MaxQuant: append error log files to stderr #575
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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)
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MaxQuant's error output seems pretty useless for users and admins:
E.g.
But there are error file in combined/proc/ which contain more info, e.g.
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)
TODO: