutations(mutations, metadata=metadata, comments=comments)\r\n  File \"/home/Pythonmodules/lib/python2.7/site-packages/Oncotator-v1.5.1.0-py2.7.egg/oncotator/output/VcfOutputRenderer.py\", line 118, in renderMutations\r\n    dataManager = OutputDataManager(self.configTable, mutations, comments, metadata, path)\r\n  File \"/home/Pythonmodules/lib/python2.7/site-packages/Oncotator-v1.5.1.0-py2.7.egg/oncotator/output/OutputDataManager.py\", line 92, in __init__\r\n    self.chroms, self.sampleNames, self.filename = self._writeMuts2Tsv(self.mutations, path)\r\n  File \"/home/Pythonmodules/lib/python2.7/site-packages/Oncotator-v1.5.1.0-py2.7.egg/oncotator/output/OutputDataManager.py\", line 160, in _writeMuts2Tsv\r\n    for mut in muts:\r\n  File \"/home/Pythonmodules/lib/python2.7/site-packages/Oncotator-v1.5.1.0-py2.7.egg/oncotator/Annotator.py\", line 414, in _applyManualAnnotations\r\n    for m in mutations:\r\n  File \"/home/Pythonmodules/lib/python2.7/site-packages/Oncotator-v1.5.1.0-py2.7.egg/oncotator/Annotator.py\", line 422, in _applyDefaultAnnotations\r\n    for m in mutations:\r\n  File \"/home/Pythonmodules/lib/python2.7/site-packages/Oncotator-v1.5.1.0-py2.7.egg/oncotator/Annotator.py\", line 470, in _annotate_mutations_using_datasources\r\n    for m in mutations:\r\n  File \"/home/Pythonmodules/lib/python2.7/site-packages/Oncotator-v1.5.1.0-py2.7.egg/oncotator/input/VcfInputMutationCreator.py\", line 306, in createMutations\r\n    sampleMut = self._addGenotypeData2Mutation(sampleMut, record, index)\r\n  File \"/home/Pythonmodules/lib/python2.7/site-packages/Oncotator-v1.5.1.0-py2.7.egg/oncotator/input/VcfInputMutationCreator.py\", line 130, in _addGenotypeData2Mutation\r\n    val = genotypeData[ID][index]\r\nIndexError: list index out of range"},"comment":{"url":"https://api.github.com/repos/broadinstitute/oncotator/issues/comments/113575998","html_url":"https://github.com/broadinstitute/oncotator/issues/321#issuecomment-113575998","issue_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/321","id":113575998,"user":{"login":"vigneshravi","id":8239398,"avatar_url":"https://avatars.githubusercontent.com/u/8239398?v=3","gravatar_id":"","url":"https://api.github.com/users/vigneshravi","html_url":"https://github.com/vigneshravi","followers_url":"https://api.github.com/users/vigneshravi/followers","following_url":"https://api.github.com/users/vigneshravi/following{/other_user}","gists_url":"https://api.github.com/users/vigneshravi/gists{/gist_id}","starred_url":"https://api.github.com/users/vigneshravi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vigneshravi/subscriptions","organizations_url":"https://api.github.com/users/vigneshravi/orgs","repos_url":"https://api.github.com/users/vigneshravi/repos","events_url":"https://api.github.com/users/vigneshravi/events{/privacy}","received_events_url":"https://api.github.com/users/vigneshravi/received_events","type":"User","site_admin":false},"created_at":"2015-06-19T16:59:24Z","updated_at":"2015-06-19T16:59:24Z","body":"I think I found it!"}}