System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
.NET Core Info: 6.0.7


Version info:
FragPipe version 21.1
MSFragger version 4.0
IonQuant version 1.10.12
Philosopher version 5.1.0


LCMS files:
  Experiment/Group: 
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03.raw	DDA+
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02.raw	DIA
  - D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02.raw	DIA


5011 commands to execute:
CheckCentroid
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.raw 20
WorkspaceCleanInit [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ni9566\AppData\Local\Temp\aa74d6af-ebde-4813-8396-865d14fa41ae
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02675-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02676-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02677-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02678-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02679-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02680-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02681-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02682-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02683-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02684-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02685-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02686-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02687-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02688-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02689-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02690-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02691-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02692-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02693-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02694-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02695-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02696-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02697-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02698-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02699-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02700-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02716-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02717-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02718-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02719-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02720-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02721-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02722-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02723-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_INT001-02724-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02701-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02702-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02703-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02704-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02705-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02706-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02707-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02708-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02709-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02710-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02711-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02712-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02713-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02714-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02715-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02725-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02726-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02727-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_INT001-02728-HLAIp_R03_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02674-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02675-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02676-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02677-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02678-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02679-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02680-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02681-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02682-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02683-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02684-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02685-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02686-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02687-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_DIA_INT001-02688-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02689-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02690-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02691-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02692-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02693-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02694-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02695-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02696-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02697-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02698-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02699-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02700-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02716-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02717-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02718-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02719-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02720-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02721-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02722-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02723-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230828_DIA_INT001-02724-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02701-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02702-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02703-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02704-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02705-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02706-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02707-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02708-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02709-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02710-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02711-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02712-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02713-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02714-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02715-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02725-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02726-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\diaumpire_se.log D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diaumpire_se.log
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02_Peak D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02.DIAWindowsFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02.RTidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02.ScanClusterMapping_Q1 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02.ScanClusterMapping_Q2 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02.ScanClusterMapping_Q3 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02.ScanidxFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02.ScanPosFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02.ScanRTFS D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02_diasetting.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02_params.ser D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02_Q1.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02_Q2.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02_Q3.mgf D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q3.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q1.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q2.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/C:/DATA/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\Nicolas\Drug_treatments\Class1\raw_files\20230829_DIA_INT001-02727-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q3.mzML
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Peak
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.DIAWindowsFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.RTidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.ScanClusterMapping_Q1
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.ScanClusterMapping_Q2
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.ScanClusterMapping_Q3
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.ScanidxFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.ScanPosFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02.ScanRTFS
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_diasetting.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_params.ser
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q1.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q2.mgf
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q3.mgf
MSFragger [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx100G C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\MSFragger-4.0.jar D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\fragger_dda.params D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q2.mzML 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D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q1.mzML 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D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q3.mzML
MSFragger [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx100G C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\MSFragger-4.0.jar D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\fragger_dda.params D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q3.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q1.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q2.mzML D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q3.mzML
MSBooster [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\msbooster-1.1.28.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar Features.MainClass --paramsList D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\msbooster_params.txt
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02722-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02722-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02722-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02692-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02692-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02692-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02724-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02724-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02724-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02713-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02713-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02713-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02713-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02713-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02713-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02682-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02682-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02682-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02684-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02684-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02684-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02718-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02718-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02718-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02704-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02704-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02704-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02682-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02682-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02682-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02706-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02706-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02706-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02689-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02689-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02689-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02706-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02706-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02706-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02720-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02720-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02720-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02675-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02675-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02675-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02696-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02696-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02696-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02675-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02675-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02675-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02713-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02713-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02713-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02690-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02690-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02690-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02727-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02727-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02727-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02677-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02677-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02677-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02724-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02724-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02724-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02704-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02704-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02704-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02711-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02711-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02711-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02699-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02699-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02699-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02691-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02691-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02691-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02711-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02711-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02711-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02706-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02706-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02706-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02689-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02689-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02689-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02680-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02680-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02680-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02684-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02684-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02684-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02696-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02696-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02696-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02675-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02675-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02675-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02718-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02718-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02718-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02720-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02720-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02720-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02675-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02675-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02675-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02692-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02692-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02692-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02694-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02694-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02694-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02698-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02698-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02698-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02690-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02690-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02690-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02711-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02711-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02711-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02709-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02709-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02709-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02687-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02687-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02687-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02723-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02723-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02723-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02722-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02722-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02722-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02682-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02682-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02682-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02715-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02715-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02715-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02675-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02675-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02675-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02682-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02682-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02682-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02708-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02708-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02708-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02716-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02716-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02716-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02702-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02702-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02702-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02704-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02704-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02704-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02722-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02722-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02722-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02724-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02724-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02724-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02706-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02706-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02706-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02709-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02709-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02709-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02713-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02713-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02713-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02675-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02675-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02675-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02680-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02680-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02680-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02684-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02684-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02684-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02697-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02697-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02697-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02718-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02718-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02718-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02715-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02715-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02715-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02680-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02680-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