Dear Skyline

I have an issue with a skyline document failing to re-integrate peaks and attribute q-values following successful model training.

The re-integration progress bar completes and then I get the error below. All other aspects of the document seem fine. I have tried closing skyline re-starting the PC and opening again with out solving the problem. A lot of work has gone into getting the analysis at this point and I would rather fix this issue than start again.

Is there any advise you can offer on how to fix the problem?


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Skyline
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Failed attempting to reintegrate peaks.
The index 6 must be between 0 and 3
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OK More Info
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System.Reflection.TargetInvocationException: The index 6 must be between 0 and 3 ---> System.Reflection.TargetInvocationException: The index 6 must be between 0 and 3 ---> System.IndexOutOfRangeException: The index 6 must be between 0 and 3
   at pwiz.Skyline.Model.Results.ChromatogramInfo.GetPeak(Int32 peakIndex) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Model\Results\ChromHeaderInfo.cs:line 2508
   at pwiz.Skyline.Model.TransitionGroupDocNode.UpdateResults(SrmSettings settingsNew, SrmSettingsDiff diff, PeptideDocNode nodePep, TransitionGroupDocNode nodePrevious) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Model\TransitionGroupDocNode.cs:line 1361
   at pwiz.Skyline.Model.TransitionGroupDocNode.ChangeSettings(SrmSettings settingsNew, PeptideDocNode nodePep, ExplicitMods mods, SrmSettingsDiff diff) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Model\TransitionGroupDocNode.cs:line 1018
   at pwiz.Skyline.Model.PeptideDocNode.ChangeSettings(SrmSettings settingsNew, SrmSettingsDiff diff, Boolean recurse) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Model\PeptideDocNode.cs:line 903
   at pwiz.Skyline.Model.SrmDocument.<>c__DisplayClass134_5.<ChangeSettingsInternal>b__7(Int32 i) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1057
   at pwiz.Skyline.Util.ParallelEx.<>c__DisplayClass4_0.<For>b__0(Int32 i) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Util\Util.cs:line 2040
   at pwiz.Skyline.Util.ParallelEx.<>c__DisplayClass4_0.<For>b__2(IntHolder h, Int32 i) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Util\Util.cs:line 2044
   at pwiz.Common.SystemUtil.ProducerConsumerWorker`2.Consume(Object threadIndex) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Shared\Common\SystemUtil\ProducerConsumerWorker.cs:line 184
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Util\Util.cs:line 1854
   at pwiz.Skyline.Util.ParallelEx.LoopWithExceptionHandling(Action loop, Action`1 catchClause) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Util\Util.cs:line 2114
   at pwiz.Skyline.Util.ParallelEx.For(Int32 fromInclusive, Int32 toExclusive, Action`1 body, Action`1 catchClause, Nullable`1 maxThreads) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Util\Util.cs:line 2042
   at pwiz.Skyline.Model.SrmDocument.ChangeSettingsInternal(SrmSettings settingsNew, SrmSettingsChangeMonitor progressMonitor) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1045
   at pwiz.Skyline.Model.SrmDocument.ChangeSettings(SrmSettings settingsNew, SrmSettingsChangeMonitor progressMonitor) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Model\SrmDocument.cs:line 911
   at pwiz.Skyline.Model.MProphetResultsHandler.ChangePeaks(IProgressMonitor progressMonitor) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Model\MProphetResultsHandler.cs:line 180
   at pwiz.Skyline.EditUI.ReintegrateDlg.<>c__DisplayClass12_1.<OkDialog>b__1(IProgressMonitor pm) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\EditUI\ReintegrateDlg.cs:line 133
   at pwiz.Skyline.Util.ProgressWaitBroker.PerformWork(ILongWaitBroker broker) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Util\UtilUI.cs:line 123
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 232
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Util\Util.cs:line 1854
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 180
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 132
   at pwiz.Skyline.EditUI.ReintegrateDlg.OkDialog() in C:\Users\nicksh\git\skyline_42_installer\pwiz_tools\Skyline\EditUI\ReintegrateDlg.cs:line 126
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