"C:\Program Files\R\R-4.0.3\bin\R.exe" -f "C:\Users\alejandrolp\AppData\Local\Apps\2.0\2VHH9Y75.Q2T\GD9YQJ5E.902\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\Tools\AvG_skylineexternaltool_v0.0.1.5_(4)\AvantGardeDIA_SkylineTool_Prep1_Params_QExactive_DIA.r" "D:\210607_DIA_Ftsz_levadura" "C:\Users\alejandrolp\AppData\Local\Apps\2.0\2VHH9Y75.Q2T\GD9YQJ5E.902\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\Tools\AvG_skylineexternaltool_v0.0.1.5_(4)" R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > args <- commandArgs() > print(args) [1] "C:\\PROGRA~1\\R\\R-40~1.3/bin/x64/Rterm.exe" [2] "-f" [3] "C:\\Users\\alejandrolp\\AppData\\Local\\Apps\\2.0\\2VHH9Y75.Q2T\\GD9YQJ5E.902\\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\\Tools\\AvG_skylineexternaltool_v0.0.1.5_(4)\\AvantGardeDIA_SkylineTool_Prep1_Params_QExactive_DIA.r" [4] "D:\\210607_DIA_Ftsz_levadura" [5] "C:\\Users\\alejandrolp\\AppData\\Local\\Apps\\2.0\\2VHH9Y75.Q2T\\GD9YQJ5E.902\\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\\Tools\\AvG_skylineexternaltool_v0.0.1.5_(4)" > setwd(file.path(args[4])) > getwd() [1] "D:/210607_DIA_Ftsz_levadura" > dir.create(file.path(getwd(),"AvantGardeDIA"),showWarnings = F) > setwd("AvantGardeDIA/") > > # Create AvantGardeDIA Parameters file > A<-" + Name_Tag='Name_Tag' #Short Name that will be added to all output files. (Must be in quotes) + + # I- DataFormating Parameters + MinimalInitialNumberOfTransitions_Filter=5 # Peptides with less than N transitions will be removed and not included in the SQLite Database + RemoveTransitionBelowOrdinal_Filter=3 # Transition ordinal below or equal to this value will be removed (for example if Max_TransitionIonOrdinal=3 transitions b1,b2,b3,y1,y2,y3 are removed) + RemoveSharedTransitionsBetweenLightAndHeavy_Filter=TRUE # Should be TRUE for DIA,FALSE for PRM. + ReadNumberOfLines=20000 # The CSV file is read in chunks. This parameter sets the number of lines in each chunk. + + # II- Optimization Parameters + NonZeroBaselineChromatogram=FALSE # TRUE for data having high noise baseline level (e.g. SWATH data on Q-TOF), FALSE (noise-reduced data, e.g demultiplexed Overlap DIA Data acquired on Q-Exactive series) + MinimalNumberOfTransitionsAfterOptimization=4 # The optimization will find the best solution that will have at least this number of transitions. + KeepPeptidesWithLowerNumberOfTransitions=FALSE # Keep (or not) a peptide if it has a lower number of transitions than the limit above (recomended FALSE for DIA). The transition refinement refinement will not be done on these peptides but the peak boundary refienement and scoring will be performed. + TopN_RankedbyIntensity=6 # Number of most intense transitions in teh spectral library (N) among which at least n transitions need to be present. + MinimalNumberOfTransitionsAmongTopN=2 # Number of transitions (n) that need to be present among the N most intense transitions in the spectral library. + alpha=0.005 + Beta=0.05 + SpectralLibraryDotProduct_limit=0.7 # + MassError_Tolerance=10 # Mass error tolerance (in PPM) + MassError_CutOff=20 # Mass error cut-off (in PPM) + MinimalNumberOfConsecutivePoints=3 # Minimal number of consecutive points above the limit of noise to consider a signal as a potential peptide. + MinimalIntensityPercentagePerTransition=3 # Minimal percentage of the maximum intensity of each transtion below which any point is no longer considered. + UseHeavyPeakBoundariesForLight=FALSE # Use the heavy peptide peak boundaries for the light peptides. + + ## Folders + Folder_1='DataFormatting' + Output.file=file.path(getwd(),Folder_1) + MultiFile.path=file.path(Output.file,'MultiFile') + Folder_2='TempFiles' + dir.output=file.path(getwd(),Folder_1,Folder_2) + Multifile_path=file.path(Output.file,'MultiFile') + RefinementWorkflow='GlobalRefinement'" > > write.table(A,file = "AvG_Params.R",row.names = F,col.names = F,quote = F) > > ### Installing Latest version of the AvantGardeDIA R package > install_Latest_AvG_RPackage<-file.path(args[5],"Update_AvG_RPackage.r") > source(install_Latest_AvG_RPackage) > > > print("Create AvantGardeDIA parameters file: Done!") [1] "Create AvantGardeDIA parameters file: Done!" > > "C:\Program Files\R\R-4.0.3\bin\R.exe" -f "C:\Users\alejandrolp\AppData\Local\Apps\2.0\2VHH9Y75.Q2T\GD9YQJ5E.902\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\Tools\AvG_skylineexternaltool_v0.0.1.5_(4)\AvantGardeDIA_SkylineTool_Prep2_DB.r" "C:\Users\alejandrolp\AppData\Local\Temp\AvantGardeDIA_Prep_2_Create_SQL_Database_From_Current_Skyline_File_AvantGardeDIA_Export.csv" "D:\210607_DIA_Ftsz_levadura" R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > rm(list=ls()) > library(dplyr) Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Warning message: package 'dplyr' was built under R version 4.0.5 > library(tidyr) Warning message: package 'tidyr' was built under R version 4.0.5 > library(stringr) Warning message: > library(data.table) package 'stringr' was built under R version 4.0.5 Attaching package: 'data.table' The following objects are masked from 'package:dplyr': > library(sqldf) between, first, last Warning message: package 'data.table' was built under R version 4.0.5 Loading required package: gsubfn Loading required package: proto Loading required package: RSQLite Warning messages: 1: package 'sqldf' was built under R version 4.0.5 2: package 'gsubfn' was built under R version 4.0.5 3: package 'proto' was built under R version 4.0.5 > library(foreach) 4: package 'RSQLite' was built under R version 4.0.5 Warning message: package 'foreach' was built under R version 4.0.5 > library(doSNOW) Loading required package: iterators Loading required package: snow Warning messages: > library(GA, quietly = T) 1: package 'doSNOW' was built under R version 4.0.5 2: package 'iterators' was built under R version 4.0.5 3: package 'snow' was built under R version 4.0.5 Package 'GA' version 3.2.1 Type 'citation("GA")' for citing this R package in publications. Attaching package: 'GA' The following object is masked from 'package:utils': de Warning message: package 'GA' was built under R version 4.0.5 > library(parallel) Attaching package: 'parallel' The following objects are masked from 'package:snow': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, makeCluster, parApply, parCapply, parLapply, parRapply, parSapply, splitIndices, stopCluster > library(readr) Warning message: > > args <- commandArgs() > print(args) package 'readr' was built under R version 4.0.5 [1] "C:\\PROGRA~1\\R\\R-40~1.3/bin/x64/Rterm.exe" [2] "-f" [3] "C:\\Users\\alejandrolp\\AppData\\Local\\Apps\\2.0\\2VHH9Y75.Q2T\\GD9YQJ5E.902\\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\\Tools\\AvG_skylineexternaltool_v0.0.1.5_(4)\\AvantGardeDIA_SkylineTool_Prep2_DB.r" [4] "C:\\Users\\alejandrolp\\AppData\\Local\\Temp\\AvantGardeDIA_Prep_2_Create_SQL_Database_From_Current_Skyline_File_AvantGardeDIA_Export.csv" [5] "D:\\210607_DIA_Ftsz_levadura" > setwd(file.path(args[5])) > getwd() [1] "D:/210607_DIA_Ftsz_levadura" > setwd("AvantGardeDIA/") > > ### source parameters file > ParamsFile="AvG_Params.R" > source(ParamsFile) > > D.file.name=args[4] > > ## Folders > Folder_1="DataFormatting" > dir.create(file.path(getwd(),Folder_1),showWarnings = F) > Output.file=file.path(getwd(),Folder_1) > dir.create(file.path(Output.file,"MultiFile"),showWarnings = F) > MultiFile.path=file.path(Output.file,"MultiFile") > Folder_2="TempFiles" > dir.create(file.path(getwd(),Folder_1,Folder_2),showWarnings = F) > dir.output=file.path(getwd(),Folder_1,Folder_2) > Multifile_path=file.path(Output.file,"MultiFile") > > ### Run AvG > library(AvantGardeDIA) > AvantGardeDIA::AvantGardeDIA_InChunks_DB(D.file.name = D.file.name,RefinementWorkflow = "GlobalRefinement") -- Column specification -------------------------------------------------------- cols( .default = col_character(), IsDecoy = col_logical(), PrecursorCharge = col_double(), PrecursorMz = col_double(), ProductCharge = col_double(), ProductMz = col_double(), Quantitative = col_logical(), LibraryDotProduct = col_double(), MinStartTime = col_double(), MaxEndTime = col_double(), Area = col_double(), LibraryIntensity = col_logical() ) i Use `spec()` for the full column specifications. [1] 1 [1] 2 [1] 3 [1] 4 [1] 5 [1] 6 [1] 7 [1] 8 [1] 9 [1] 10 [1] 11 [1] 12 [1] 13 [1] 14 [1] 15 [1] 16 [1] 17 [1] 18 [1] 19 [1] 20 [1] 21 [1] 22 [1] 23 [1] 24 Error: cannot allocate vector of size 835.0 Mb In addition: Warning message: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0. Please `group_by()` first This warning is displayed once every 8 hours. Call `lifecycle::last_warnings()` to see where this warning was generated. Execution halted "C:\Program Files\R\R-4.0.3\bin\R.exe" -f "C:\Users\alejandrolp\AppData\Local\Apps\2.0\2VHH9Y75.Q2T\GD9YQJ5E.902\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\Tools\AvG_skylineexternaltool_v0.0.1.5_(4)\AvantGardeDIA_SkylineTool_Prep1_Params_QExactive_DIA.r" "D:\210607_DIA_Ftsz_levadura" "C:\Users\alejandrolp\AppData\Local\Apps\2.0\2VHH9Y75.Q2T\GD9YQJ5E.902\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\Tools\AvG_skylineexternaltool_v0.0.1.5_(4)" R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > args <- commandArgs() > print(args) [1] "C:\\PROGRA~1\\R\\R-40~1.3/bin/x64/Rterm.exe" [2] "-f" [3] "C:\\Users\\alejandrolp\\AppData\\Local\\Apps\\2.0\\2VHH9Y75.Q2T\\GD9YQJ5E.902\\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\\Tools\\AvG_skylineexternaltool_v0.0.1.5_(4)\\AvantGardeDIA_SkylineTool_Prep1_Params_QExactive_DIA.r" [4] "D:\\210607_DIA_Ftsz_levadura" [5] "C:\\Users\\alejandrolp\\AppData\\Local\\Apps\\2.0\\2VHH9Y75.Q2T\\GD9YQJ5E.902\\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\\Tools\\AvG_skylineexternaltool_v0.0.1.5_(4)" > setwd(file.path(args[4])) > getwd() [1] "D:/210607_DIA_Ftsz_levadura" > dir.create(file.path(getwd(),"AvantGardeDIA"),showWarnings = F) > setwd("AvantGardeDIA/") > > # Create AvantGardeDIA Parameters file > A<-" + Name_Tag='Name_Tag' #Short Name that will be added to all output files. (Must be in quotes) + + # I- DataFormating Parameters + MinimalInitialNumberOfTransitions_Filter=5 # Peptides with less than N transitions will be removed and not included in the SQLite Database + RemoveTransitionBelowOrdinal_Filter=3 # Transition ordinal below or equal to this value will be removed (for example if Max_TransitionIonOrdinal=3 transitions b1,b2,b3,y1,y2,y3 are removed) + RemoveSharedTransitionsBetweenLightAndHeavy_Filter=TRUE # Should be TRUE for DIA,FALSE for PRM. + ReadNumberOfLines=20000 # The CSV file is read in chunks. This parameter sets the number of lines in each chunk. + + # II- Optimization Parameters + NonZeroBaselineChromatogram=FALSE # TRUE for data having high noise baseline level (e.g. SWATH data on Q-TOF), FALSE (noise-reduced data, e.g demultiplexed Overlap DIA Data acquired on Q-Exactive series) + MinimalNumberOfTransitionsAfterOptimization=4 # The optimization will find the best solution that will have at least this number of transitions. + KeepPeptidesWithLowerNumberOfTransitions=FALSE # Keep (or not) a peptide if it has a lower number of transitions than the limit above (recomended FALSE for DIA). The transition refinement refinement will not be done on these peptides but the peak boundary refienement and scoring will be performed. + TopN_RankedbyIntensity=6 # Number of most intense transitions in teh spectral library (N) among which at least n transitions need to be present. + MinimalNumberOfTransitionsAmongTopN=2 # Number of transitions (n) that need to be present among the N most intense transitions in the spectral library. + alpha=0.005 + Beta=0.05 + SpectralLibraryDotProduct_limit=0.7 # + MassError_Tolerance=10 # Mass error tolerance (in PPM) + MassError_CutOff=20 # Mass error cut-off (in PPM) + MinimalNumberOfConsecutivePoints=3 # Minimal number of consecutive points above the limit of noise to consider a signal as a potential peptide. + MinimalIntensityPercentagePerTransition=3 # Minimal percentage of the maximum intensity of each transtion below which any point is no longer considered. + UseHeavyPeakBoundariesForLight=FALSE # Use the heavy peptide peak boundaries for the light peptides. + + ## Folders + Folder_1='DataFormatting' + Output.file=file.path(getwd(),Folder_1) + MultiFile.path=file.path(Output.file,'MultiFile') + Folder_2='TempFiles' + dir.output=file.path(getwd(),Folder_1,Folder_2) + Multifile_path=file.path(Output.file,'MultiFile') + RefinementWorkflow='GlobalRefinement'" > > write.table(A,file = "AvG_Params.R",row.names = F,col.names = F,quote = F) > > ### Installing Latest version of the AvantGardeDIA R package > install_Latest_AvG_RPackage<-file.path(args[5],"Update_AvG_RPackage.r") > source(install_Latest_AvG_RPackage) > > > print("Create