02680-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02694-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02694-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02694-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02686-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02686-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02686-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02700-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02700-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02700-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02727-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02727-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02727-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02677-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02677-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02677-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02699-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02699-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02699-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02691-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02691-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02691-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02710-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02710-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02710-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02717-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02717-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02717-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02726-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02726-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02726-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02694-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02694-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02694-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02696-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02696-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02696-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02677-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02677-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02677-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02704-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02704-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02704-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02709-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02709-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02709-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02687-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02687-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02687-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02718-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02718-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02718-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02681-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02681-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02681-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02685-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02685-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02685-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02686-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02686-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02686-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02688-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02688-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02688-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02691-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02691-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02691-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02710-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02710-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02710-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02701-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02701-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02701-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02678-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02678-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02678-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02702-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02702-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02702-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02695-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02695-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02695-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02680-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02680-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02680-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02722-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02722-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02722-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02677-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02677-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02677-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02727-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02727-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02727-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02697-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02697-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02697-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02701-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02701-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02701-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02727-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02727-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02727-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02679-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02679-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02679-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02724-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02724-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02724-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02701-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02701-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02701-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02707-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02707-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02707-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02687-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02687-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02687-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02698-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02698-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02698-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02720-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02720-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02720-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02708-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02708-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02708-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02715-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02715-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02715-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02681-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02681-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02681-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02708-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02708-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02708-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02686-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02686-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02686-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02718-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02718-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02718-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02693-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02693-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02693-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02678-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02678-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02678-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02712-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02712-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02712-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02726-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02726-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02726-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02697-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02697-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02697-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02679-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02679-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02679-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02725-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02725-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02725-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02700-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02700-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02700-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02724-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02724-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02724-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02725-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02725-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02725-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02683-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02683-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02683-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02699-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02699-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02699-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02727-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02727-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02727-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02693-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02693-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02693-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02700-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02700-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02700-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02699-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02699-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02699-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02720-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02720-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02720-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02684-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02684-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02684-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02706-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02706-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02706-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02710-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02710-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02710-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02683-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02683-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02683-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02677-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02677-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02677-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02725-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02725-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02725-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02714-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02714-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02714-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02720-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02720-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02720-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02703-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02703-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02703-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02700-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02700-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02700-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02693-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02693-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02693-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02679-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02679-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02679-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02703-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02703-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02703-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02722-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02722-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02722-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02716-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02716-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02716-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02725-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02725-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02725-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02685-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02685-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02685-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02689-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02689-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02689-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02711-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02711-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02711-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02688-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02688-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02688-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02712-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02712-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02712-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02716-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02716-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02716-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02676-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02676-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02676-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02722-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02722-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02722-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02695-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02695-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02695-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02701-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02701-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02701-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02689-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02689-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02689-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02690-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02690-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02690-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02679-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02679-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02679-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02695-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02695-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02695-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02708-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02708-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02708-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02707-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02707-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02707-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02723-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02723-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02723-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02691-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02691-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02691-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02712-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02712-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02712-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02676-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02676-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02676-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02697-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02697-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02697-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02703-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02703-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02703-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02728-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02728-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02728-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02712-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02712-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02712-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02681-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02681-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02681-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02690-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02690-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02690-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02714-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02714-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02714-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02698-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02698-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02698-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02714-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02714-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02714-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02719-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02719-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02719-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02685-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02685-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02685-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02717-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02717-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02717-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02705-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02705-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02705-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02716-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02716-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02716-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02674-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02674-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02674-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02728-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02728-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02728-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02695-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02695-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02695-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02705-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02705-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02705-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02674-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02674-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02674-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02693-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02693-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02693-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02674-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02674-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02674-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02721-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02721-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02721-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02723-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02723-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02723-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02693-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02693-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02693-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02683-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02683-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