{"action":"created","issue":{"url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/issues/1239","repository_url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus","labels_url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/issues/1239/labels{/name}","comments_url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/issues/1239/comments","events_url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/issues/1239/events","html_url":"https://github.com/smith-chem-wisc/MetaMorpheus/issues/1239","id":336289172,"node_id":"MDU6SXNzdWUzMzYyODkxNzI=","number":1239,"title":"Agilent .d Crash (precursorSpectrum.Size == 0)","user":{"login":"rmillikin","id":24705713,"node_id":"MDQ6VXNlcjI0NzA1NzEz","avatar_url":"https://avatars3.githubusercontent.com/u/24705713?v=4","gravatar_id":"","url":"https://api.github.com/users/rmillikin","html_url":"https://github.com/rmillikin","followers_url":"https://api.github.com/users/rmillikin/followers","following_url":"https://api.github.com/users/rmillikin/following{/other_user}","gists_url":"https://api.github.com/users/rmillikin/gists{/gist_id}","starred_url":"https://api.github.com/users/rmillikin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rmillikin/subscriptions","organizations_url":"https://api.github.com/users/rmillikin/orgs","repos_url":"https://api.github.com/users/rmillikin/repos","events_url":"https://api.github.com/users/rmillikin/events{/privacy}","received_events_url":"https://api.github.com/users/rmillikin/received_events","type":"User","site_admin":false},"labels":[{"id":659928031,"node_id":"MDU6TGFiZWw2NTk5MjgwMzE=","url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/labels/Crash","name":"Crash","color":"b60205","default":false}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-06-27T15:53:54Z","updated_at":"2018-06-28T19:07:01Z","closed_at":"2018-06-28T19:07:01Z","author_association":"CONTRIBUTOR","body":"A user has reported a crash with the following error message when converting an Agilent .d file in MSConvert to centroid mzML and running through MetaMorpheus:\r\n\r\n```\r\nCould not refine selected m/z and intensity because precursorSpectrum.Size == 0 \r\nSystem.Collections.ListDictionaryInternal \r\n   at MassSpectrometry.MsDataScan.RefineSelectedMzAndIntensity(MzSpectrum precursorSpectrum) \r\n   at TaskLayer.MetaMorpheusTask.<GetMs2Scans>d__42.MoveNext() in C:\\projects\\metamorpheus\\TaskLayer\\MetaMorpheusTask.cs:line 123\r\n   at System.Linq.Buffer`1..ctor(IEnumerable`1 source) \r\n   at System.Linq.OrderedEnumerable`1.<GetEnumerator>d__1.MoveNext() \r\n   at System.Linq.Buffer`1..ctor(IEnumerable`1 source) \r\n   at System.Linq.Enumerable.ToArray[TSource](IEnumerable`1 source) \r\n   at TaskLayer.CalibrationTask.GetDataAcquisitionResults(MsDataFile myMsDataFile, String currentDataFile, List`1 variableModifications, List`1 fixedModifications, List`1 proteinList, String taskId, CommonParameters combinedParameters, Tolerance initPrecTol, Tolerance initProdTol) in C:\\projects\\metamorpheus\\TaskLayer\\CalibrationTask\\CalibrationTask.cs:line 317\r\n   at TaskLayer.CalibrationTask.RunSpecific(String OutputFolder, List`1 dbFilenameList, List`1 currentRawFileList, String taskId, FileSpecificParameters[] fileSettingsList) in C:\\projects\\metamorpheus\\TaskLayer\\CalibrationTask\\CalibrationTask.cs:line 122\r\n   at TaskLayer.MetaMorpheusTask.RunTask(String output_folder, List`1 currentProteinDbFilenameList, List`1 currentRawDataFilepathList, String displayName) in C:\\projects\\metamorpheus\\TaskLayer\\MetaMorpheusTask.cs:line 258\r\n   at TaskLayer.EverythingRunnerEngine.Run() in C:\\projects\\metamorpheus\\TaskLayer\\EverythingRunnerEngine.cs:line 97 \r\n   at System.Threading.Tasks.Task.Execute() \r\nMassSpectrometry \r\n```\r\n\r\nI'm guessing that the precursor scan has no peaks, and MM crashes trying to deconvolute the isolation window. Or at least the isolation window has no peaks in it. Or the isolation window is messed up in the mzML."},"comment":{"url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/issues/comments/401141091","html_url":"https://github.com/smith-chem-wisc/MetaMorpheus/issues/1239#issuecomment-401141091","issue_url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/issues/1239","id":401141091,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMTE0MTA5MQ==","user":{"login":"rmillikin","id":24705713,"node_id":"MDQ6VXNlcjI0NzA1NzEz","avatar_url":"https://avatars3.githubusercontent.com/u/24705713?v=4","gravatar_id":"","url":"https://api.github.com/users/rmillikin","html_url":"https://github.com/rmillikin","followers_url":"https://api.github.com/users/rmillikin/followers","following_url":"https://api.github.com/users/rmillikin/following{/other_user}","gists_url":"https://api.github.com/users/rmillikin/gists{/gist_id}","starred_url":"https://api.github.com/users/rmillikin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rmillikin/subscriptions","organizations_url":"https://api.github.com/users/rmillikin/orgs","repos_url":"https://api.github.com/users/rmillikin/repos","events_url":"https://api.github.com/users/rmillikin/events{/privacy}","received_events_url":"https://api.github.com/users/rmillikin/received_events","type":"User","site_admin":false},"created_at":"2018-06-28T19:07:01Z","updated_at":"2018-06-28T19:07:01Z","author_association":"CONTRIBUTOR","body":"crash likely fixed in #1243 with appropriate error message. unable to test directly because of data confidentiality. will reopen this issue if it ends up not being a valid fix."}}
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