Commits on Mar 15, 2021

1. MaxQuant: append error log files to stderr …

   MaxQuant's error output seems pretty useless for users and admins:
   
   E.g.
   
   ```
   Unhandled Exception:
   System.Exception: Exception during execution of external process: 27929
     at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x001a1] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0
     at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0
     at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <3fc1eb7cc45041de8ce7f41aa00f3311>: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: 27929
     at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x001a1] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0
     at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0
     at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <3fc1eb7cc45041de8ce7f41aa00f3311>: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
   ```
   
   But there are error file in combined/proc/ which contain more info, e.g.
   
   ```
   id	0
   start	15/03/2021 13:22:03
   title	Testing_raw_files (4/6)
   description	/gpfs1/work/songalax/galaxy/database/jobs_directory/000/107/107504/working/2016-04-05_NJ_Groundwater_5_1.raw.thermo.raw
   error	/gpfs1/work/songalax/galaxy/database/jobs_directory/000/107/107504/working/2016-04-05_NJ_Groundwater_5_1.raw.thermo.raw_The file '/gpfs1/work/songalax/galaxy/database/jobs_directory/000/107/107504/working/2016-04-05_NJ_Groundwater_5_1.raw.thermo.raw' appears to be corrupt. Try to open it with vendor software. Error message: RunHeaderEx_  at MaxQuantPLibS.Basic.MaxQuantTasks.TestFile (System.Int32 taskIndex, System.String mqparFile) [0x00080] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantPLibS.Work.RawFileTester.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x00009] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantPLibS.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantTask.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x00012] in <a9a7ab44566440088bf38b1365d644dc>:0 _  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x000af] in <13cd68fb3f5d4831b26fc0f070437c6f>:0
   end	15/03/2021 13:22:04
   ```
   
   Which contains the slightly more useful message: `2016-04-05_NJ_Groundwater_5_1.raw.thermo.raw' appears to be corrupt. Try to open it with vendor software.`
   
   While this might still overwhelm end users its certainly useful for
   admins (and they do not need to remember where the error are kept for
   MaxQuant)

   

   bernt-matthias committed Mar 15, 2021
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