02683-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02714-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02714-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02714-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02700-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02700-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02700-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02714-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02714-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02714-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02717-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02717-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02717-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02683-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02683-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02683-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02728-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02728-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02728-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02703-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02703-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02703-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02728-HLAIp_R03_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02728-HLAIp_R03_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02728-HLAIp_R03_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02688-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02688-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02688-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02674-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02674-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02674-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02705-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02705-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02705-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02697-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02697-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02697-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02705-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02705-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02705-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02710-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02710-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02710-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02697-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02697-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02697-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02705-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02705-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02705-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02688-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02688-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02688-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02714-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02714-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02714-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02674-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02674-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02674-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02689-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02689-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02689-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02716-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02716-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02716-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02685-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02685-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02685-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02688-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02688-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02688-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02692-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02692-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02692-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02681-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02681-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02681-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02719-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02719-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02719-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02685-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02685-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02685-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02717-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02717-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02717-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02676-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02676-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02676-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02728-HLAIp_R03_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02728-HLAIp_R03_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02728-HLAIp_R03_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02695-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02695-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02695-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02687-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02687-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02687-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02728-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02728-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02728-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02698-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02698-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02698-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02690-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02690-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02690-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02719-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02719-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02719-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02718-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02718-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02718-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02676-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02676-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02676-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02725-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02725-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02725-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02695-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02695-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02695-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02703-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02703-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02703-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02691-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02691-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02691-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02699-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02699-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02699-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02700-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02700-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02700-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02712-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02712-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02712-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02686-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02686-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02686-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02721-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02721-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02721-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02724-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02724-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02724-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02683-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02683-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02683-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02681-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02681-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02681-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02696-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02696-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02696-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02674-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02674-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02674-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02703-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02703-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02703-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02707-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02707-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02707-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02683-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02683-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02683-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02728-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02728-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02728-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02701-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02701-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02701-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02723-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02723-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02723-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02721-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02721-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02721-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02686-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02686-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02686-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02708-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02708-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02708-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02707-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02707-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02707-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02719-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02719-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02719-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02702-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02702-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02702-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02687-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02687-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02687-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02710-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02710-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02710-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02680-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02680-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02680-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02720-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02720-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02720-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02717-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02717-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02717-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02725-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02725-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02725-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02692-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02692-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02692-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02711-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02711-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02711-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02693-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02693-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02693-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02726-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02726-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02726-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02696-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02696-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02696-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02723-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02723-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02723-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02709-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02709-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02709-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02679-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02679-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02679-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02699-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02699-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02699-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02678-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02678-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02678-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02689-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02689-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02689-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02687-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02687-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02687-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02717-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02717-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02717-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02684-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02684-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02684-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02680-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02680-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02680-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02726-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02726-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02726-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02694-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02694-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02694-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02686-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02686-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02686-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02710-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02710-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02710-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02716-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02716-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02716-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02723-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02723-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02723-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02728-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02728-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02728-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02681-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02681-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02681-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02679-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02679-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02679-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02702-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02702-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02702-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02715-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02715-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02715-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02676-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02676-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02676-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02721-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02721-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02721-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02707-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02707-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02707-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02696-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02696-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02696-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02701-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02701-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02701-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02709-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02709-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02709-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02690-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02690-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02690-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02702-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02702-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02702-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02678-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02678-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02678-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02726-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02726-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02726-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02706-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02706-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02706-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02678-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02678-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02678-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02721-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02721-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02721-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02715-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02715-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02715-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02709-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02709-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02709-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02712-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02712-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02712-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02684-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02684-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02684-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02711-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02711-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02711-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02677-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02677-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02677-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02721-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02721-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02721-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02694-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02694-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02694-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02713-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02713-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02713-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02727-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02727-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02727-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02702-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02702-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02702-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02678-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02678-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02678-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02694-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02694-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02694-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02704-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02704-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02704-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02691-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02691-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02691-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02707-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02707-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02707-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02708-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02708-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02708-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02719-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02719-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02719-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02688-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02688-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02688-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02698-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02698-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02698-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02682-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02682-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02682-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_DIA_INT001-02682-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_DIA_INT001-02682-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_DIA_INT001-02682-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02685-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02685-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02685-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02692-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02692-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02692-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02715-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02715-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02715-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02705-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02705-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02705-HLAIp_R01_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02698-HLAIp_R02_Q1_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02698-HLAIp_R02_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02698-HLAIp_R02_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_DIA_INT001-02719-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230828_DIA_INT001-02719-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_DIA_INT001-02719-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02713-HLAIp_R02_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02713-HLAIp_R02_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02713-HLAIp_R02_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_DIA_INT001-02704-HLAIp_R02_Q2_percolator_target_psms.tsv --decoy-results-psms 20230829_DIA_INT001-02704-HLAIp_R02_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_DIA_INT001-02704-HLAIp_R02_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02728-HLAIp_R03_Q3_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02728-HLAIp_R03_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02728-HLAIp_R03_Q3_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230829_INT001-02726-HLAIp_R01_Q1_percolator_target_psms.tsv --decoy-results-psms 20230829_INT001-02726-HLAIp_R01_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230829_INT001-02726-HLAIp_R01_Q1_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230825_INT001-02676-HLAIp_R01_Q2_percolator_target_psms.tsv --decoy-results-psms 20230825_INT001-02676-HLAIp_R01_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230825_INT001-02676-HLAIp_R01_Q2_edited.pin
Percolator [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20230828_INT001-02692-HLAIp_R01_Q3_percolator_target_psms.tsv --decoy-results-psms 20230828_INT001-02692-HLAIp_R01_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230828_INT001-02692-HLAIp_R01_Q3_edited.pin
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02722-HLAIp_R01_Q3.pin 20230828_INT001-02722-HLAIp_R01_Q3 20230828_INT001-02722-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02722-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02722-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02692-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02692-HLAIp_R02_Q2 20230828_DIA_INT001-02692-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02692-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02692-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02724-HLAIp_R01_Q1.pin 20230828_INT001-02724-HLAIp_R01_Q1 20230828_INT001-02724-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02724-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02724-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02713-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02713-HLAIp_R02_Q2 20230829_DIA_INT001-02713-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02713-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02713-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02713-HLAIp_R01_Q2.pin 20230829_INT001-02713-HLAIp_R01_Q2 20230829_INT001-02713-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02713-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02713-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02682-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02682-HLAIp_R02_Q2 20230825_DIA_INT001-02682-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02682-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02682-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02684-HLAIp_R01_Q2.pin 20230825_INT001-02684-HLAIp_R01_Q2 20230825_INT001-02684-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02684-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02684-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02718-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02718-HLAIp_R02_Q2 20230828_DIA_INT001-02718-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02718-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02718-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02704-HLAIp_R01_Q3.pin 20230829_INT001-02704-HLAIp_R01_Q3 20230829_INT001-02704-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02704-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02704-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02682-HLAIp_R01_Q3.pin 20230825_INT001-02682-HLAIp_R01_Q3 20230825_INT001-02682-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02682-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02682-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02706-HLAIp_R01_Q1.pin 20230829_INT001-02706-HLAIp_R01_Q1 20230829_INT001-02706-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02706-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02706-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02689-HLAIp_R01_Q1.pin 20230828_INT001-02689-HLAIp_R01_Q1 20230828_INT001-02689-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02689-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02689-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02706-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02706-HLAIp_R02_Q1 20230829_DIA_INT001-02706-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02706-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02706-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02720-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02720-HLAIp_R02_Q1 20230828_DIA_INT001-02720-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02720-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02720-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02675-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02675-HLAIp_R02_Q1 20230825_DIA_INT001-02675-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02675-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02675-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02696-HLAIp_R01_Q2.pin 20230828_INT001-02696-HLAIp_R01_Q2 20230828_INT001-02696-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02696-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02696-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02675-HLAIp_R01_Q2.pin 20230825_INT001-02675-HLAIp_R01_Q2 20230825_INT001-02675-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02675-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02675-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02713-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02713-HLAIp_R02_Q1 20230829_DIA_INT001-02713-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02713-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02713-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02690-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02690-HLAIp_R02_Q3 20230828_DIA_INT001-02690-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02690-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02690-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02727-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02727-HLAIp_R02_Q3 20230829_DIA_INT001-02727-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02727-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02727-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02677-HLAIp_R01_Q1.pin 20230825_INT001-02677-HLAIp_R01_Q1 20230825_INT001-02677-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02677-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02677-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02724-HLAIp_R01_Q2.pin 20230828_INT001-02724-HLAIp_R01_Q2 20230828_INT001-02724-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02724-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02724-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02704-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02704-HLAIp_R02_Q3 20230829_DIA_INT001-02704-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02704-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02704-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02711-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02711-HLAIp_R02_Q3 20230829_DIA_INT001-02711-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02711-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02711-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02699-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02699-HLAIp_R02_Q3 20230828_DIA_INT001-02699-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02699-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02699-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02691-HLAIp_R01_Q1.pin 20230828_INT001-02691-HLAIp_R01_Q1 20230828_INT001-02691-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02691-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02691-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02711-HLAIp_R01_Q3.pin 20230829_INT001-02711-HLAIp_R01_Q3 20230829_INT001-02711-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02711-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02711-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02706-HLAIp_R01_Q2.pin 20230829_INT001-02706-HLAIp_R01_Q2 20230829_INT001-02706-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02706-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02706-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02689-HLAIp_R01_Q2.pin 20230828_INT001-02689-HLAIp_R01_Q2 20230828_INT001-02689-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02689-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02689-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02680-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02680-HLAIp_R02_Q3 20230825_DIA_INT001-02680-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02680-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02680-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02684-HLAIp_R01_Q1.pin 20230825_INT001-02684-HLAIp_R01_Q1 20230825_INT001-02684-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02684-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02684-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02696-HLAIp_R01_Q1.pin 20230828_INT001-02696-HLAIp_R01_Q1 20230828_INT001-02696-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02696-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02696-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02675-HLAIp_R01_Q3.pin 20230825_INT001-02675-HLAIp_R01_Q3 20230825_INT001-02675-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02675-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02675-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02718-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02718-HLAIp_R02_Q3 20230828_DIA_INT001-02718-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02718-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02718-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02720-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02720-HLAIp_R02_Q2 20230828_DIA_INT001-02720-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02720-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02720-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02675-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02675-HLAIp_R02_Q2 20230825_DIA_INT001-02675-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02675-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02675-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02692-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02692-HLAIp_R02_Q1 20230828_DIA_INT001-02692-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02692-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02692-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02694-HLAIp_R01_Q3.pin 20230828_INT001-02694-HLAIp_R01_Q3 20230828_INT001-02694-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02694-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02694-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02698-HLAIp_R01_Q2.pin 20230828_INT001-02698-HLAIp_R01_Q2 20230828_INT001-02698-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02698-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02698-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02690-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02690-HLAIp_R02_Q2 20230828_DIA_INT001-02690-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02690-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02690-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02711-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02711-HLAIp_R02_Q2 20230829_DIA_INT001-02711-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02711-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02711-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02709-HLAIp_R01_Q3.pin 20230829_INT001-02709-HLAIp_R01_Q3 20230829_INT001-02709-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02709-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02709-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02687-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02687-HLAIp_R02_Q3 20230825_DIA_INT001-02687-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02687-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02687-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02723-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02723-HLAIp_R02_Q3 20230828_DIA_INT001-02723-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02723-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02723-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02722-HLAIp_R01_Q1.pin 20230828_INT001-02722-HLAIp_R01_Q1 20230828_INT001-02722-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02722-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02722-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02682-HLAIp_R01_Q2.pin 20230825_INT001-02682-HLAIp_R01_Q2 20230825_INT001-02682-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02682-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02682-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02715-HLAIp_R01_Q2.pin 20230829_INT001-02715-HLAIp_R01_Q2 20230829_INT001-02715-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02715-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02715-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02675-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02675-HLAIp_R02_Q3 20230825_DIA_INT001-02675-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02675-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02675-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02675-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02682-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02682-HLAIp_R02_Q1 20230825_DIA_INT001-02682-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02682-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02682-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02708-HLAIp_R01_Q1.pin 20230829_INT001-02708-HLAIp_R01_Q1 20230829_INT001-02708-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02708-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02708-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02716-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02716-HLAIp_R02_Q2 20230828_DIA_INT001-02716-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02716-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02716-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02702-HLAIp_R01_Q3.pin 20230829_INT001-02702-HLAIp_R01_Q3 20230829_INT001-02702-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02702-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02702-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02704-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02704-HLAIp_R02_Q1 20230829_DIA_INT001-02704-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02704-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02704-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02722-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02722-HLAIp_R02_Q1 20230828_DIA_INT001-02722-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02722-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02722-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02724-HLAIp_R01_Q3.pin 20230828_INT001-02724-HLAIp_R01_Q3 20230828_INT001-02724-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02724-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02724-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02724-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02706-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02706-HLAIp_R02_Q3 20230829_DIA_INT001-02706-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02706-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02706-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02709-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02709-HLAIp_R02_Q2 20230829_DIA_INT001-02709-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02709-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02709-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02713-HLAIp_R01_Q3.pin 20230829_INT001-02713-HLAIp_R01_Q3 20230829_INT001-02713-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02713-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02713-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02675-HLAIp_R01_Q1.pin 20230825_INT001-02675-HLAIp_R01_Q1 20230825_INT001-02675-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02675-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02675-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02675-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02680-HLAIp_R01_Q3.pin 20230825_INT001-02680-HLAIp_R01_Q3 20230825_INT001-02680-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02680-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02680-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02684-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02684-HLAIp_R02_Q1 20230825_DIA_INT001-02684-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02684-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02684-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02697-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02697-HLAIp_R02_Q3 20230828_DIA_INT001-02697-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02697-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02697-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02718-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02718-HLAIp_R02_Q1 20230828_DIA_INT001-02718-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02718-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02718-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02718-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02715-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02715-HLAIp_R02_Q1 20230829_DIA_INT001-02715-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02715-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02715-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02680-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02680-HLAIp_R02_Q2 20230825_DIA_INT001-02680-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02680-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02680-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02694-HLAIp_R01_Q1.pin 20230828_INT001-02694-HLAIp_R01_Q1 20230828_INT001-02694-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02694-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02694-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02686-HLAIp_R01_Q1.pin 20230825_INT001-02686-HLAIp_R01_Q1 20230825_INT001-02686-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02686-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02686-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02700-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02700-HLAIp_R02_Q3 20230828_DIA_INT001-02700-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02700-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02700-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02727-HLAIp_R01_Q2.pin 20230829_INT001-02727-HLAIp_R01_Q2 