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atc3 / maxquant_linux_guide

A guide to running MaxQuant in Linux
http://atchen.me/research/2019/03/21/mq-linux.html
MIT License
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System.Exception: Exception during execution of external process: 229605 #11

Open littlenapleon opened 2 years ago

littlenapleon commented 2 years ago

My Maxquant analysis runs well then it fails at the Writing tables stage. What could be causing this problem? My fasta file was constructed by myself. Errors are as below, Configuring Assemble run info Finish run info Testing fasta files Testing raw files Feature detection Deisotoping MS/MS preparation Calculating peak properties Combining apl files for first search Preparing searches MS/MS first search Read search results for recalibration Mass recalibration Calculating masses MS/MS preparation for main search Combining apl files for main search MS/MS main search Preparing combined folder
Correcting errors Reading search engine results Preparing reverse hits Finish search engine results Filter identifications (MS/MS) Calculating PEP Copying identifications Applying FDR Assembling second peptide MS/MS Combining second peptide files Second peptide search Reading search engine results (SP) Finish search engine results (SP) Filtering identifications (SP) Applying FDR (SP) Re-quantification Reporter quantification Prepare protein assembly Assembling proteins Assembling unidentified peptides Finish protein assembly Updating identifications Estimating complexity Prepare writing tables
Writing tables

Unhandled Exception: System.Exception: Exception during execution of external process: 229605 Unhandled Exception: System.IndexOutOfRangeException: Index was outside the bounds of the array. at BaseLibS.Ms.RawFileLayer.GetDiaMs2Indices () [0x00037] in <8513301686fe48d39ba1f2bf0804617e>:0 at BaseLibS.Ms.RawFileLayer.GetDiaRanges (System.Double[]& mzMin, System.Double[]& mzMax) [0x00001] in <8513301686fe48d39ba1f2bf0804617e>:0 at MaxQuantLibS.Domains.Peptides.Dia.Data.DiaRangeCombination.GetCount (MaxQuantLibS.Domains.Peptides.Data.Run run) [0x0000f] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Dia.Data.DiaRangeCombination.GetCount (MaxQuantLibS.Domains.Peptides.Data.GenericRun run) [0x00016] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.MsScansTable.FillTable (BaseLibS.Table.IDataTable table, System.String rawFile, System.Int32 rawFileIndex, MaxQuantLibS.Domains.Peptides.Basic.GroupParams param, MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams mqpar, MaxQuantLibS.Domains.Peptides.Data.CombinedData data) [0x00044] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.FillMsScansTable (System.String filenameTxt, System.String filenameSer, MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams mqpar, System.Int32 index, System.String combinedFolder) [0x00037] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteRemainingTables (System.Int32 jobIndex, System.String mqparFile, System.String combinedFolder, System.String txtFolder, System.String serFolder) [0x0021d] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteTablesImpl (System.String combinedFolder, System.String txtFolder, System.String serFolder, System.String mqparFile, System.Int32 taskIndex) [0x0016b] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteTables (System.String combinedFolder, System.String mqparFile, System.Int32 taskIndex) [0x00015] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Work.WriteTable.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x00036] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0003e] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantTask.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <7ba895466ed6424bbd152d1a31fcf271>:0 at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in <7b96395895e442fea6f0a41d98060a6c>:0 at MaxQuantTask.Program.Main (System.String[] args) [0x00007] in <7ba895466ed6424bbd152d1a31fcf271>:0 [ERROR] FATAL UNHANDLED EXCEPTION: System.IndexOutOfRangeException: Index was outside the bounds of the array. at BaseLibS.Ms.RawFileLayer.GetDiaMs2Indices () [0x00037] in <8513301686fe48d39ba1f2bf0804617e>:0 at BaseLibS.Ms.RawFileLayer.GetDiaRanges (System.Double[]& mzMin, System.Double[]& mzMax) [0x00001] in <8513301686fe48d39ba1f2bf0804617e>:0 at MaxQuantLibS.Domains.Peptides.Dia.Data.DiaRangeCombination.GetCount (MaxQuantLibS.Domains.Peptides.Data.Run run) [0x0000f] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Dia.Data.DiaRangeCombination.GetCount (MaxQuantLibS.Domains.Peptides.Data.GenericRun run) [0x00016] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.MsScansTable.FillTable (BaseLibS.Table.IDataTable table, System.String rawFile, System.Int32 rawFileIndex, MaxQuantLibS.Domains.Peptides.Basic.GroupParams param, MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams mqpar, MaxQuantLibS.Domains.Peptides.Data.CombinedData data) [0x00044] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.FillMsScansTable (System.String filenameTxt, System.String filenameSer, MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams mqpar, System.Int32 index, System.String combinedFolder) [0x00037] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteRemainingTables (System.Int32 jobIndex, System.String mqparFile, System.String combinedFolder, System.String txtFolder, System.String serFolder) [0x0021d] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteTablesImpl (System.String combinedFolder, System.String txtFolder, System.String serFolder, System.String mqparFile, System.Int32 taskIndex) [0x0016b] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteTables (System.String combinedFolder, System.String mqparFile, System.Int32 taskIndex) [0x00015] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Work.WriteTable.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x00036] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0003e] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantTask.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <7ba895466ed6424bbd152d1a31fcf271>:0 at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in <7b96395895e442fea6f0a41d98060a6c>:0 at MaxQuantTask.Program.Main (System.String[] args) [0x00007] in <7ba895466ed6424bbd152d1a31fcf271>:0

