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Topic: MS-DIAL V5.1.23 : crashes after adding a .msp/.txt file for identification (Read 4397 times) previous topic - next topic

MS-DIAL V5.1.23 : crashes after adding a .msp/.txt file for identification

Hi,

I have a SWATH-MS/MS metabolomics dataset processed with v4.9 and I want to compare the results with v5.1.23. When I try to process the data with MS-DIAL 5 the software crashes before doing anything after clicking "Run". I figured out that it was because of the "Identification" module. If I don't use it, the software works properly: I effectively end up with aligned spot and etc. But I can't seem to be able to identify my MS/MS spectra with a .msp/.txt database as it always crashes the software even when doing it after processing (peak peaking, adduct identification, deconvolution, alignement, etc.).
Does anyone else have this issue and could enlighten me?
Thanks.

Thomas B.

Re: MS-DIAL V5.1.23 : crashes after adding a .msp/.txt file for identification

Reply #1
Hi,

MS-DIAL 5.123 also crashes often! It crashes after the alignment is finished. No error pop-up, the program just stops.  (please find below the error)
I tried/checked several things to figure out what the problem could be. It seems no multiuser problem and CPU max. is not reached during processing.
So far, the software was able to process 2 lipidomics datasets and 1 metabolomics (.msp Fiehn HILIC).  I want to process the latter with an additional .msp file. However, it crashed three times in a row.

What can/check/change to fix this?

Please help! Thanks a lot!