20230829_INT001-02727-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02727-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02727-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02677-HLAIp_R01_Q3.pin 20230825_INT001-02677-HLAIp_R01_Q3 20230825_INT001-02677-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02677-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02677-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02699-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02699-HLAIp_R02_Q2 20230828_DIA_INT001-02699-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02699-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02699-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02691-HLAIp_R01_Q2.pin 20230828_INT001-02691-HLAIp_R01_Q2 20230828_INT001-02691-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02691-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02691-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02710-HLAIp_R01_Q1.pin 20230829_INT001-02710-HLAIp_R01_Q1 20230829_INT001-02710-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02710-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02710-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02717-HLAIp_R01_Q1.pin 20230828_INT001-02717-HLAIp_R01_Q1 20230828_INT001-02717-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02717-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02717-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02726-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02726-HLAIp_R02_Q1 20230829_DIA_INT001-02726-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02726-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02726-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02694-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02694-HLAIp_R02_Q1 20230828_DIA_INT001-02694-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02694-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02694-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02696-HLAIp_R01_Q3.pin 20230828_INT001-02696-HLAIp_R01_Q3 20230828_INT001-02696-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02696-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02696-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02696-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02677-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02677-HLAIp_R02_Q2 20230825_DIA_INT001-02677-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02677-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02677-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02704-HLAIp_R01_Q2.pin 20230829_INT001-02704-HLAIp_R01_Q2 20230829_INT001-02704-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02704-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02704-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02709-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02709-HLAIp_R02_Q1 20230829_DIA_INT001-02709-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02709-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02709-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02687-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02687-HLAIp_R02_Q1 20230825_DIA_INT001-02687-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02687-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02687-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02718-HLAIp_R01_Q2.pin 20230828_INT001-02718-HLAIp_R01_Q2 20230828_INT001-02718-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02718-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02718-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02681-HLAIp_R01_Q1.pin 20230825_INT001-02681-HLAIp_R01_Q1 20230825_INT001-02681-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02681-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02681-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02685-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02685-HLAIp_R02_Q3 20230825_DIA_INT001-02685-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02685-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02685-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02686-HLAIp_R01_Q3.pin 20230825_INT001-02686-HLAIp_R01_Q3 20230825_INT001-02686-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02686-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02686-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02688-HLAIp_R01_Q1.pin 20230825_INT001-02688-HLAIp_R01_Q1 20230825_INT001-02688-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02688-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02688-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02691-HLAIp_R01_Q3.pin 20230828_INT001-02691-HLAIp_R01_Q3 20230828_INT001-02691-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02691-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02691-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02691-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02710-HLAIp_R01_Q2.pin 20230829_INT001-02710-HLAIp_R01_Q2 20230829_INT001-02710-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02710-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02710-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02701-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02701-HLAIp_R02_Q2 20230829_DIA_INT001-02701-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02701-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02701-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02678-HLAIp_R01_Q3.pin 20230825_INT001-02678-HLAIp_R01_Q3 20230825_INT001-02678-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02678-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02678-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02702-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02702-HLAIp_R02_Q1 20230829_DIA_INT001-02702-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02702-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02702-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02695-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02695-HLAIp_R02_Q3 20230828_DIA_INT001-02695-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02695-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02695-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02680-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02680-HLAIp_R02_Q1 20230825_DIA_INT001-02680-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02680-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02680-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02680-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02722-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02722-HLAIp_R02_Q3 20230828_DIA_INT001-02722-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02722-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02722-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02677-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02677-HLAIp_R02_Q3 20230825_DIA_INT001-02677-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02677-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02677-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02727-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02727-HLAIp_R02_Q1 20230829_DIA_INT001-02727-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02727-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02727-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02697-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02697-HLAIp_R02_Q1 20230828_DIA_INT001-02697-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02697-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02697-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02701-HLAIp_R01_Q2.pin 20230829_INT001-02701-HLAIp_R01_Q2 20230829_INT001-02701-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02701-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02701-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02727-HLAIp_R01_Q1.pin 20230829_INT001-02727-HLAIp_R01_Q1 20230829_INT001-02727-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02727-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02727-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02679-HLAIp_R01_Q2.pin 20230825_INT001-02679-HLAIp_R01_Q2 20230825_INT001-02679-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02679-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02679-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02724-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02724-HLAIp_R02_Q1 20230828_DIA_INT001-02724-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02724-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02724-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02701-HLAIp_R01_Q1.pin 20230829_INT001-02701-HLAIp_R01_Q1 20230829_INT001-02701-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02701-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02701-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02707-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02707-HLAIp_R02_Q2 20230829_DIA_INT001-02707-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02707-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02707-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02687-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02687-HLAIp_R02_Q2 20230825_DIA_INT001-02687-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02687-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02687-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02687-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02698-HLAIp_R01_Q3.pin 20230828_INT001-02698-HLAIp_R01_Q3 20230828_INT001-02698-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02698-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02698-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02720-HLAIp_R01_Q2.pin 20230828_INT001-02720-HLAIp_R01_Q2 20230828_INT001-02720-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02720-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02720-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02708-HLAIp_R01_Q3.pin 20230829_INT001-02708-HLAIp_R01_Q3 20230829_INT001-02708-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02708-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02708-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02715-HLAIp_R01_Q3.pin 20230829_INT001-02715-HLAIp_R01_Q3 20230829_INT001-02715-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02715-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02715-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02681-HLAIp_R01_Q2.pin 20230825_INT001-02681-HLAIp_R01_Q2 20230825_INT001-02681-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02681-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02681-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02708-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02708-HLAIp_R02_Q3 20230829_DIA_INT001-02708-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02708-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02708-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02686-HLAIp_R01_Q2.pin 20230825_INT001-02686-HLAIp_R01_Q2 20230825_INT001-02686-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02686-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02686-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02686-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02718-HLAIp_R01_Q3.pin 20230828_INT001-02718-HLAIp_R01_Q3 20230828_INT001-02718-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02718-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02718-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02693-HLAIp_R01_Q2.pin 20230828_INT001-02693-HLAIp_R01_Q2 20230828_INT001-02693-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02693-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02693-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02678-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02678-HLAIp_R02_Q1 20230825_DIA_INT001-02678-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02678-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02678-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02712-HLAIp_R01_Q1.pin 20230829_INT001-02712-HLAIp_R01_Q1 20230829_INT001-02712-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02712-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02712-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02726-HLAIp_R01_Q3.pin 20230829_INT001-02726-HLAIp_R01_Q3 20230829_INT001-02726-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02726-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02726-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02697-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02697-HLAIp_R02_Q2 20230828_DIA_INT001-02697-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02697-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02697-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02697-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02679-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02679-HLAIp_R02_Q2 20230825_DIA_INT001-02679-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02679-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02679-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02725-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02725-HLAIp_R02_Q2 20230829_DIA_INT001-02725-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02725-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02725-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02700-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02700-HLAIp_R02_Q1 20230828_DIA_INT001-02700-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02700-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02700-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02724-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02724-HLAIp_R02_Q2 20230828_DIA_INT001-02724-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02724-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02724-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02725-HLAIp_R01_Q2.pin 20230829_INT001-02725-HLAIp_R01_Q2 20230829_INT001-02725-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02725-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02725-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02683-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02683-HLAIp_R02_Q3 20230825_DIA_INT001-02683-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02683-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02683-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02699-HLAIp_R01_Q1.pin 20230828_INT001-02699-HLAIp_R01_Q1 20230828_INT001-02699-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02699-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02699-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02727-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02727-HLAIp_R02_Q2 20230829_DIA_INT001-02727-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02727-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02727-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02727-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02693-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02693-HLAIp_R02_Q3 20230828_DIA_INT001-02693-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02693-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02693-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02700-HLAIp_R01_Q2.pin 20230828_INT001-02700-HLAIp_R01_Q2 20230828_INT001-02700-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02700-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02700-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02699-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02699-HLAIp_R02_Q1 20230828_DIA_INT001-02699-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02699-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02699-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02699-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02720-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02720-HLAIp_R02_Q3 20230828_DIA_INT001-02720-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02720-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02720-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02720-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02684-HLAIp_R01_Q3.pin 20230825_INT001-02684-HLAIp_R01_Q3 20230825_INT001-02684-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02684-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02684-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02684-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02706-HLAIp_R01_Q3.pin 20230829_INT001-02706-HLAIp_R01_Q3 20230829_INT001-02706-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02706-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02706-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02706-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02710-HLAIp_R01_Q3.pin 20230829_INT001-02710-HLAIp_R01_Q3 20230829_INT001-02710-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02710-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02710-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02710-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02683-HLAIp_R01_Q1.pin 20230825_INT001-02683-HLAIp_R01_Q1 20230825_INT001-02683-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02683-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02683-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02677-HLAIp_R01_Q2.pin 20230825_INT001-02677-HLAIp_R01_Q2 20230825_INT001-02677-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02677-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02677-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02677-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02725-HLAIp_R01_Q1.pin 20230829_INT001-02725-HLAIp_R01_Q1 20230829_INT001-02725-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02725-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02725-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02714-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02714-HLAIp_R02_Q3 20230829_DIA_INT001-02714-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02714-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02714-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02720-HLAIp_R01_Q3.pin 20230828_INT001-02720-HLAIp_R01_Q3 20230828_INT001-02720-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02720-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02720-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02703-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02703-HLAIp_R02_Q2 20230829_DIA_INT001-02703-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02703-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02703-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02700-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02700-HLAIp_R02_Q2 20230828_DIA_INT001-02700-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02700-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02700-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02700-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02693-HLAIp_R01_Q3.pin 20230828_INT001-02693-HLAIp_R01_Q3 20230828_INT001-02693-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02693-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02693-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02679-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02679-HLAIp_R02_Q3 20230825_DIA_INT001-02679-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02679-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02679-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02703-HLAIp_R01_Q1.pin 20230829_INT001-02703-HLAIp_R01_Q1 20230829_INT001-02703-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02703-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02703-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02722-HLAIp_R01_Q2.pin 20230828_INT001-02722-HLAIp_R01_Q2 20230828_INT001-02722-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02722-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02722-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02722-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02716-HLAIp_R01_Q3.pin 20230828_INT001-02716-HLAIp_R01_Q3 20230828_INT001-02716-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02716-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02716-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02725-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02725-HLAIp_R02_Q3 20230829_DIA_INT001-02725-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02725-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02725-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02685-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02685-HLAIp_R02_Q2 20230825_DIA_INT001-02685-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02685-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02685-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02689-HLAIp_R01_Q3.pin 20230828_INT001-02689-HLAIp_R01_Q3 20230828_INT001-02689-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02689-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02689-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02689-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02711-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02711-HLAIp_R02_Q1 20230829_DIA_INT001-02711-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02711-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02711-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02711-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02688-HLAIp_R01_Q2.pin 20230825_INT001-02688-HLAIp_R01_Q2 20230825_INT001-02688-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02688-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02688-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02712-HLAIp_R01_Q2.pin 20230829_INT001-02712-HLAIp_R01_Q2 