"C:\Program Files\R\R-3.6.3\bin\R.exe" -f "C:\Program Files\Skyline\Application Files\Skyline-daily_20_1_1_83\Tools\AvG_skylineexternaltool_v0.0.1.4\AvantGardeDIA_SkylineTool_Prep1_Params_QTOF_DIA.r" "C:\Users\tim_v\Downloads\ExampleAvG.sky" "C:\Program Files\Skyline\Application Files\Skyline-daily_20_1_1_83\Tools\AvG_skylineexternaltool_v0.0.1.4"
ARGUMENT 'C:\Users\tim_v\Downloads\ExampleAvG.sky' __ignored__

ARGUMENT 'C:\Program Files\Skyline\Application Files\Skyline-daily_20_1_1_83\Tools\AvG_skylineexternaltool_v0.0.1.4' __ignored__


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

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-36~1.3/bin/x64/Rterm.exe"                                                                                                                       
[2] "-f"                                                                                                                                                                
[3] "C:\\Program Files\\Skyline\\Application Files\\Skyline-daily_20_1_1_83\\Tools\\AvG_skylineexternaltool_v0.0.1.4\\AvantGardeDIA_SkylineTool_Prep1_Params_QTOF_DIA.r"
[4] "C:\\Users\\tim_v\\Downloads\\ExampleAvG.sky"                                                                                                                       
[5] "C:\\Program Files\\Skyline\\Application Files\\Skyline-daily_20_1_1_83\\Tools\\AvG_skylineexternaltool_v0.0.1.4"                                                   
> setwd(file.path(args[4]))
> getwd()
[1] "C:/Users/tim_v/Downloads/ExampleAvG.sky"
> 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=TRUE # 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=0.9 # 
+ 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-3.6.3\bin\R.exe" -f "C:\Program Files\Skyline\Application Files\Skyline-daily_20_1_1_83\Tools\AvG_skylineexternaltool_v0.0.1.4\AvantGardeDIA_SkylineTool_Prep2_DB.r" "C:\Users\tim_v\AppData\Local\Temp\AvantGardeDIA_Prep_2_Create_SQL_Database_From_Current_Skyline_File_AvantGardeDIA_Export.csv" "C:\Users\tim_v\Downloads\ExampleAvG.sky"
ARGUMENT 'C:\Users\tim_v\AppData\Local\Temp\AvantGardeDIA_Prep_2_Create_SQL_Database_From_Current_Skyline_File_AvantGardeDIA_Export.csv' __ignored__

ARGUMENT 'C:\Users\tim_v\Downloads\ExampleAvG.sky' __ignored__


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

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

> library(tidyr)
> library(stringr)
> library(data.table)

Attaching package: 'data.table'

The following objects are masked from 'package:dplyr':

    between, first, last

> library(sqldf)
Loading required package: gsubfn
Loading required package: proto
Loading required package: RSQLite
> library(foreach)
> library(doSNOW)
Loading required package: iterators
Loading required package: snow
> library(GA, quietly = T)
Package 'GA' version 3.2
Type 'citation("GA")' for citing this R package in publications.

Attaching package: 'GA'

The following object is masked from 'package:utils':

    de

> 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)
> 
> args <- commandArgs()
> print(args)
[1] "C:\\PROGRA~1\\R\\R-36~1.3/bin/x64/Rterm.exe"                                                                                                          
[2] "-f"                                                                                                                                                   
[3] "C:\\Program Files\\Skyline\\Application Files\\Skyline-daily_20_1_1_83\\Tools\\AvG_skylineexternaltool_v0.0.1.4\\AvantGardeDIA_SkylineTool_Prep2_DB.r"
[4] "C:\\Users\\tim_v\\AppData\\Local\\Temp\\AvantGardeDIA_Prep_2_Create_SQL_Database_From_Current_Skyline_File_AvantGardeDIA_Export.csv"                  
[5] "C:\\Users\\tim_v\\Downloads\\ExampleAvG.sky"                                                                                                          
> setwd(file.path(args[5]))
> getwd()
[1] "C:/Users/tim_v/Downloads/ExampleAvG.sky"
> 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")
Parsed with 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_double()
)
See spec(...) for full column specifications.
[1] "The SQLite database called: 'DB_Name_Tag.sqlite' already exists in the working directory. Erase it or change the Name_Tag in the parameters file."
> 
> 
> rm(list=ls())
> 




"C:\Program Files\R\R-3.6.3\bin\R.exe" -f "C:\Program Files\Skyline\Application Files\Skyline-daily_20_1_1_83\Tools\AvG_skylineexternaltool_v0.0.1.4\AvantGardeDIA_SkylineTool_Go_GlobalRefinement.r" "C:\Users\tim_v\Downloads\ExampleAvG.sky"
ARGUMENT 'C:\Users\tim_v\Downloads\ExampleAvG.sky' __ignored__


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

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.

> 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

> library(tidyr)
> library(stringr)
> library(data.table)

Attaching package: 'data.table'
> library(sqldf)

The following objects are masked from 'package:dplyr':

    between, first, last

Loading required package: gsubfn
Loading required package: proto
Loading required package: RSQLite
> library(foreach)
> library(doSNOW)
Loading required package: iterators
Loading required package: snow
> library(GA, quietly = T)
Package 'GA' version 3.2
Type 'citation("GA")' for citing this R package in publications.

Attaching package: 'GA'

The following object is masked from 'package:utils':

    de

> 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)
> library(ggplot2)
> library(gridExtra)

Attaching package: 'gridExtra'

> 
The following object is masked from 'package:dplyr':
> args <- commandArgs()

> setwd(file.path(args[4]))
    combine
> setwd("AvantGardeDIA/")

> getwd()
[1] "C:/Users/tim_v/Downloads/ExampleAvG.sky/AvantGardeDIA"
> 
> #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")
> 
> ParamsFile="AvG_Params.R"
> source(ParamsFile)
> RefinementWorkflow="GlobalRefinement"
> write.table(paste0("RefinementWorkflow='",RefinementWorkflow,"'"),
+             file = file.path(getwd(),"AvG_Params.R"),
+             append = T,quote = F,row.names = F,col.names = F)
> 
> 
> library(AvantGardeDIA,quietly = T)
> cat(paste(paste0("AvantGardeDIA_",RefinementWorkflow," is running."),"The analisis is done using N-1 cores where N is the number of cores detected in this device. This might take a few minutes.",sep="\n"))
AvantGardeDIA_GlobalRefinement is running.
The analisis is done using N-1 cores where N is the number of cores detected in this device. This might take a few minutes.> 
> 
> LaunchParallelTasks_ReadFromDB(ParamsFile,RefinementWorkflow)
Warning messages:
[1] "Parallel: Done!"
1: In connection_release(conn@ptr) :
> Read_AndFormatResults()
  There are 1 result in use. The connection will be released when they are closed
2: In connection_release(conn@ptr) : Already disconnected
Error in file(file, "rt") : cannot open the connection
Calls: Read_AndFormatResults -> read.csv -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'C:/Users/tim_v/Downloads/ExampleAvG.sky/AvantGardeDIA/DataFormatting/TempFiles/Report_GR_ColNamesName_Tag.csv': No such file or directory
Execution halted