XLMS search run failed: HELP

[bluemooninvestor]

I am getting the following error

"Runtime error, Run failed: Value cannot be null (Parameter 'source')

Would you like to report this crash?

I am running XLMS mode. I am putting "Common Fixed and Common Variable" - both of these as variable modifications. That is the only thing I am doing differently. I have tried with custom crosslinker that binds to cysteine residues (put C and C as amino acid/amino acid2 in custom crosslinker box.

Uniprot human fasta (attached)

Thermo RAW (without calibration)
mzml (after calibration)

I am putting "Common Fixed and Common Variable" - both of these as variable modifications. That is the only thing I am doing differently. I have tried with custom crosslinker that binds to cysteine residues (put C and C as amino acid/amino acid2 in custom crosslinker box. But the crash also happens with DSS (inbuilt crosslinker) although that may be because the sample doesn't contain DSS.

• Example datafiles
  It's private. Do you really need it? Data quality is good. I am getting 2500 proteins on Fragpipe.

Expected behavior for GUI
NA

Screenshots
Explained in detail.

Desktop information

MetaMorpheus: version 1.0.5
Data files were processed on a computer running Microsoft Windows 10.0.22631 with a 64-bit Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz processor with 12 threads and 32GB installed RAM.
.NET version: .NET 6.0.33
e: System.ArgumentNullException: Value cannot be null. (Parameter 'source')
at System.Linq.ThrowHelper.ThrowArgumentNullException(ExceptionArgument argument)
at System.Linq.Enumerable.Select[TSource,TResult](IEnumerable1 source, Func2 selector)
at EngineLayer.CrosslinkSearch.CrosslinkSearchEngine..ctor(List1[] globalCsms, Ms2ScanWithSpecificMass[] listOfSortedms2Scans, List1 peptideIndex, List1[] fragmentIndex, List1[] secondFragmentIndex, Int32 currentPartition, CommonParameters commonParameters, List1 fileSpecificParameters, Crosslinker crosslinker, Int32 CrosslinkSearchTopNum, Boolean CleaveAtCrosslinkSite, Boolean quench_H2O, Boolean quench_NH2, Boolean quench_Tris, List1 nestedIds, List1[] candidates, Int32 nextPartition, List1 nextPeptideIndex, List1 precursorss) in C:\projects\metamorpheus\MetaMorpheus\EngineLayer\CrosslinkSearch\CrosslinkSearchEngine.cs:line 48 at TaskLayer.XLSearchTask.RunSpecific(String OutputFolder, List1 dbFilenameList, List1 currentRawFileList, String taskId, FileSpecificParameters[] fileSettingsList) in C:\projects\metamorpheus\MetaMorpheus\TaskLayer\XLSearchTask\XLSearchTask.cs:line 191 at TaskLayer.MetaMorpheusTask.RunTask(String output_folder, List1 currentProteinDbFilenameList, List1 currentRawDataFilepathList, String displayName) in C:\projects\metamorpheus\MetaMorpheus\TaskLayer\MetaMorpheusTask.cs:line 509e.Message: Value cannot be null. (Parameter 'source')e.InnerException: e.Source: System.Linqe.StackTrace: at System.Linq.ThrowHelper.ThrowArgumentNullException(ExceptionArgument argument) at System.Linq.Enumerable.Select[TSource,TResult](IEnumerable1 source, Func2 selector) at EngineLayer.CrosslinkSearch.CrosslinkSearchEngine..ctor(List1[] globalCsms, Ms2ScanWithSpecificMass[] listOfSortedms2Scans, List1 peptideIndex, List1[] fragmentIndex, List1[] secondFragmentIndex, Int32 currentPartition, CommonParameters commonParameters, List1 fileSpecificParameters, Crosslinker crosslinker, Int32 CrosslinkSearchTopNum, Boolean CleaveAtCrosslinkSite, Boolean quench_H2O, Boolean quench_NH2, Boolean quench_Tris, List1 nestedIds, List1[] candidates, Int32 nextPartition, List1 nextPeptideIndex, List1 precursorss) in C:\projects\metamorpheus\MetaMorpheus\EngineLayer\CrosslinkSearch\CrosslinkSearchEngine.cs:line 48
at TaskLayer.XLSearchTask.RunSpecific(String OutputFolder, List1 dbFilenameList, List1 currentRawFileList, String taskId, FileSpecificParameters[] fileSettingsList) in C:\projects\metamorpheus\MetaMorpheus\TaskLayer\XLSearchTask\XLSearchTask.cs:line 191
at TaskLayer.MetaMorpheusTask.RunTask(String output_folder, List1 currentProteinDbFilenameList, List1 currentRawDataFilepathList, String displayName) in C:\projects\metamorpheus\MetaMorpheus\TaskLayer\MetaMorpheusTask.cs:line 509e.TargetSite: Void ThrowArgumentNullException(System.Linq.ExceptionArgument)

Additional context

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[bluemooninvestor]

Update:

This error was happening when I was using a human.fasta, which contained proteins overlapping with the contaminants.fasta generated by the software. This problem ceased when I stopped using the contaminants.fasta.

However, upon most recent update(1.0.6), now this issue is occuring even when I use the human.fasta alone without the contaminants.fasta.

Kindly look into it.

[nbollis]

Thank you for this update. One simple troubleshooting step would be to delete the database index folder found in the same directory as your database.