Problem with galaxy's Maxquant
0
0
Entering edit mode
4 months ago
Chris K ▴ 10

Hello everyone,

I am facing a problem with i am trying to do a mass spec analysis with galaxys Maxquant. I initially used the .raw files from this experiment (PRIDE id:PXD027714) and imported them on galaxy and followed an used pipeline. Then i got this error:

Unhandled Exception:
System.Exception: Exception during execution of external process: 1300689 
Unhandled Exception:
ThermoFisher.CommonCore.Data.Business.NoSelectedDeviceException: RunHeaderEx
  at ThermoFisher.CommonCore.RawFileReader.RawFileAccessBase.RequireDevice (System.String reason) [0x0001c] in <7b20930f488c4a50a6b41afdf3646c13>:0 
  at ThermoFisher.CommonCore.RawFileReader.RawFileAccessBase.get_RunHeaderEx () [0x00000] in <7b20930f488c4a50a6b41afdf3646c13>:0 
  at PluginRawThermo.ThermoRawFile.get_FirstScanNumber () [0x00017] in <63f726adc13d42dab92b89022cfbd864>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFileImpl () [0x00020] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFile () [0x00017] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.Init (System.String path1) [0x00058] in <2a783505a9324377a912fbc866234a84>:0 
  at MsLib.Raw.RawFileUtil.CreateRawFile (System.String path) [0x00047] in <c7996a5d247b4a82ba72a2553c25246f>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun+<>c__DisplayClass10_0.<.ctor>b__0 () [0x00000] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun.get_RawFile () [0x0000a] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRunLayer.get_RawFileLayer () [0x00006] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at

after a quick search i found that a possible solution would be to convert the .raw files to the .mzML format which i did using proteoWizard's MS converter with these parameters: enter image description here

And after i uploaded it and re-run it in Maxquant i got the error message bellow:

Unhandled Exception:
System.Exception: Exception during execution of external process: 829937 
Unhandled Exception:
System.ArgumentException: Could not identify mass analyzer for spectrum 0.
  at PluginRawMzMl.MzMLRawFile.MassAnalyzer (System.Int32 scanNumber, PluginRawMzMl.ScanType scan) [0x00091] in <43a575582d27438f841a4c61dc554bbc>:0 
  at PluginRawMzMl.MzMLRawFile.GetInfoForScanNumber (System.Int32 scanNumber) [0x0009e] in <43a575582d27438f841a4c61dc554bbc>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFileImpl () [0x00048] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFile () [0x00017] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.Init (System.String path1) [0x00058] in <2a783505a9324377a912fbc866234a84>:0 
  at MsLib.Raw.RawFileUtil.CreateRawFile (System.String path) [0x00047] in <c7996a5d247b4a82ba72a2553c25246f>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun+<>c__DisplayClass10_0.<.ctor>b__0 () [0x00000] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun.get_RawFile () [0x0000a] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRunLayer.get_RawFileLayer () [0x00006] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Features.FeatureDetectionUtil.AssembleRunInfo (System.String mqparFile, System.Int32 fileIndex) [0x000a4] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.AssembleRunInfo.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x0000c] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0002d] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantTaskCore.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <1c54eed30d1e45488ee6c9e61d204782>:0 
  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in <94cd7968dc654c259fccb9053e84841e>:0 
  at MaxQuantTaskCore.Program.Main (System.String[] args) [0x00007] in <1c54eed30d1e45488ee6c9e61d204782>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.ArgumentException: Could not identify mass analyzer for spectrum 0.
  at PluginRawMzMl.MzMLRawFile.MassAnalyzer (System.Int32 scanNumber, PluginRawMzMl.ScanType scan) [0x00091] in <43a575582d27438f841a4c61dc554bbc>:0 
  at PluginRawMzMl.MzMLRawFile.GetInfoForScanNumber (System.Int32 scanNumber) [0x0009e] in <43a575582d27438f841a4c61dc554bbc>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFileImpl () [0x00048] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFile () [0x00017] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.Init (System.String path1) [0x00058] in <2a783505a9324377a912fbc866234a84>:0 
  at MsLib.Raw.RawFileUtil.CreateRawFile (System.String path) [0x00047] in <c7996a5d247b4a82ba72a2553c25246f>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun+<>c__DisplayClass10_0.<.ctor>b__0 () [0x00000] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun.get_RawFile () [0x0000a] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRunLayer.get_RawFileLayer () [0x00006] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Features.FeatureDetectionUtil.AssembleRunInfo (System.String mqparFile, System.Int32 fileIndex) [0x000a4] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.AssembleRunInfo.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x0000c] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0002d] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantTaskCore.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <1c54eed30d1e45488ee6c9e61d204782>:0 
  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in <94cd7968dc654c259fccb9053e84841e>:0 
  at MaxQuantTaskCore.Program.Main (System.String[] args) [0x00007] in <1c54eed30d1e45488ee6c9e61d204782>:0 