20230829_INT001-02712-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02712-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02712-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02716-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02716-HLAIp_R02_Q3 20230828_DIA_INT001-02716-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02716-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02716-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02676-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02676-HLAIp_R02_Q1 20230825_DIA_INT001-02676-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02676-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02676-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02722-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02722-HLAIp_R02_Q2 20230828_DIA_INT001-02722-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02722-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02722-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02722-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02695-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02695-HLAIp_R02_Q2 20230828_DIA_INT001-02695-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02695-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02695-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02701-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02701-HLAIp_R02_Q3 20230829_DIA_INT001-02701-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02701-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02701-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02689-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02689-HLAIp_R02_Q3 20230828_DIA_INT001-02689-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02689-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02689-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02690-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02690-HLAIp_R02_Q1 20230828_DIA_INT001-02690-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02690-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02690-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02690-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02679-HLAIp_R01_Q1.pin 20230825_INT001-02679-HLAIp_R01_Q1 20230825_INT001-02679-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02679-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02679-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02695-HLAIp_R01_Q2.pin 20230828_INT001-02695-HLAIp_R01_Q2 20230828_INT001-02695-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02695-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02695-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02708-HLAIp_R01_Q2.pin 20230829_INT001-02708-HLAIp_R01_Q2 20230829_INT001-02708-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02708-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02708-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02708-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02707-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02707-HLAIp_R02_Q1 20230829_DIA_INT001-02707-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02707-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02707-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02723-HLAIp_R01_Q2.pin 20230828_INT001-02723-HLAIp_R01_Q2 20230828_INT001-02723-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02723-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02723-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02691-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02691-HLAIp_R02_Q3 20230828_DIA_INT001-02691-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02691-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02691-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02712-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02712-HLAIp_R02_Q3 20230829_DIA_INT001-02712-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02712-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02712-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02676-HLAIp_R01_Q1.pin 20230825_INT001-02676-HLAIp_R01_Q1 20230825_INT001-02676-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02676-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02676-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02697-HLAIp_R01_Q1.pin 20230828_INT001-02697-HLAIp_R01_Q1 20230828_INT001-02697-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02697-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02697-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02703-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02703-HLAIp_R02_Q3 20230829_DIA_INT001-02703-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02703-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02703-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02728-HLAIp_R01_Q3.pin 20230829_INT001-02728-HLAIp_R01_Q3 20230829_INT001-02728-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02728-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02728-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02712-HLAIp_R01_Q3.pin 20230829_INT001-02712-HLAIp_R01_Q3 20230829_INT001-02712-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02712-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02712-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02712-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02681-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02681-HLAIp_R02_Q3 20230825_DIA_INT001-02681-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02681-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02681-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02690-HLAIp_R01_Q1.pin 20230828_INT001-02690-HLAIp_R01_Q1 20230828_INT001-02690-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02690-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02690-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02714-HLAIp_R01_Q1.pin 20230829_INT001-02714-HLAIp_R01_Q1 20230829_INT001-02714-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02714-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02714-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02698-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02698-HLAIp_R02_Q3 20230828_DIA_INT001-02698-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02698-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02698-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02714-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02714-HLAIp_R02_Q1 20230829_DIA_INT001-02714-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02714-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02714-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02719-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02719-HLAIp_R02_Q1 20230828_DIA_INT001-02719-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02719-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02719-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02685-HLAIp_R01_Q1.pin 20230825_INT001-02685-HLAIp_R01_Q1 20230825_INT001-02685-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02685-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02685-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02717-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02717-HLAIp_R02_Q3 20230828_DIA_INT001-02717-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02717-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02717-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02705-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02705-HLAIp_R02_Q2 20230829_DIA_INT001-02705-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02705-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02705-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02716-HLAIp_R01_Q1.pin 20230828_INT001-02716-HLAIp_R01_Q1 20230828_INT001-02716-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02716-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02716-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02674-HLAIp_R01_Q3.pin 20230825_INT001-02674-HLAIp_R01_Q3 20230825_INT001-02674-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02674-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02674-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02728-HLAIp_R02_Q2.pin 20230829_INT001-02728-HLAIp_R02_Q2 20230829_INT001-02728-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_INT001-02728-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02728-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02695-HLAIp_R01_Q3.pin 20230828_INT001-02695-HLAIp_R01_Q3 20230828_INT001-02695-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02695-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02695-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02705-HLAIp_R01_Q2.pin 20230829_INT001-02705-HLAIp_R01_Q2 20230829_INT001-02705-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02705-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02705-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02674-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02674-HLAIp_R02_Q2 20230825_DIA_INT001-02674-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02674-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02674-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02693-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02693-HLAIp_R02_Q1 20230828_DIA_INT001-02693-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02693-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02693-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02674-HLAIp_R01_Q2.pin 20230825_INT001-02674-HLAIp_R01_Q2 20230825_INT001-02674-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02674-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02674-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02721-HLAIp_R01_Q3.pin 20230828_INT001-02721-HLAIp_R01_Q3 20230828_INT001-02721-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02721-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02721-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02723-HLAIp_R01_Q1.pin 20230828_INT001-02723-HLAIp_R01_Q1 20230828_INT001-02723-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02723-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02723-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02693-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02693-HLAIp_R02_Q2 20230828_DIA_INT001-02693-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02693-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02693-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02693-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02683-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02683-HLAIp_R02_Q2 20230825_DIA_INT001-02683-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02683-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02683-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02714-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02714-HLAIp_R02_Q2 20230829_DIA_INT001-02714-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02714-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02714-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02714-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02700-HLAIp_R01_Q1.pin 20230828_INT001-02700-HLAIp_R01_Q1 20230828_INT001-02700-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02700-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02700-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02714-HLAIp_R01_Q2.pin 20230829_INT001-02714-HLAIp_R01_Q2 20230829_INT001-02714-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02714-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02714-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02717-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02717-HLAIp_R02_Q2 20230828_DIA_INT001-02717-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02717-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02717-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02683-HLAIp_R01_Q3.pin 20230825_INT001-02683-HLAIp_R01_Q3 20230825_INT001-02683-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02683-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02683-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02728-HLAIp_R02_Q1.pin 20230829_INT001-02728-HLAIp_R02_Q1 20230829_INT001-02728-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_INT001-02728-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02728-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02703-HLAIp_R01_Q3.pin 20230829_INT001-02703-HLAIp_R01_Q3 20230829_INT001-02703-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02703-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02703-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02728-HLAIp_R03_Q1.pin 20230829_INT001-02728-HLAIp_R03_Q1 20230829_INT001-02728-HLAIp_R03_Q1_percolator_target_psms.tsv 20230829_INT001-02728-HLAIp_R03_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02728-HLAIp_R03_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02688-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02688-HLAIp_R02_Q3 20230825_DIA_INT001-02688-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02688-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02688-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02674-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02674-HLAIp_R02_Q1 20230825_DIA_INT001-02674-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02674-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02674-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02705-HLAIp_R01_Q1.pin 20230829_INT001-02705-HLAIp_R01_Q1 20230829_INT001-02705-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02705-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02705-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02697-HLAIp_R01_Q2.pin 20230828_INT001-02697-HLAIp_R01_Q2 20230828_INT001-02697-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02697-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02697-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02705-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02705-HLAIp_R02_Q1 20230829_DIA_INT001-02705-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02705-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02705-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02710-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02710-HLAIp_R02_Q3 20230829_DIA_INT001-02710-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02710-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02710-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02697-HLAIp_R01_Q3.pin 20230828_INT001-02697-HLAIp_R01_Q3 20230828_INT001-02697-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02697-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02697-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02697-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02705-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02705-HLAIp_R02_Q3 20230829_DIA_INT001-02705-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02705-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02705-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02705-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02688-HLAIp_R01_Q3.pin 20230825_INT001-02688-HLAIp_R01_Q3 20230825_INT001-02688-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02688-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02688-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02688-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02714-HLAIp_R01_Q3.pin 20230829_INT001-02714-HLAIp_R01_Q3 20230829_INT001-02714-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02714-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02714-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02714-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02674-HLAIp_R01_Q1.pin 20230825_INT001-02674-HLAIp_R01_Q1 20230825_INT001-02674-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02674-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02674-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02674-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02689-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02689-HLAIp_R02_Q2 20230828_DIA_INT001-02689-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02689-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02689-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02716-HLAIp_R01_Q2.pin 20230828_INT001-02716-HLAIp_R01_Q2 20230828_INT001-02716-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02716-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02716-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02716-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02685-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02685-HLAIp_R02_Q1 20230825_DIA_INT001-02685-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02685-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02685-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02685-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02688-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02688-HLAIp_R02_Q2 20230825_DIA_INT001-02688-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02688-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02688-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02692-HLAIp_R01_Q1.pin 20230828_INT001-02692-HLAIp_R01_Q1 20230828_INT001-02692-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02692-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02692-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02681-HLAIp_R01_Q3.pin 20230825_INT001-02681-HLAIp_R01_Q3 20230825_INT001-02681-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02681-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02681-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02681-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02719-HLAIp_R01_Q3.pin 20230828_INT001-02719-HLAIp_R01_Q3 20230828_INT001-02719-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02719-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02719-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02685-HLAIp_R01_Q2.pin 20230825_INT001-02685-HLAIp_R01_Q2 20230825_INT001-02685-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02685-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02685-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02717-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02717-HLAIp_R02_Q1 20230828_DIA_INT001-02717-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02717-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02717-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02717-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02676-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02676-HLAIp_R02_Q2 20230825_DIA_INT001-02676-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02676-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02676-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02728-HLAIp_R03_Q2.pin 20230829_INT001-02728-HLAIp_R03_Q2 20230829_INT001-02728-HLAIp_R03_Q2_percolator_target_psms.tsv 20230829_INT001-02728-HLAIp_R03_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02728-HLAIp_R03_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02695-HLAIp_R01_Q1.pin 20230828_INT001-02695-HLAIp_R01_Q1 20230828_INT001-02695-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02695-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02695-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02695-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02687-HLAIp_R01_Q1.pin 20230825_INT001-02687-HLAIp_R01_Q1 20230825_INT001-02687-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02687-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02687-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02728-HLAIp_R01_Q2.pin 20230829_INT001-02728-HLAIp_R01_Q2 20230829_INT001-02728-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02728-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02728-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02698-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02698-HLAIp_R02_Q2 20230828_DIA_INT001-02698-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02698-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02698-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02690-HLAIp_R01_Q2.pin 20230828_INT001-02690-HLAIp_R01_Q2 20230828_INT001-02690-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02690-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02690-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02719-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02719-HLAIp_R02_Q3 20230828_DIA_INT001-02719-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02719-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02719-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02718-HLAIp_R01_Q1.pin 20230828_INT001-02718-HLAIp_R01_Q1 20230828_INT001-02718-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02718-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02718-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02718-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02676-HLAIp_R01_Q3.pin 20230825_INT001-02676-HLAIp_R01_Q3 20230825_INT001-02676-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02676-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02676-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02725-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02725-HLAIp_R02_Q1 20230829_DIA_INT001-02725-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02725-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02725-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02725-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02695-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02695-HLAIp_R02_Q1 