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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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Index was outside the bounds of the array #2331

Open animesh opened 5 months ago

animesh commented 5 months ago

I am trying to run the latest version but facing following error results.txt at the very first stage of calibration Task1-CalibrateTaskconfig - Copy.toml.txt , any ideas how to proceed?

MetaMorpheus: version 1.0.5
Data files were processed on a computer running Microsoft Windows 10.0.22635 with a 64-bit Intel(R) Xeon(R) CPU E5-2643 v3 @ 3.40GHz processor with 24 threads and 128GB installed RAM.
.NET version: .NET 6.0.26
e: System.AggregateException: One or more errors occurred. (Index was outside the bounds of the array.) (Index was outside the bounds of the array.) (Index was outside the bounds of the array.) (Index was outside the bounds of the array.) (Index was outside the bounds of the array.)
 ---> System.IndexOutOfRangeException: Index was outside the bounds of the array.
   at Readers.Mzml.GetOneBasedPrecursorScanNumber(mzMLType _mzMLConnection, Int32 oneBasedSpectrumNumber)
   at Readers.Mzml.GetMsDataOneBasedScanFromConnection(mzMLType _mzMLConnection, Int32 oneBasedIndex, IFilteringParams filterParams)
   at Readers.Mzml.<>c__DisplayClass29_0.<LoadAllStaticData>b__0(Tuple`2 fff)
   at System.Threading.Tasks.Parallel.<>c__DisplayClass44_0`2.<PartitionerForEachWorker>b__1(IEnumerator& partitionState, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion)
--- End of stack trace from previous location ---
   at System.Threading.Tasks.Parallel.<>c__DisplayClass44_0`2.<PartitionerForEachWorker>b__1(IEnumerator& partitionState, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion)
   at System.Threading.Tasks.TaskReplicator.Replica`1.ExecuteAction(Boolean& yieldedBeforeCompletion)
   at System.Threading.Tasks.TaskReplicator.Replica.Execute()
   --- End of inner exception stack trace ---
   at System.Threading.Tasks.TaskReplicator.Run[TState](ReplicatableUserAction`1 action, ParallelOptions options, Boolean stopOnFirstFailure)
   at System.Threading.Tasks.Parallel.PartitionerForEachWorker[TSource,TLocal](Partitioner`1 source, ParallelOptions parallelOptions, Action`1 simpleBody, Action`2 bodyWithState, Action`3 bodyWithStateAndIndex, Func`4 bodyWithStateAndLocal, Func`5 bodyWithEverything, Func`1 localInit, Action`1 localFinally)
--- End of stack trace from previous location ---
   at System.Threading.Tasks.Parallel.ThrowSingleCancellationExceptionOrOtherException(ICollection exceptions, CancellationToken cancelToken, Exception otherException)
   at System.Threading.Tasks.Parallel.PartitionerForEachWorker[TSource,TLocal](Partitioner`1 source, ParallelOptions parallelOptions, Action`1 simpleBody, Action`2 bodyWithState, Action`3 bodyWithStateAndIndex, Func`4 bodyWithStateAndLocal, Func`5 bodyWithEverything, Func`1 localInit, Action`1 localFinally)
   at System.Threading.Tasks.Parallel.ForEach[TSource](Partitioner`1 source, ParallelOptions parallelOptions, Action`1 body)
   at Readers.Mzml.LoadAllStaticData(FilteringParams filterParams, Int32 maxThreads)
   at TaskLayer.MyFileManager.LoadFile(String origDataFile, CommonParameters commonParameters) in C:\projects\metamorpheus\MetaMorpheus\TaskLayer\MyFileManager.cs:line 53
   at TaskLayer.CalibrationTask.RunSpecific(String OutputFolder, List`1 dbFilenameList, List`1 currentRawFileList, String taskId, FileSpecificParameters[] fileSettingsList) in C:\projects\metamorpheus\MetaMorpheus\TaskLayer\CalibrationTask\CalibrationTask.cs:line 90
   at TaskLayer.MetaMorpheusTask.RunTask(String output_folder, List`1 currentProteinDbFilenameList, List`1 currentRawDataFilepathList, String displayName) in C:\projects\metamorpheus\MetaMorpheus\TaskLayer\MetaMorpheusTask.cs:line 509
 ---> (Inner Exception #1) System.IndexOutOfRangeException: Index was outside the bounds of the array.
   at Readers.Mzml.GetOneBasedPrecursorScanNumber(mzMLType _mzMLConnection, Int32 oneBasedSpectrumNumber)
   at Readers.Mzml.GetMsDataOneBasedScanFromConnection(mzMLType _mzMLConnection, Int32 oneBasedIndex, IFilteringParams filterParams)
   at Readers.Mzml.<>c__DisplayClass29_0.<LoadAllStaticData>b__0(Tuple`2 fff)
   at System.Threading.Tasks.Parallel.<>c__DisplayClass44_0`2.<PartitionerForEachWorker>b__1(IEnumerator& partitionState, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion)
--- End of stack trace from previous location ---
   at System.Threading.Tasks.Parallel.<>c__DisplayClass44_0`2.<PartitionerForEachWorker>b__1(IEnumerator& partitionState, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion)
   at System.Threading.Tasks.TaskReplicator.Replica`1.ExecuteAction(Boolean& yieldedBeforeCompletion)
   at System.Threading.Tasks.TaskReplicator.Replica.Execute()<---

