Issue 128: Topograph throws exceptions during search for replicates w/o MS2 IDs, and those replicates are not accessible

issues
Status:closed
Assigned To:Guest
Type:Defect
Area:Topograph
Priority:2
Milestone:1.2
Opened:2011-12-13 by Evvie Vincow
Changed:2017-10-18 by Brendan MacLean
Resolved:2017-10-18 by Brendan MacLean
Resolution:Won't Fix
Closed:2017-10-18 by Brendan MacLean
2011-12-13 Evvie Vincow
Title»Topograph throws exceptions during search for replicates w/o MS2 IDs, and those replicates are not accessible
Assigned To»nicksh@u.washington.edu
Type»Defect
Area»Topograph
Priority»2
Milestone»1.2
Topograph has been throwing a lot of exceptions lately in general. Today I tried to generate replicates without MS2 IDs for the October 17 PINK1 nulls workspace. I have pasted below a few of the exceptions thrown (they run for pages and pages, so let me know if you want them). Topograph appeared to complete the process of generating the additional values, as shown by the increase in chromatogram/result numbers in the Recalculate Results dialog and the end of activity in Running Jobs. However, many peptides were still displayed as having 1-23 files instead of 24. I closed the program, restarted it, and reopened the workspace. No change. I am now rerunning the process of generating the extra replicates, and hoping that this will render them visible.

12/13/2011 2:20:24 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.ProteowizardWrapper.MsDataFileImpl.ToArray(IList`1 list)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Spectrum spectrum)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex, Double[]& mzArray, Double[]& intensityArray)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()