20230828_DIA_INT001-02695-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02695-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02695-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02695-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02703-HLAIp_R01_Q2.pin 20230829_INT001-02703-HLAIp_R01_Q2 20230829_INT001-02703-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02703-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02703-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02703-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02691-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02691-HLAIp_R02_Q2 20230828_DIA_INT001-02691-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02691-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02691-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02699-HLAIp_R01_Q2.pin 20230828_INT001-02699-HLAIp_R01_Q2 20230828_INT001-02699-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02699-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02699-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02700-HLAIp_R01_Q3.pin 20230828_INT001-02700-HLAIp_R01_Q3 20230828_INT001-02700-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02700-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02700-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02700-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02712-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02712-HLAIp_R02_Q2 20230829_DIA_INT001-02712-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02712-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02712-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02686-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02686-HLAIp_R02_Q3 20230825_DIA_INT001-02686-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02686-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02686-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02721-HLAIp_R01_Q1.pin 20230828_INT001-02721-HLAIp_R01_Q1 20230828_INT001-02721-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02721-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02721-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02724-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02724-HLAIp_R02_Q3 20230828_DIA_INT001-02724-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02724-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02724-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02724-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02683-HLAIp_R01_Q2.pin 20230825_INT001-02683-HLAIp_R01_Q2 20230825_INT001-02683-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02683-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02683-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02683-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02681-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02681-HLAIp_R02_Q2 20230825_DIA_INT001-02681-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02681-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02681-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02696-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02696-HLAIp_R02_Q3 20230828_DIA_INT001-02696-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02696-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02696-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02674-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02674-HLAIp_R02_Q3 20230825_DIA_INT001-02674-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02674-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02674-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02674-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02703-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02703-HLAIp_R02_Q1 20230829_DIA_INT001-02703-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02703-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02703-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02703-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02707-HLAIp_R01_Q1.pin 20230829_INT001-02707-HLAIp_R01_Q1 20230829_INT001-02707-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02707-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02707-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02683-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02683-HLAIp_R02_Q1 20230825_DIA_INT001-02683-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02683-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02683-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02683-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02728-HLAIp_R02_Q3.pin 20230829_INT001-02728-HLAIp_R02_Q3 20230829_INT001-02728-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_INT001-02728-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02728-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02701-HLAIp_R01_Q3.pin 20230829_INT001-02701-HLAIp_R01_Q3 20230829_INT001-02701-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02701-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02701-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02701-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02723-HLAIp_R01_Q3.pin 20230828_INT001-02723-HLAIp_R01_Q3 20230828_INT001-02723-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02723-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02723-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02723-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02721-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02721-HLAIp_R02_Q1 20230828_DIA_INT001-02721-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02721-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02721-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02686-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02686-HLAIp_R02_Q2 20230825_DIA_INT001-02686-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02686-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02686-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02708-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02708-HLAIp_R02_Q2 20230829_DIA_INT001-02708-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02708-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02708-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02707-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02707-HLAIp_R02_Q3 20230829_DIA_INT001-02707-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02707-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02707-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02707-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02719-HLAIp_R01_Q1.pin 20230828_INT001-02719-HLAIp_R01_Q1 20230828_INT001-02719-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02719-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02719-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02702-HLAIp_R01_Q1.pin 20230829_INT001-02702-HLAIp_R01_Q1 20230829_INT001-02702-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02702-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02702-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02687-HLAIp_R01_Q2.pin 20230825_INT001-02687-HLAIp_R01_Q2 20230825_INT001-02687-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02687-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02687-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02710-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02710-HLAIp_R02_Q1 20230829_DIA_INT001-02710-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02710-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02710-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02680-HLAIp_R01_Q2.pin 20230825_INT001-02680-HLAIp_R01_Q2 20230825_INT001-02680-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02680-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02680-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02720-HLAIp_R01_Q1.pin 20230828_INT001-02720-HLAIp_R01_Q1 20230828_INT001-02720-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02720-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02720-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02720-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02717-HLAIp_R01_Q3.pin 20230828_INT001-02717-HLAIp_R01_Q3 20230828_INT001-02717-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02717-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02717-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02725-HLAIp_R01_Q3.pin 20230829_INT001-02725-HLAIp_R01_Q3 20230829_INT001-02725-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02725-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02725-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02725-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02692-HLAIp_R01_Q2.pin 20230828_INT001-02692-HLAIp_R01_Q2 20230828_INT001-02692-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02692-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02692-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02711-HLAIp_R01_Q1.pin 20230829_INT001-02711-HLAIp_R01_Q1 20230829_INT001-02711-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02711-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02711-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02693-HLAIp_R01_Q1.pin 20230828_INT001-02693-HLAIp_R01_Q1 20230828_INT001-02693-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02693-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02693-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02693-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02726-HLAIp_R01_Q2.pin 20230829_INT001-02726-HLAIp_R01_Q2 20230829_INT001-02726-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02726-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02726-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02696-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02696-HLAIp_R02_Q2 20230828_DIA_INT001-02696-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02696-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02696-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02723-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02723-HLAIp_R02_Q2 20230828_DIA_INT001-02723-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02723-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02723-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02709-HLAIp_R01_Q2.pin 20230829_INT001-02709-HLAIp_R01_Q2 20230829_INT001-02709-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02709-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02709-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02679-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02679-HLAIp_R02_Q1 20230825_DIA_INT001-02679-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02679-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02679-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02679-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02699-HLAIp_R01_Q3.pin 20230828_INT001-02699-HLAIp_R01_Q3 20230828_INT001-02699-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02699-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02699-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02699-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02678-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02678-HLAIp_R02_Q2 20230825_DIA_INT001-02678-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02678-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02678-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02689-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02689-HLAIp_R02_Q1 20230828_DIA_INT001-02689-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02689-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02689-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02689-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02687-HLAIp_R01_Q3.pin 20230825_INT001-02687-HLAIp_R01_Q3 20230825_INT001-02687-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02687-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02687-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02687-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02717-HLAIp_R01_Q2.pin 20230828_INT001-02717-HLAIp_R01_Q2 20230828_INT001-02717-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02717-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02717-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02717-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02684-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02684-HLAIp_R02_Q3 20230825_DIA_INT001-02684-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02684-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02684-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02680-HLAIp_R01_Q1.pin 20230825_INT001-02680-HLAIp_R01_Q1 20230825_INT001-02680-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02680-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02680-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02680-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02726-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02726-HLAIp_R02_Q2 20230829_DIA_INT001-02726-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02726-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02726-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02694-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02694-HLAIp_R02_Q3 20230828_DIA_INT001-02694-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02694-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02694-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02686-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02686-HLAIp_R02_Q1 20230825_DIA_INT001-02686-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02686-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02686-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02686-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02710-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02710-HLAIp_R02_Q2 20230829_DIA_INT001-02710-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02710-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02710-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02710-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02716-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02716-HLAIp_R02_Q1 20230828_DIA_INT001-02716-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02716-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02716-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02716-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02723-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02723-HLAIp_R02_Q1 20230828_DIA_INT001-02723-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02723-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02723-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02723-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02728-HLAIp_R01_Q1.pin 20230829_INT001-02728-HLAIp_R01_Q1 20230829_INT001-02728-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02728-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02728-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02681-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02681-HLAIp_R02_Q1 20230825_DIA_INT001-02681-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02681-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02681-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02681-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02679-HLAIp_R01_Q3.pin 20230825_INT001-02679-HLAIp_R01_Q3 20230825_INT001-02679-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02679-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02679-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02679-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02702-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02702-HLAIp_R02_Q2 20230829_DIA_INT001-02702-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02702-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02702-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02715-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02715-HLAIp_R02_Q3 20230829_DIA_INT001-02715-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02715-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02715-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02676-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02676-HLAIp_R02_Q3 20230825_DIA_INT001-02676-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02676-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02676-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02676-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02721-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02721-HLAIp_R02_Q3 20230828_DIA_INT001-02721-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02721-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02721-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02707-HLAIp_R01_Q3.pin 20230829_INT001-02707-HLAIp_R01_Q3 20230829_INT001-02707-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02707-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02707-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02696-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02696-HLAIp_R02_Q1 20230828_DIA_INT001-02696-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02696-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02696-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02696-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02701-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02701-HLAIp_R02_Q1 20230829_DIA_INT001-02701-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02701-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02701-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02701-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02709-HLAIp_R01_Q1.pin 20230829_INT001-02709-HLAIp_R01_Q1 20230829_INT001-02709-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02709-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02709-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02709-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02690-HLAIp_R01_Q3.pin 20230828_INT001-02690-HLAIp_R01_Q3 20230828_INT001-02690-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02690-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02690-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02690-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02702-HLAIp_R01_Q2.pin 20230829_INT001-02702-HLAIp_R01_Q2 20230829_INT001-02702-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02702-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02702-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02702-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02678-HLAIp_R01_Q2.pin 20230825_INT001-02678-HLAIp_R01_Q2 20230825_INT001-02678-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02678-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02678-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02726-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02726-HLAIp_R02_Q3 20230829_DIA_INT001-02726-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02726-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02726-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02726-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02706-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02706-HLAIp_R02_Q2 20230829_DIA_INT001-02706-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02706-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02706-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02706-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02678-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02678-HLAIp_R02_Q3 20230825_DIA_INT001-02678-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02678-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02678-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02678-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02721-HLAIp_R01_Q2.pin 20230828_INT001-02721-HLAIp_R01_Q2 20230828_INT001-02721-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02721-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02721-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02721-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02715-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02715-HLAIp_R02_Q2 20230829_DIA_INT001-02715-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02715-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02715-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02715-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02709-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02709-HLAIp_R02_Q3 20230829_DIA_INT001-02709-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02709-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02709-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02709-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02712-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02712-HLAIp_R02_Q1 20230829_DIA_INT001-02712-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02712-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02712-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02712-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02684-HLAIp_R02_Q2.pin 20230825_DIA_INT001-02684-HLAIp_R02_Q2 20230825_DIA_INT001-02684-HLAIp_R02_Q2_percolator_target_psms.tsv 20230825_DIA_INT001-02684-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02684-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02684-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02711-HLAIp_R01_Q2.pin 20230829_INT001-02711-HLAIp_R01_Q2 20230829_INT001-02711-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02711-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02711-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02711-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02677-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02677-HLAIp_R02_Q1 