Framework Version: v4.0.30319
Description: The process was terminated due to an unhandled exception.
Exception Info: System.InvalidOperationException
   at MessagePack.MessagePackBinary.WriteString(Byte[] ByRef, Int32, System.String)
   at MessagePack.Formatters.CompMs_Common_DataObj_Property_IsotopicPeakFormatter65.Serialize(Byte[] ByRef, Int32, CompMs.Common.DataObj.Property.IsotopicPeak, MessagePack.IFormatterResolver)
   at MessagePack.Formatters.ListFormatter`1[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]].Serialize(Byte[] ByRef, Int32, System.Collections.Generic.List`1<System.__Canon>, MessagePack.IFormatterResolver)
   at MessagePack.Formatters.CompMs_MsdialCore_DataObj_AlignmentSpotPropertyFormatter74.Serialize(Byte[] ByRef, Int32, CompMs.MsdialCore.DataObj.AlignmentSpotProperty, MessagePack.IFormatterResolver)
   at MessagePack.Formatters.CollectionFormatterBase`4[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089],[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089],[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089],[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]].Serialize(Byte[] ByRef, Int32, System.__Canon, MessagePack.IFormatterResolver)
   at MessagePack.Formatters.CompMs_MsdialCore_DataObj_AlignmentResultContainerFormatter73.Serialize(Byte[] ByRef, Int32, CompMs.MsdialCore.DataObj.AlignmentResultContainer, MessagePack.IFormatterResolver)
   at MessagePack.MessagePackSerializer.SerializeUnsafe[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]](System.__Canon, MessagePack.IFormatterResolver)
   at MessagePack.LZ4MessagePackSerializer.SerializeCore[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]](System.__Canon, MessagePack.IFormatterResolver)
   at MessagePack.LZ4MessagePackSerializer.Serialize[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]](System.IO.Stream, System.__Canon, MessagePack.IFormatterResolver)
   at CompMs.Common.MessagePack.MessagePackDefaultHandler.SaveToFile[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]](System.__Canon, System.String)
   at CompMs.Common.MessagePack.MessagePackHandler.SaveToFile[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]](System.__Canon, System.String)
   at CompMs.MsdialCore.DataObj.AlignmentResultContainer.Save(CompMs.MsdialCore.DataObj.AlignmentFileBean)
   at CompMs.App.Msdial.Model.DataObj.AlignmentFileBeanModel+<SaveAlignmentResultAsync>d__12.MoveNext()
   at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
   at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
   at CompMs.App.Msdial.Model.Lcms.LcmsMethodModel+<>c__DisplayClass34_0+<<ProcessAlignment>b__0>d.MoveNext()
   at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
   at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
   at CompMs.App.Msdial.View.Core.MainWindow+<>c__DisplayClass7_0+<<ShowProgressBarWindow>b__0>d.MoveNext()
   at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
   at System.Windows.Threading.ExceptionWrapper.InternalRealCall(System.Delegate, System.Object, Int32)
   at System.Windows.Threading.ExceptionWrapper.TryCatchWhen(System.Object, System.Delegate, System.Object, Int32, System.Delegate)
   at System.Windows.Threading.DispatcherOperation.InvokeImpl()
   at MS.Internal.CulturePreservingExecutionContext.CallbackWrapper(System.Object)
   at System.Threading.ExecutionContext.RunInternal(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object, Boolean)
   at System.Threading.ExecutionContext.Run(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object, Boolean)
   at System.Threading.ExecutionContext.Run(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object)
   at MS.Internal.CulturePreservingExecutionContext.Run(MS.Internal.CulturePreservingExecutionContext, System.Threading.ContextCallback, System.Object)
   at System.Windows.Threading.DispatcherOperation.Invoke()
   at System.Windows.Threading.Dispatcher.ProcessQueue()
   at System.Windows.Threading.Dispatcher.WndProcHook(IntPtr, Int32, IntPtr, IntPtr, Boolean ByRef)
   at MS.Win32.HwndWrapper.WndProc(IntPtr, Int32, IntPtr, IntPtr, Boolean ByRef)
   at MS.Win32.HwndSubclass.DispatcherCallbackOperation(System.Object)
   at System.Windows.Threading.ExceptionWrapper.InternalRealCall(System.Delegate, System.Object, Int32)
   at System.Windows.Threading.ExceptionWrapper.TryCatchWhen(System.Object, System.Delegate, System.Object, Int32, System.Delegate)
   at System.Windows.Threading.Dispatcher.LegacyInvokeImpl(System.Windows.Threading.DispatcherPriority, System.TimeSpan, System.Delegate, System.Object, Int32)
   at MS.Win32.HwndSubclass.SubclassWndProc(IntPtr, Int32, IntPtr, IntPtr)
   at MS.Win32.UnsafeNativeMethods.DispatchMessage(System.Windows.Interop.MSG ByRef)
   at System.Windows.Threading.Dispatcher.PushFrameImpl(System.Windows.Threading.DispatcherFrame)
   at System.Windows.Window.ShowHelper(System.Object)
   at System.Windows.Window.ShowDialog()
   at CompMs.App.Msdial.View.Core.MainWindow.ShowProgressBarWindow(CompMs.Graphics.UI.ProgressBar.ProgressBarRequest)
   at System.Reactive.ObserverBase`1[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]].OnNext(System.__Canon)
   at System.Reactive.AutoDetachObserver`1[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]].OnNextCore(System.__Canon)
   at System.Reactive.ObserverBase`1[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]].OnNext(System.__Canon)
   at Reactive.Bindings.Notifiers.MessageBrokerExtensions+<>c__DisplayClass0_1`1[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]].<ToObservable>b__1(System.__Canon)
   at Reactive.Bindings.Notifiers.MessageBroker.Publish[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]](System.__Canon)
   at CompMs.App.Msdial.Model.Lcms.LcmsMethodModel.ProcessAlignment(CompMs.MsdialCore.DataObj.IMsdialDataStorage`1<CompMs.MsdialLcmsApi.Parameter.MsdialLcmsParameter>)
   at CompMs.App.Msdial.Model.Lcms.LcmsMethodModel+<RunAsync>d__27.MoveNext()
   at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
   at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
   at CompMs.App.Msdial.Model.Setting.MethodSettingModel+<TryRunAsync>d__44.MoveNext()
   at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
   at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
   at CompMs.App.Msdial.Model.Setting.ProcessSettingModel+<RunProcessAsync>d__10.MoveNext()
   at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
   at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
   at CompMs.App.Msdial.ViewModel.Core.MainWindowVM+<RunProcess>d__28.MoveNext()
   at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
   at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
   at CompMs.App.Msdial.ViewModel.Core.MainWindowVM+<ExecuteIdentificationMethodProcess>d__40.MoveNext()
   at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
   at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
   at Reactive.Bindings.AsyncReactiveCommand+<>c__DisplayClass6_0+<<Subscribe>b__0>d.MoveNext()
   at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
   at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
   at Reactive.Bindings.AsyncReactiveCommand`1+<ExecuteAsync>d__16[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]].MoveNext()
   at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
   at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
   at Reactive.Bindings.AsyncReactiveCommand`1+<Execute>d__15[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]].MoveNext()
   at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
   at System.Windows.Threading.ExceptionWrapper.InternalRealCall(System.Delegate, System.Object, Int32)
   at System.Windows.Threading.ExceptionWrapper.TryCatchWhen(System.Object, System.Delegate, System.Object, Int32, System.Delegate)
   at System.Windows.Threading.DispatcherOperation.InvokeImpl()
   at MS.Internal.CulturePreservingExecutionContext.CallbackWrapper(System.Object)
   at System.Threading.ExecutionContext.RunInternal(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object, Boolean)
   at System.Threading.ExecutionContext.Run(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object, Boolean)
   at System.Threading.ExecutionContext.Run(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object)
   at MS.Internal.CulturePreservingExecutionContext.Run(MS.Internal.CulturePreservingExecutionContext, System.Threading.ContextCallback, System.Object)
   at System.Windows.Threading.DispatcherOperation.Invoke()
   at System.Windows.Threading.Dispatcher.ProcessQueue()
   at System.Windows.Threading.Dispatcher.WndProcHook(IntPtr, Int32, IntPtr, IntPtr, Boolean ByRef)
   at MS.Win32.HwndWrapper.WndProc(IntPtr, Int32, IntPtr, IntPtr, Boolean ByRef)
   at MS.Win32.HwndSubclass.DispatcherCallbackOperation(System.Object)
   at System.Windows.Threading.ExceptionWrapper.InternalRealCall(System.Delegate, System.Object, Int32)
   at System.Windows.Threading.ExceptionWrapper.TryCatchWhen(System.Object, System.Delegate, System.Object, Int32, System.Delegate)
   at System.Windows.Threading.Dispatcher.LegacyInvokeImpl(System.Windows.Threading.DispatcherPriority, System.TimeSpan, System.Delegate, System.Object, Int32)
   at MS.Win32.HwndSubclass.SubclassWndProc(IntPtr, Int32, IntPtr, IntPtr)
   at MS.Win32.UnsafeNativeMethods.DispatchMessage(System.Windows.Interop.MSG ByRef)
   at System.Windows.Threading.Dispatcher.PushFrameImpl(System.Windows.Threading.DispatcherFrame)
   at System.Windows.Application.RunDispatcher(System.Object)
   at System.Windows.Application.RunInternal(System.Windows.Window)
   at CompMs.App.Msdial.App.Main()
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Re: MS-DIAL V5.1.23 : crashes after adding a .msp/.txt file for identification

Reply #2
I ran a comparison between v4.92 and v5.1 for my AIF data. v5.1 crashed during processing so I'm sticking with v4.92. I haven't found any version of MS-DIAL 5 to be stable.