12/12/2011 5:06:03 PM    Unhandled exception    System.FormatException: Input string was not in a correct format.
   at System.Number.StringToNumber(String str, NumberStyles options, NumberBuffer& number, NumberFormatInfo info, Boolean parseDecimal)
   at System.Number.ParseDouble(String value, NumberStyles options, NumberFormatInfo numfmt)
   at System.Double.Parse(String s, NumberStyles style, NumberFormatInfo info)
   at pwiz.Topograph.ui.Forms.ResultsPerGroupForm.btnRequery_Click(Object sender, EventArgs e)
   at System.Windows.Forms.Control.OnClick(EventArgs e)
   at System.Windows.Forms.Button.OnClick(EventArgs e)
   at System.Windows.Forms.Button.OnMouseUp(MouseEventArgs mevent)
   at System.Windows.Forms.Control.WmMouseUp(Message& m, MouseButtons button, Int32 clicks)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.ButtonBase.WndProc(Message& m)
   at System.Windows.Forms.Button.WndProc(Message& m)
   at System.Windows.Forms.Control.ControlNativeWindow.OnMessage(Message& m)
   at System.Windows.Forms.Control.ControlNativeWindow.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
12/13/2011 1:43:10 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.ProteowizardWrapper.MsDataFileImpl.ToArray(IList`1 list)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Spectrum spectrum)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex, Double[]& mzArray, Double[]& intensityArray)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:43:29 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.Topograph.Data.ArrayConverter.ToBytes[T](T[] array)
   at pwiz.Topograph.Data.DbMsDataFile.set_Times(Double[] value)
   at NHibernate.Proxy.DefaultLazyInitializer.Intercept(InvocationInfo info)
   at DbMsDataFileProxy.set_Times(Double[] )
   at pwiz.Topograph.Model.MsDataFileData.UpdateDbEntity(ISession session)
   at pwiz.Topograph.Model.EntityModel`1.Save(ISession session)
   at pwiz.Topograph.MsData.ChromatogramGenerator.SaveChromatograms(ChromatogramTask chromatogramTask, ICollection`1 analyses, Boolean finished)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:43:41 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.ProteowizardWrapper.MsDataFileImpl.ToArray(IList`1 list)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Spectrum spectrum)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex, Double[]& mzArray, Double[]& intensityArray)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:43:52 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at System.Collections.Generic.List`1.set_Capacity(Int32 value)
   at System.Collections.Generic.List`1.EnsureCapacity(Int32 min)
   at pwiz.ProteowizardWrapper.Centroider.GetCentroidedData(Double[]& centroidedMzs, Double[]& centroidedIntensities)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:44:32 PM        System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at System.Collections.ArrayList..ctor(Int32 capacity)
   at NHibernate.Util.IdentityMap.get_EntryList()
   at NHibernate.Util.IdentityMap.ConcurrentEntries(IDictionary map)
   at NHibernate.Event.Default.AbstractFlushingEventListener.PrepareEntityFlushes(IEventSource session)
   at NHibernate.Event.Default.AbstractFlushingEventListener.FlushEverythingToExecutions(FlushEvent event)
   at NHibernate.Event.Default.DefaultFlushEventListener.OnFlush(FlushEvent event)
   at NHibernate.Impl.SessionImpl.Flush()
   at NHibernate.Transaction.AdoTransaction.Commit()
   at pwiz.Topograph.ui.Forms.AnalyzePeptidesForm.DoCreateAnalyses(Char[] excludeAas, Int32 minTracerCount)
   at pwiz.Topograph.ui.Forms.AnalyzePeptidesForm.CreateAnalyses()
12/13/2011 1:44:34 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.ProteowizardWrapper.MsDataFileImpl.ToArray(IList`1 list)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Spectrum spectrum)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex, Double[]& mzArray, Double[]& intensityArray)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:44:51 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.ProteowizardWrapper.MsDataFileImpl.ToArray(IList`1 list)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Spectrum spectrum)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex, Double[]& mzArray, Double[]& intensityArray)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:45:01 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.ProteowizardWrapper.MsDataFileImpl.ToArray(IList`1 list)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Spectrum spectrum)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex, Double[]& mzArray, Double[]& intensityArray)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:45:24 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.ProteowizardWrapper.MsDataFileImpl.ToArray(IList`1 list)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Spectrum spectrum)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex, Double[]& mzArray, Double[]& intensityArray)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:45:41 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.ProteowizardWrapper.MsDataFileImpl.ToArray(IList`1 list)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Spectrum spectrum)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex, Double[]& mzArray, Double[]& intensityArray)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:46:02 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.ProteowizardWrapper.MsDataFileImpl.ToArray(IList`1 list)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Spectrum spectrum)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex, Double[]& mzArray, Double[]& intensityArray)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:46:23 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.ProteowizardWrapper.MsDataFileImpl.ToArray(IList`1 list)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Spectrum spectrum)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex, Double[]& mzArray, Double[]& intensityArray)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:46:37 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.ProteowizardWrapper.MsDataFileImpl.ToArray(IList`1 list)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Spectrum spectrum)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex, Double[]& mzArray, Double[]& intensityArray)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:46:56 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at System.Collections.Generic.List`1.set_Capacity(Int32 value)
   at System.Collections.Generic.List`1.EnsureCapacity(Int32 min)
   at pwiz.ProteowizardWrapper.Centroider.GetCentroidedData(Double[]& centroidedMzs, Double[]& centroidedIntensities)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()
12/13/2011 1:47:13 PM    Exception generating chromatograms    System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at pwiz.ProteowizardWrapper.MsDataFileImpl.ToArray(IList`1 list)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Spectrum spectrum)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 scanIndex, Double[]& mzArray, Double[]& intensityArray)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateChromatograms(ChromatogramTask chromatogramTask)
   at pwiz.Topograph.MsData.ChromatogramGenerator.GenerateSavedChromatograms()

2017-10-18 Brendan MacLean
resolve as Won't Fix
Statusopen»resolved
Assigned ToNick Shulman»Evvie Vincow
Not really maintaining Topograph any longer.

2017-10-18 Brendan MacLean
close
Statusresolved»closed
Assigned ToEvvie Vincow»Guest