  at QueueingSystem.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0009d] in <9c0f25807e814cdb9d19b5c1d7b1d72f>:0 
  at QueueingSystem.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <9c0f25807e814cdb9d19b5c1d7b1d72f>:0 
  at QueueingSystem.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <9c0f25807e814cdb9d19b5c1d7b1d72f>:0 
  at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <7cd4deb8302a478d9d393f24754841da>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 829937 
Unhandled Exception:
System.ArgumentException: Could not identify mass analyzer for spectrum 0.
  at PluginRawMzMl.MzMLRawFile.MassAnalyzer (System.Int32 scanNumber, PluginRawMzMl.ScanType scan) [0x00091] in <43a575582d27438f841a4c61dc554bbc>:0 
  at PluginRawMzMl.MzMLRawFile.GetInfoForScanNumber (System.Int32 scanNumber) [0x0009e] in <43a575582d27438f841a4c61dc554bbc>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFileImpl () [0x00048] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFile () [0x00017] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.Init (System.String path1) [0x00058] in <2a783505a9324377a912fbc866234a84>:0 
  at MsLib.Raw.RawFileUtil.CreateRawFile (System.String path) [0x00047] in <c7996a5d247b4a82ba72a2553c25246f>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun+<>c__DisplayClass10_0.<.ctor>b__0 () [0x00000] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun.get_RawFile () [0x0000a] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRunLayer.get_RawFileLayer () [0x00006] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Features.FeatureDetectionUtil.AssembleRunInfo (System.String mqparFile, System.Int32 fileIndex) [0x000a4] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.AssembleRunInfo.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x0000c] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0002d] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantTaskCore.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <1c54eed30d1e45488ee6c9e61d204782>:0 
  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in <94cd7968dc654c259fccb9053e84841e>:0 
  at MaxQuantTaskCore.Program.Main (System.String[] args) [0x00007] in <1c54eed30d1e45488ee6c9e61d204782>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.ArgumentException: Could not identify mass analyzer for spectrum 0.
  at PluginRawMzMl.MzMLRawFile.MassAnalyzer (System.Int32 scanNumber, PluginRawMzMl.ScanType scan) [0x00091] in <43a575582d27438f841a4c61dc554bbc>:0 
  at PluginRawMzMl.MzMLRawFile.GetInfoForScanNumber (System.Int32 scanNumber) [0x0009e] in <43a575582d27438f841a4c61dc554bbc>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFileImpl () [0x00048] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFile () [0x00017] in <2a783505a9324377a912fbc866234a84>:0 
  at BaseLibS.Ms.RawFile.Init (System.String path1) [0x00058] in <2a783505a9324377a912fbc866234a84>:0 
  at MsLib.Raw.RawFileUtil.CreateRawFile (System.String path) [0x00047] in <c7996a5d247b4a82ba72a2553c25246f>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun+<>c__DisplayClass10_0.<.ctor>b__0 () [0x00000] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRun.get_RawFile () [0x0000a] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Data.GenericRunLayer.get_RawFileLayer () [0x00006] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Features.FeatureDetectionUtil.AssembleRunInfo (System.String mqparFile, System.Int32 fileIndex) [0x000a4] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.AssembleRunInfo.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x0000c] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0002d] in <6a6754cab5cf48c89c9c64e9dafc7e21>:0 
  at MaxQuantTaskCore.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <1c54eed30d1e45488ee6c9e61d204782>:0 
  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in <94cd7968dc654c259fccb9053e84841e>:0 
  at MaxQuantTaskCore.Program.Main (System.String[] args) [0x00007] in <1c54eed30d1e45488ee6c9e61d204782>:0 

  at QueueingSystem.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0009d] in <9c0f25807e814cdb9d19b5c1d7b1d72f>:0 
  at QueueingSystem.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <9c0f25807e814cdb9d19b5c1d7b1d72f>:0 
  at QueueingSystem.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <9c0f25807e814cdb9d19b5c1d7b1d72f>:0 
  at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <7cd4deb8302a478d9d393f24754841da>:0 
  at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <7cd4deb8302a478d9d393f24754841da>:0

Could it be something wrong native in the provided files, that i can not change? Thank you very much in advance!
Proteomics Maxquant Galaxy • 533 views
ADD COMMENT •
1
Entering edit mode

Please post galaxy related questions to their help forum for prompt help: https://help.galaxyproject.org/

ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 4015 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6