 ---> (Inner Exception #2) System.IndexOutOfRangeException: Index was outside the bounds of the array.
   at Readers.Mzml.GetOneBasedPrecursorScanNumber(mzMLType _mzMLConnection, Int32 oneBasedSpectrumNumber)
   at Readers.Mzml.GetMsDataOneBasedScanFromConnection(mzMLType _mzMLConnection, Int32 oneBasedIndex, IFilteringParams filterParams)
   at Readers.Mzml.<>c__DisplayClass29_0.<LoadAllStaticData>b__0(Tuple`2 fff)
   at System.Threading.Tasks.Parallel.<>c__DisplayClass44_0`2.<PartitionerForEachWorker>b__1(IEnumerator& partitionState, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion)
--- End of stack trace from previous location ---
   at System.Threading.Tasks.Parallel.<>c__DisplayClass44_0`2.<PartitionerForEachWorker>b__1(IEnumerator& partitionState, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion)
   at System.Threading.Tasks.TaskReplicator.Replica`1.ExecuteAction(Boolean& yieldedBeforeCompletion)
   at System.Threading.Tasks.TaskReplicator.Replica.Execute()<---

 ---> (Inner Exception #3) System.IndexOutOfRangeException: Index was outside the bounds of the array.
   at Readers.Mzml.GetOneBasedPrecursorScanNumber(mzMLType _mzMLConnection, Int32 oneBasedSpectrumNumber)
   at Readers.Mzml.GetMsDataOneBasedScanFromConnection(mzMLType _mzMLConnection, Int32 oneBasedIndex, IFilteringParams filterParams)
   at Readers.Mzml.<>c__DisplayClass29_0.<LoadAllStaticData>b__0(Tuple`2 fff)
   at System.Threading.Tasks.Parallel.<>c__DisplayClass44_0`2.<PartitionerForEachWorker>b__1(IEnumerator& partitionState, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion)
--- End of stack trace from previous location ---
   at System.Threading.Tasks.Parallel.<>c__DisplayClass44_0`2.<PartitionerForEachWorker>b__1(IEnumerator& partitionState, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion)
   at System.Threading.Tasks.TaskReplicator.Replica`1.ExecuteAction(Boolean& yieldedBeforeCompletion)
   at System.Threading.Tasks.TaskReplicator.Replica.Execute()<---

 ---> (Inner Exception #4) System.IndexOutOfRangeException: Index was outside the bounds of the array.
   at Readers.Mzml.GetOneBasedPrecursorScanNumber(mzMLType _mzMLConnection, Int32 oneBasedSpectrumNumber)
   at Readers.Mzml.GetMsDataOneBasedScanFromConnection(mzMLType _mzMLConnection, Int32 oneBasedIndex, IFilteringParams filterParams)
   at Readers.Mzml.<>c__DisplayClass29_0.<LoadAllStaticData>b__0(Tuple`2 fff)
   at System.Threading.Tasks.Parallel.<>c__DisplayClass44_0`2.<PartitionerForEachWorker>b__1(IEnumerator& partitionState, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion)
--- End of stack trace from previous location ---
   at System.Threading.Tasks.Parallel.<>c__DisplayClass44_0`2.<PartitionerForEachWorker>b__1(IEnumerator& partitionState, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion)
   at System.Threading.Tasks.TaskReplicator.Replica`1.ExecuteAction(Boolean& yieldedBeforeCompletion)
   at System.Threading.Tasks.TaskReplicator.Replica.Execute()<---
e.Message: One or more errors occurred. (Index was outside the bounds of the array.) (Index was outside the bounds of the array.) (Index was outside the bounds of the array.) (Index was outside the bounds of the array.) (Index was outside the bounds of the array.)e.InnerException: System.IndexOutOfRangeException: Index was outside the bounds of the array.
   at Readers.Mzml.GetOneBasedPrecursorScanNumber(mzMLType _mzMLConnection, Int32 oneBasedSpectrumNumber)
   at Readers.Mzml.GetMsDataOneBasedScanFromConnection(mzMLType _mzMLConnection, Int32 oneBasedIndex, IFilteringParams filterParams)
   at Readers.Mzml.<>c__DisplayClass29_0.<LoadAllStaticData>b__0(Tuple`2 fff)
   at System.Threading.Tasks.Parallel.<>c__DisplayClass44_0`2.<PartitionerForEachWorker>b__1(IEnumerator& partitionState, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion)
--- End of stack trace from previous location ---
   at System.Threading.Tasks.Parallel.<>c__DisplayClass44_0`2.<PartitionerForEachWorker>b__1(IEnumerator& partitionState, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion)
   at System.Threading.Tasks.TaskReplicator.Replica`1.ExecuteAction(Boolean& yieldedBeforeCompletion)
   at System.Threading.Tasks.TaskReplicator.Replica.Execute()e.Source: System.Threading.Tasks.Parallele.StackTrace:    at System.Threading.Tasks.TaskReplicator.Run[TState](ReplicatableUserAction`1 action, ParallelOptions options, Boolean stopOnFirstFailure)
   at System.Threading.Tasks.Parallel.PartitionerForEachWorker[TSource,TLocal](Partitioner`1 source, ParallelOptions parallelOptions, Action`1 simpleBody, Action`2 bodyWithState, Action`3 bodyWithStateAndIndex, Func`4 bodyWithStateAndLocal, Func`5 bodyWithEverything, Func`1 localInit, Action`1 localFinally)
--- End of stack trace from previous location ---
   at System.Threading.Tasks.Parallel.ThrowSingleCancellationExceptionOrOtherException(ICollection exceptions, CancellationToken cancelToken, Exception otherException)
   at System.Threading.Tasks.Parallel.PartitionerForEachWorker[TSource,TLocal](Partitioner`1 source, ParallelOptions parallelOptions, Action`1 simpleBody, Action`2 bodyWithState, Action`3 bodyWithStateAndIndex, Func`4 bodyWithStateAndLocal, Func`5 bodyWithEverything, Func`1 localInit, Action`1 localFinally)
   at System.Threading.Tasks.Parallel.ForEach[TSource](Partitioner`1 source, ParallelOptions parallelOptions, Action`1 body)
   at Readers.Mzml.LoadAllStaticData(FilteringParams filterParams, Int32 maxThreads)
   at TaskLayer.MyFileManager.LoadFile(String origDataFile, CommonParameters commonParameters) in C:\projects\metamorpheus\MetaMorpheus\TaskLayer\MyFileManager.cs:line 53
   at TaskLayer.CalibrationTask.RunSpecific(String OutputFolder, List`1 dbFilenameList, List`1 currentRawFileList, String taskId, FileSpecificParameters[] fileSettingsList) in C:\projects\metamorpheus\MetaMorpheus\TaskLayer\CalibrationTask\CalibrationTask.cs:line 90
   at TaskLayer.MetaMorpheusTask.RunTask(String output_folder, List`1 currentProteinDbFilenameList, List`1 currentRawDataFilepathList, String displayName) in C:\projects\metamorpheus\MetaMorpheus\TaskLayer\MetaMorpheusTask.cs:line 509e.TargetSite: Void Run[TState](ReplicatableUserAction`1, System.Threading.Tasks.ParallelOptions, Boolean)