AvantGardeDIA parameters file: Done!") [1] "Create AvantGardeDIA parameters file: Done!" > > "C:\Program Files\R\R-4.0.3\bin\R.exe" -f "C:\Users\alejandrolp\AppData\Local\Apps\2.0\2VHH9Y75.Q2T\GD9YQJ5E.902\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\Tools\AvG_skylineexternaltool_v0.0.1.5_(4)\AvantGardeDIA_SkylineTool_Prep2_DB_LargeDataset.r" "210607_Ftsz_levadura_iRT.sky" "D:\210607_DIA_Ftsz_levadura" R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > rm(list=ls()) > library(dplyr) Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': > library(tidyr) intersect, setdiff, setequal, union Warning message: package 'dplyr' was built under R version 4.0.5 Warning message: > library(stringr) package 'tidyr' was built under R version 4.0.5 Warning message: package 'stringr' was built under R version 4.0.5 > library(data.table) Attaching package: 'data.table' The following objects are masked from 'package:dplyr': > library(sqldf) between, first, last Warning message: package 'data.table' was built under R version 4.0.5 Loading required package: gsubfn Loading required package: proto Loading required package: RSQLite Warning messages: 1: package 'sqldf' was built under R version 4.0.5 2: package 'gsubfn' was built under R version 4.0.5 > library(foreach) 3: package 'proto' was built under R version 4.0.5 4: package 'RSQLite' was built under R version 4.0.5 Warning message: package 'foreach' was built under R version 4.0.5 > library(doSNOW) Loading required package: iterators Loading required package: snow Warning messages: > library(GA, quietly = T) 1: package 'doSNOW' was built under R version 4.0.5 2: package 'iterators' was built under R version 4.0.5 3: package 'snow' was built under R version 4.0.5 Package 'GA' version 3.2.1 Type 'citation("GA")' for citing this R package in publications. Attaching package: 'GA' > library(parallel) The following object is masked from 'package:utils': de Warning message: package 'GA' was built under R version 4.0.5 Attaching package: 'parallel' The following objects are masked from 'package:snow': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, makeCluster, parApply, parCapply, parLapply, parRapply, parSapply, splitIndices, stopCluster > library(readr) Warning message: package 'readr' was built under R version 4.0.5 > > > args <- commandArgs() > > setwd(file.path(args[5])) > getwd() [1] "D:/210607_DIA_Ftsz_levadura" > setwd("AvantGardeDIA/") > > ### source parameters file > ParamsFile="AvG_Params.R" > source(ParamsFile) > > if(!file.exists("AvantGardeDIA_Export.csv")) {print("Please export AvantGardeDIA_Export report in the 'AvantGardeDIA' folder.")} else { + D.file.name="AvantGardeDIA_Export.csv" + + ## Folders + Folder_1="DataFormatting" + dir.create(file.path(getwd(),Folder_1),showWarnings = F) + Output.file=file.path(getwd(),Folder_1) + dir.create(file.path(Output.file,"MultiFile"),showWarnings = F) + MultiFile.path=file.path(Output.file,"MultiFile") + Folder_2="TempFiles" + dir.create(file.path(getwd(),Folder_1,Folder_2),showWarnings = F) + dir.output=file.path(getwd(),Folder_1,Folder_2) + Multifile_path=file.path(Output.file,"MultiFile") + + library(AvantGardeDIA) + AvantGardeDIA::AvantGardeDIA_InChunks_DB(D.file.name = D.file.name,RefinementWorkflow = "GlobalRefinement") + } -- Column specification -------------------------------------------------------- cols( .default = col_character(), `Is Decoy` = col_logical(), `Precursor Charge` = col_double(), `Precursor Mz` = col_double(), `Product Charge` = col_double(), `Product Mz` = col_double(), Quantitative = col_logical(), `Library Dot Product` = col_double(), `Min Start Time` = col_double(), `Max End Time` = col_double(), Area = col_double(), `Library Intensity` = col_logical() ) i Use `spec()` for the full column specifications. [1] 1 [1] 2 [1] 3 [1] 4 [1] 5 [1] 6 [1] 7 [1] 8 [1] 9 [1] 10 [1] 11 [1] 12 [1] 13 [1] 14 [1] 15 [1] 16 [1] 17 [1] 18 [1] 19 [1] 20 [1] 21 [1] 22 [1] 23 [1] 24 Error: cannot allocate vector of size 835.0 Mb In addition: Warning message: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0. Please `group_by()` first This warning is displayed once every 8 hours. Call `lifecycle::last_warnings()` to see where this warning was generated. Execution halted