Crash - Index was outside the bounds of the array - XLSearchTask

[xLinkKnight]

Running the latest release of MetaMorpheus (1.0.5).

Crash when attempting to perform a crosslink search when using MGF files. MGF files were generated by MSConvert from Bruker SCP raw files.

Error: Run failed, Exception: Index was outside the bounds of the array.

The results file contains the following:

Data files were processed on a computer running Microsoft Windows 10.0.22631 with a 64-bit AMD EPYC 9754 128-Core Processor                processor with 64 threads and 768GB installed RAM.
.NET version: .NET 6.0.30
e: System.IndexOutOfRangeException: Index was outside the bounds of the array.
   at Readers.Mgf.GetNextMsDataOneBasedScanFromConnection(StreamReader sr, HashSet`1 scanNumbersAlreadyObserved, IFilteringParams filterParams, Nullable`1 alreadyKnownScanNumber)
   at Readers.Mgf.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.XLSearchTask.RunSpecific(String OutputFolder, List`1 dbFilenameList, List`1 currentRawFileList, String taskId, FileSpecificParameters[] fileSettingsList) in C:\projects\metamorpheus\MetaMorpheus\TaskLayer\XLSearchTask\XLSearchTask.cs:line 96
   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.Message: Index was outside the bounds of the array.e.InnerException: e.Source: Readerse.StackTrace:    at Readers.Mgf.GetNextMsDataOneBasedScanFromConnection(StreamReader sr, HashSet`1 scanNumbersAlreadyObserved, IFilteringParams filterParams, Nullable`1 alreadyKnownScanNumber)
   at Readers.Mgf.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.XLSearchTask.RunSpecific(String OutputFolder, List`1 dbFilenameList, List`1 currentRawFileList, String taskId, FileSpecificParameters[] fileSettingsList) in C:\projects\metamorpheus\MetaMorpheus\TaskLayer\XLSearchTask\XLSearchTask.cs:line 96
   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: MassSpectrometry.MsDataScan GetNextMsDataOneBasedScanFromConnection(System.IO.StreamReader, System.Collections.Generic.HashSet`1[System.Int32], MassSpectrometry.IFilteringParams, System.Nullable`1[System.Int32])

XL-Task.toml:

TaskType = "XLSearch"

[XlSearchParameters]
DecoyType = "Reverse"
CrosslinkSearchTopNum = 50
CrosslinkAtCleavageSite = false
WritePepXml = true
WriteOutputForPercolator = false
WriteSpectralLibrary = false
XlQuench_H2O = true
XlQuench_Tris = false
XlQuench_NH2 = true

[XlSearchParameters.Crosslinker]
CrosslinkerModSites = "K"
CrosslinkerModSites2 = "K"
CrosslinkerName = "DSSO"
Cleavable = true
CleaveDissociationTypes = ["CID", "HCD"]
TotalMass = 158.0038
CleaveMassShort = 54.01056
CleaveMassLong = 85.982635
LoopMass = 158.0038
DeadendMassH2O = 176.0143
DeadendMassNH2 = 175.0303
DeadendMassTris = 279.0777

[CommonParameters]
TaskDescriptor = "ProteinX_DSSO"
MaxThreadsToUsePerFile = 63
ListOfModsFixed = "Common Fixed\tCarbamidomethyl on C\t\tCommon Fixed\tCarbamidomethyl on U"
ListOfModsVariable = "Common Variable\tOxidation on M"
DoPrecursorDeconvolution = true
UseProvidedPrecursorInfo = true
DeconvolutionIntensityRatio = 3.0
DeconvolutionMaxAssumedChargeState = 12
DeconvolutionMassTolerance = "±4.0000 PPM"
TotalPartitions = 1
ProductMassTolerance = "±20.0000 PPM"
PrecursorMassTolerance = "±20.0000 PPM"
AddCompIons = false
QValueThreshold = 0.01
PepQValueThreshold = 1.0
ScoreCutoff = 3.0
ReportAllAmbiguity = true
NumberOfPeaksToKeepPerWindow = 200
MinimumAllowedIntensityRatioToBasePeak = 0.01
NormalizePeaksAccrossAllWindows = false
TrimMs1Peaks = false
TrimMsMsPeaks = true
UseDeltaScore = false
CustomIons = []
AssumeOrphanPeaksAreZ1Fragments = true
MaxHeterozygousVariants = 4
MinVariantDepth = 1
AddTruncations = false
DissociationType = "HCD"
SeparationType = "HPLC"
MS2ChildScanDissociationType = "Unknown"
MS3ChildScanDissociationType = "Unknown"

[CommonParameters.DigestionParams]
MaxMissedCleavages = 3
InitiatorMethionineBehavior = "Variable"
MinPeptideLength = 5
MaxPeptideLength = 60
MaxModificationIsoforms = 1024
MaxModsForPeptide = 2
Protease = "trypsin"
SearchModeType = "Full"
FragmentationTerminus = "Both"
SpecificProtease = "trypsin"
GeneratehUnlabeledProteinsForSilac = true
KeepNGlycopeptide = false
KeepOGlycopeptide = false

System OS: Windows 11
MetaMorpheus Version: 1.0.5
Available RAM: 768 GB
CPU: EPYC 9754 128c/256t

Are there other dumps/logs I should attach?