at QueueingSystem.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0009d] in :0 at QueueingSystem.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in :0 at QueueingSystem.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in :0 at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x0002c] in <12b418a7818c4ca0893feeaaf67f1e7f>:0 at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x0008d] in <12b418a7818c4ca0893feeaaf67f1e7f>:0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <12b418a7818c4ca0893feeaaf67f1e7f>:0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x00031] in <12b418a7818c4ca0893feeaaf67f1e7f>:0 at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x00012] in <12b418a7818c4ca0893feeaaf67f1e7f>:0 [ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 229605 Unhandled Exception: System.IndexOutOfRangeException: Index was outside the bounds of the array. at BaseLibS.Ms.RawFileLayer.GetDiaMs2Indices () [0x00037] in <8513301686fe48d39ba1f2bf0804617e>:0 at BaseLibS.Ms.RawFileLayer.GetDiaRanges (System.Double[]& mzMin, System.Double[]& mzMax) [0x00001] in <8513301686fe48d39ba1f2bf0804617e>:0 at MaxQuantLibS.Domains.Peptides.Dia.Data.DiaRangeCombination.GetCount (MaxQuantLibS.Domains.Peptides.Data.Run run) [0x0000f] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Dia.Data.DiaRangeCombination.GetCount (MaxQuantLibS.Domains.Peptides.Data.GenericRun run) [0x00016] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.MsScansTable.FillTable (BaseLibS.Table.IDataTable table, System.String rawFile, System.Int32 rawFileIndex, MaxQuantLibS.Domains.Peptides.Basic.GroupParams param, MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams mqpar, MaxQuantLibS.Domains.Peptides.Data.CombinedData data) [0x00044] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.FillMsScansTable (System.String filenameTxt, System.String filenameSer, MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams mqpar, System.Int32 index, System.String combinedFolder) [0x00037] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteRemainingTables (System.Int32 jobIndex, System.String mqparFile, System.String combinedFolder, System.String txtFolder, System.String serFolder) [0x0021d] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteTablesImpl (System.String combinedFolder, System.String txtFolder, System.String serFolder, System.String mqparFile, System.Int32 taskIndex) [0x0016b] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteTables (System.String combinedFolder, System.String mqparFile, System.Int32 taskIndex) [0x00015] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Work.WriteTable.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x00036] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0003e] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantTask.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <7ba895466ed6424bbd152d1a31fcf271>:0 at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in <7b96395895e442fea6f0a41d98060a6c>:0 at MaxQuantTask.Program.Main (System.String[] args) [0x00007] in <7ba895466ed6424bbd152d1a31fcf271>:0 [ERROR] FATAL UNHANDLED EXCEPTION: System.IndexOutOfRangeException: Index was outside the bounds of the array. at BaseLibS.Ms.RawFileLayer.GetDiaMs2Indices () [0x00037] in <8513301686fe48d39ba1f2bf0804617e>:0 at BaseLibS.Ms.RawFileLayer.GetDiaRanges (System.Double[]& mzMin, System.Double[]& mzMax) [0x00001] in <8513301686fe48d39ba1f2bf0804617e>:0 at MaxQuantLibS.Domains.Peptides.Dia.Data.DiaRangeCombination.GetCount (MaxQuantLibS.Domains.Peptides.Data.Run run) [0x0000f] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Dia.Data.DiaRangeCombination.GetCount (MaxQuantLibS.Domains.Peptides.Data.GenericRun run) [0x00016] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.MsScansTable.FillTable (BaseLibS.Table.IDataTable table, System.String rawFile, System.Int32 rawFileIndex, MaxQuantLibS.Domains.Peptides.Basic.GroupParams param, MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams mqpar, MaxQuantLibS.Domains.Peptides.Data.CombinedData data) [0x00044] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.FillMsScansTable (System.String filenameTxt, System.String filenameSer, MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams mqpar, System.Int32 index, System.String combinedFolder) [0x00037] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteRemainingTables (System.Int32 jobIndex, System.String mqparFile, System.String combinedFolder, System.String txtFolder, System.String serFolder) [0x0021d] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteTablesImpl (System.String combinedFolder, System.String txtFolder, System.String serFolder, System.String mqparFile, System.Int32 taskIndex) [0x0016b] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Table.TableUtilsP.WriteTables (System.String combinedFolder, System.String mqparFile, System.Int32 taskIndex) [0x00015] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Work.WriteTable.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x00036] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0003e] in <0192019f238544f0853b98f2f971fe56>:0 at MaxQuantTask.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <7ba895466ed6424bbd152d1a31fcf271>:0 at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in <7b96395895e442fea6f0a41d98060a6c>:0 at MaxQuantTask.Program.Main (System.String[] args) [0x00007] in <7ba895466ed6424bbd152d1a31fcf271>:0

at QueueingSystem.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0009d] in :0 at QueueingSystem.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in :0 at QueueingSystem.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in :0 at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x0002c] in <12b418a7818c4ca0893feeaaf67f1e7f>:0 at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x0008d] in <12b418a7818c4ca0893feeaaf67f1e7f>:0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <12b418a7818c4ca0893feeaaf67f1e7f>:0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x00031] in <12b418a7818c4ca0893feeaaf67f1e7f>:0 at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x00012] in <12b418a7818c4ca0893feeaaf67f1e7f>:0

snail123815 commented 8 months ago

Same here. Error happens after I switch "writeMzTab" on. Using version 2.4.9.0.

atc3 commented 7 months ago

Hi,

I'm not familiar with this error. You should ask the official MaxQuant forum. The official help forum is on Google Groups here: https://groups.google.com/g/maxquant-list?pli=1

Albert