20230825_DIA_INT001-02677-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02677-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02677-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02677-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02721-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02721-HLAIp_R02_Q2 20230828_DIA_INT001-02721-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02721-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02721-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02721-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02694-HLAIp_R01_Q2.pin 20230828_INT001-02694-HLAIp_R01_Q2 20230828_INT001-02694-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02694-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02694-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02694-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02713-HLAIp_R01_Q1.pin 20230829_INT001-02713-HLAIp_R01_Q1 20230829_INT001-02713-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02713-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02713-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02713-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02727-HLAIp_R01_Q3.pin 20230829_INT001-02727-HLAIp_R01_Q3 20230829_INT001-02727-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02727-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02727-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02727-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02702-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02702-HLAIp_R02_Q3 20230829_DIA_INT001-02702-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02702-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02702-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02702-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02678-HLAIp_R01_Q1.pin 20230825_INT001-02678-HLAIp_R01_Q1 20230825_INT001-02678-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02678-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02678-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02678-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02694-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02694-HLAIp_R02_Q2 20230828_DIA_INT001-02694-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02694-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02694-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02694-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02704-HLAIp_R01_Q1.pin 20230829_INT001-02704-HLAIp_R01_Q1 20230829_INT001-02704-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02704-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02704-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02704-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02691-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02691-HLAIp_R02_Q1 20230828_DIA_INT001-02691-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02691-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02691-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02691-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02707-HLAIp_R01_Q2.pin 20230829_INT001-02707-HLAIp_R01_Q2 20230829_INT001-02707-HLAIp_R01_Q2_percolator_target_psms.tsv 20230829_INT001-02707-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230829_INT001-02707-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02707-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02708-HLAIp_R02_Q1.pin 20230829_DIA_INT001-02708-HLAIp_R02_Q1 20230829_DIA_INT001-02708-HLAIp_R02_Q1_percolator_target_psms.tsv 20230829_DIA_INT001-02708-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02708-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02708-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02719-HLAIp_R01_Q2.pin 20230828_INT001-02719-HLAIp_R01_Q2 20230828_INT001-02719-HLAIp_R01_Q2_percolator_target_psms.tsv 20230828_INT001-02719-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230828_INT001-02719-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02719-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02688-HLAIp_R02_Q1.pin 20230825_DIA_INT001-02688-HLAIp_R02_Q1 20230825_DIA_INT001-02688-HLAIp_R02_Q1_percolator_target_psms.tsv 20230825_DIA_INT001-02688-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02688-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02688-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02698-HLAIp_R01_Q1.pin 20230828_INT001-02698-HLAIp_R01_Q1 20230828_INT001-02698-HLAIp_R01_Q1_percolator_target_psms.tsv 20230828_INT001-02698-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230828_INT001-02698-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02698-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02682-HLAIp_R01_Q1.pin 20230825_INT001-02682-HLAIp_R01_Q1 20230825_INT001-02682-HLAIp_R01_Q1_percolator_target_psms.tsv 20230825_INT001-02682-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230825_INT001-02682-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02682-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_DIA_INT001-02682-HLAIp_R02_Q3.pin 20230825_DIA_INT001-02682-HLAIp_R02_Q3 20230825_DIA_INT001-02682-HLAIp_R02_Q3_percolator_target_psms.tsv 20230825_DIA_INT001-02682-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230825_DIA_INT001-02682-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_DIA_INT001-02682-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02685-HLAIp_R01_Q3.pin 20230825_INT001-02685-HLAIp_R01_Q3 20230825_INT001-02685-HLAIp_R01_Q3_percolator_target_psms.tsv 20230825_INT001-02685-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230825_INT001-02685-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02685-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02692-HLAIp_R02_Q3.pin 20230828_DIA_INT001-02692-HLAIp_R02_Q3 20230828_DIA_INT001-02692-HLAIp_R02_Q3_percolator_target_psms.tsv 20230828_DIA_INT001-02692-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02692-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02692-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02715-HLAIp_R01_Q1.pin 20230829_INT001-02715-HLAIp_R01_Q1 20230829_INT001-02715-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02715-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02715-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02715-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02705-HLAIp_R01_Q3.pin 20230829_INT001-02705-HLAIp_R01_Q3 20230829_INT001-02705-HLAIp_R01_Q3_percolator_target_psms.tsv 20230829_INT001-02705-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02705-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02705-HLAIp_R01_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02698-HLAIp_R02_Q1.pin 20230828_DIA_INT001-02698-HLAIp_R02_Q1 20230828_DIA_INT001-02698-HLAIp_R02_Q1_percolator_target_psms.tsv 20230828_DIA_INT001-02698-HLAIp_R02_Q1_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02698-HLAIp_R02_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02698-HLAIp_R02_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_DIA_INT001-02719-HLAIp_R02_Q2.pin 20230828_DIA_INT001-02719-HLAIp_R02_Q2 20230828_DIA_INT001-02719-HLAIp_R02_Q2_percolator_target_psms.tsv 20230828_DIA_INT001-02719-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230828_DIA_INT001-02719-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_DIA_INT001-02719-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02713-HLAIp_R02_Q3.pin 20230829_DIA_INT001-02713-HLAIp_R02_Q3 20230829_DIA_INT001-02713-HLAIp_R02_Q3_percolator_target_psms.tsv 20230829_DIA_INT001-02713-HLAIp_R02_Q3_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02713-HLAIp_R02_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02713-HLAIp_R02_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_DIA_INT001-02704-HLAIp_R02_Q2.pin 20230829_DIA_INT001-02704-HLAIp_R02_Q2 20230829_DIA_INT001-02704-HLAIp_R02_Q2_percolator_target_psms.tsv 20230829_DIA_INT001-02704-HLAIp_R02_Q2_percolator_decoy_psms.tsv interact-20230829_DIA_INT001-02704-HLAIp_R02_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_DIA_INT001-02704-HLAIp_R02_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02728-HLAIp_R03_Q3.pin 20230829_INT001-02728-HLAIp_R03_Q3 20230829_INT001-02728-HLAIp_R03_Q3_percolator_target_psms.tsv 20230829_INT001-02728-HLAIp_R03_Q3_percolator_decoy_psms.tsv interact-20230829_INT001-02728-HLAIp_R03_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02728-HLAIp_R03_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230829_INT001-02726-HLAIp_R01_Q1.pin 20230829_INT001-02726-HLAIp_R01_Q1 20230829_INT001-02726-HLAIp_R01_Q1_percolator_target_psms.tsv 20230829_INT001-02726-HLAIp_R01_Q1_percolator_decoy_psms.tsv interact-20230829_INT001-02726-HLAIp_R01_Q1 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q1.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q1_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230829_INT001-02726-HLAIp_R01_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230825_INT001-02676-HLAIp_R01_Q2.pin 20230825_INT001-02676-HLAIp_R01_Q2 20230825_INT001-02676-HLAIp_R01_Q2_percolator_target_psms.tsv 20230825_INT001-02676-HLAIp_R01_Q2_percolator_decoy_psms.tsv interact-20230825_INT001-02676-HLAIp_R01_Q2 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q2.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q2_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230825_INT001-02676-HLAIp_R01_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230828_INT001-02692-HLAIp_R01_Q3.pin 20230828_INT001-02692-HLAIp_R01_Q3 20230828_INT001-02692-HLAIp_R01_Q3_percolator_target_psms.tsv 20230828_INT001-02692-HLAIp_R01_Q3_percolator_decoy_psms.tsv interact-20230828_INT001-02692-HLAIp_R01_Q3 DDA 0.5 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q3.mzML
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q3_percolator_target_psms.tsv
Percolator: Delete temp
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\20230828_INT001-02692-HLAIp_R01_Q3_percolator_decoy_psms.tsv
ProteinProphet [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate D:\Nicolas\2023-11-28-decoys-contam-gencode.v38lift37.pc_translations_with_noncanonicalEBV.fa.fas --prefix rev_
PhilosopherFilter [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 1 --ion 0.03 --psm 0.03 --pep 0.03 --group --tag rev_ --pepxml D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA --protxml D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\combined.prot.xml --razor
PhilosopherReport [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report
SpecLibGen [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\ProgramData\Anaconda3\python.exe -u C:\DATA\FragPipe-jre-21.1\fragpipe\tools\speclib\gen_con_spec_lib.py D:\Nicolas\2023-11-28-decoys-contam-gencode.v38lift37.pc_translations_with_noncanonicalEBV.fa.fas D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA unused D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA True unused use_easypqp noiRT;noIM 20 "--unimod C:/DATA/FragPipe-jre-21.1/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.0" delete_intermediate_files D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\filelist_speclibgen.txt
DIA-NN [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib library.tsv --threads 20 --verbose 1 --out diann-output\report.tsv --qvalue 0.03 --matrix-qvalue 0.03 --matrix-spec-q --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --cfg D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\filelist_diann.txt
DIA-NN [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\diann\1.8.2_beta_8\win\dia-nn-plotter.exe diann-output\report.stats.tsv diann-output\report.tsv diann-output\report.pdf
DIA-NN: Propagate localization [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diann-output]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.dmtavt.fragpipe.tools.diann.Localization D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA
DIA-NN: Convert DIA-NN output to MSstats.csv [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\diann-output]
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\commons-io-2.15.1.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.dmtavt.fragpipe.tools.diann.DiannToMsstats report.tsv msstats.csv 0.03 0.03 0.03 0.03 D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\fragpipe-files.fp-manifest
WorkspaceClean [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [CheckCentroid], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [UmpireSe], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [MSFragger], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [MSBooster], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [Percolator], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [ProteinProphet], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [PhilosopherFilter], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [PhilosopherReport], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [SpecLibGen], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [DIA-NN], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
    Cmd: [WorkspaceClean], Work dir: [D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]

~~~~~~~~~~~~~~~~~~~~~~

~~~~~~Sample of D:\Nicolas\2023-11-28-decoys-contam-gencode.v38lift37.pc_translations_with_noncanonicalEBV.fa.fas~~~~~~~
>rev_sp|1-non-canonical|LMP-2A_1_1171-1539 LMP-2A OS=NC_007605.1 GN=3783751 PE=2 SV=2
>rev_sp|ENSP00000306920.4|GLB1-201 GLB1 OS=human GN=ENSG00000170266.16_1 PE=1 SV=1
>rev_sp|ENSP00000359665.3|PI4K2A-201 PI4K2A OS=human GN=ENSG00000155252.13_1 PE=1 SV=1
>rev_sp|ENSP00000385766.1|LRRC32-202 LRRC32 OS=human GN=ENSG00000137507.11_1 PE=1 SV=1
>rev_sp|ENSP00000407315.2|SCML2-203 SCML2 OS=human GN=ENSG00000102098.19_1 PE=1 SV=1
>rev_sp|ENSP00000425215.1|EMB-204 EMB OS=human GN=ENSG00000170571.12_1 PE=1 SV=1
>rev_sp|ENSP00000439694.1|SYT7-203 SYT7 OS=human GN=ENSG00000011347.10_1 PE=1 SV=1
>rev_sp|ENSP00000457701.1|RP11-195F19.5-003 RP11-195F19.5 OS=human GN=ENSG00000187186.15_1 PE=1 SV=1
>rev_sp|ENSP00000476327.1|UCK2-206 UCK2 OS=human GN=ENSG00000143179.16_1 PE=1 SV=1
>rev_sp|ENSP00000496572.1|UBE2T-203 UBE2T OS=human GN=ENSG00000077152.11_1 PE=1 SV=1
>rev_sp|YP_401721.1|YP_401721.1 BNLF2a OS=Human_gammaherpesvirus_4 GN=3783720 PE=1 SV=1
>sp|ENSP00000306898.4|DCDC1-201 DCDC1 OS=human GN=ENSG00000170959.15_1 PE=1 SV=1
>sp|ENSP00000359656.1|ARHGEF6-203 ARHGEF6 OS=human GN=ENSG00000129675.16_1 PE=1 SV=1
>sp|ENSP00000385756.2|EIPR1-203 EIPR1 OS=human GN=ENSG00000032389.13_1 PE=1 SV=1
>sp|ENSP00000407304.1|SLC4A7-209 SLC4A7 OS=human GN=ENSG00000033867.16_1 PE=1 SV=1
>sp|ENSP00000425203.1|CXXC5-206 CXXC5 OS=human GN=ENSG00000171604.12_1 PE=1 SV=1
>sp|ENSP00000439676.1|GSG1-207 GSG1 OS=human GN=ENSG00000111305.19_1 PE=1 SV=1
>sp|ENSP00000457694.1|JPT2-206 JPT2 OS=human GN=ENSG00000206053.13_1 PE=1 SV=1
>sp|ENSP00000476319.1|RIT1-203 RIT1 OS=human GN=ENSG00000143622.11_1 PE=1 SV=1
>sp|ENSP00000496564.2|OTOA-208 OTOA OS=human GN=ENSG00000155719.18_1 PE=1 SV=1
>sp|YP_401715.3|YP_401715.3 BALF3 OS=Human_gammaherpesvirus_4 GN=3783679 PE=1 SV=1
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v21.1ui state cache


# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\Nicolas\\2023-11-28-decoys-contam-gencode.v38lift37.pc_translations_with_noncanonicalEBV.fa.fas

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.03
diann.quantification-strategy=3
diann.quantification-strategy-2=QuantUMS (high accuracy)
diann.run-dia-nn=true
diann.run-dia-plex=false
diann.run-specific-protein-q-value=true
diann.unrelated-runs=false
diann.use-predicted-spectra=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=true
fpop.fpop-tmt=false
fpop.label_control=
fpop.label_fpop=
fpop.region_size=1
fpop.run-fpop=false
fpop.subtract-control=false
fragpipe-config.bin-diann=C\:\\DATA\\FragPipe-jre-21.1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=C\:\\DATA\\FragPipe-jre-21.1\\fragpipe\\tools\\IonQuant-1.10.12.jar
fragpipe-config.bin-msfragger=C\:\\DATA\\FragPipe-jre-21.1\\fragpipe\\tools\\MSFragger-4.0\\MSFragger-4.0.jar
fragpipe-config.bin-philosopher=C\:\\DATA\\FragPipe-jre-21.1\\fragpipe\\tools\\philosopher_v5.1.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=true
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=25
msfragger.digest_min_length=8
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.group_variable=2
msfragger.intensity_transform=1
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=5
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.00
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=200
msfragger.misc.fragger.enzyme-dropdown-1=nonspecific
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=0
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
msfragger.output_report_topN_dia2=3
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=15
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=-18.01056 79.96633
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=true
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=-
msfragger.search_enzyme_cut_2=-
msfragger.search_enzyme_name=nonspecific
msfragger.search_enzyme_name_1=nonspecific
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),false,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,2; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQ,true,1; -18.0106,nE,true,1; 119.0041,C,true,1; 0.98402,N,false,1; 8.014199,K,false,1; 10.008269,R,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=300
msfragger.write_calibrated_mgf=false
msfragger.write_calibrated_mzml=false
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=4
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 1 --ion 0.03 --psm 0.03 --pep 0.03  --group
phi-report.pep-level-summary=true
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.assign_glycans=true
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=00.2
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=00.1
ptmshepherd.diagmine_fragMinSpecDiff=00.1
ptmshepherd.diagmine_minIons=25
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=00.2
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=2,0.5,0.1
ptmshepherd.prob_dhexY=2,0.5
ptmshepherd.prob_neuacOx=2,0.05,0.2
ptmshepherd.prob_neugcOx=2,0.05,0.2
ptmshepherd.prob_phosphoOx=2,0.05,0.2
ptmshepherd.prob_regY=5,0.5
ptmshepherd.prob_sulfoOx=2,0.05,0.2
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-diaumpire=false
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=true
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
sub_mzml_prob_threshold=0
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=D\:\\Nicolas\\Drug_treatments\\Class1\\fdr_3percent_noncanonical_DDAplus\\DIA
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.misc.save-sdrf=true
workflow.ram=100
workflow.threads=20

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -cp C:\DATA\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.raw 20
Done in 0,0 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[11:18:59] Executing Workspace  v5.1.0                  
INFO[11:18:59] Removing workspace                           
INFO[11:18:59] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA]
C:\DATA\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ni9566\AppData\Local\Temp\aa74d6af-ebde-4813-8396-865d14fa41ae
INFO[11:19:00] Executing Workspace  v5.1.0                  
INFO[11:19:00] Creating workspace                           
INFO[11:19:00] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
UmpireSe
C:\DATA\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx100G -Dlibs.thermo.dir=C:\DATA\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp C:\DATA\FragPipe-jre-21.1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\DATA\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar dia_umpire_se.DIA_Umpire_SE D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.raw D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
=================================================================================================
DIA-Umpire signal extraction analysis  (version: v2.3.2)
(c) University of Michigan
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
2024-02-21 11:19:01,229 INFO  [main] Version: v2.3.2
2024-02-21 11:19:01,229 INFO  [main] Parameter file:D:\Nicolas\Drug_treatments\Class1\fdr_3percent_noncanonical_DDAplus\DIA\umpire-se.params
2024-02-21 11:19:01,229 INFO  [main] Spectra file:D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.raw
2024-02-21 11:19:01,229 INFO  [main] 
2024-02-21 11:19:01,229 INFO  [main] ####################################################################################################
2024-02-21 11:19:01,229 INFO  [main] #No of threads
2024-02-21 11:19:01,229 INFO  [main] Thread = 20
2024-02-21 11:19:01,229 INFO  [main] ####################################################################################################
2024-02-21 11:19:01,229 INFO  [main] 
2024-02-21 11:19:01,229 INFO  [main] ## omit Thread
2024-02-21 11:19:01,229 INFO  [main] 
2024-02-21 11:19:01,229 INFO  [main] #Precursor-fragments grouping parameters
2024-02-21 11:19:01,229 INFO  [main] RPmax = 25
2024-02-21 11:19:01,229 INFO  [main] RFmax = 500
2024-02-21 11:19:01,229 INFO  [main] CorrThreshold = 0
2024-02-21 11:19:01,229 INFO  [main] DeltaApex = 0.2
2024-02-21 11:19:01,229 INFO  [main] RTOverlap = 0.3
2024-02-21 11:19:01,229 INFO  [main] 
2024-02-21 11:19:01,229 INFO  [main] #Fragment intensity adjustments
2024-02-21 11:19:01,229 INFO  [main] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2024-02-21 11:19:01,229 INFO  [main] AdjustFragIntensity = true
2024-02-21 11:19:01,229 INFO  [main] BoostComplementaryIon = false
2024-02-21 11:19:01,229 INFO  [main] 
2024-02-21 11:19:01,229 INFO  [main] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2024-02-21 11:19:01,229 INFO  [main] ExportPrecursorPeak = false
2024-02-21 11:19:01,229 INFO  [main] 
2024-02-21 11:19:01,229 INFO  [main] Q1 = true
2024-02-21 11:19:01,229 INFO  [main] Q2 = true
2024-02-21 11:19:01,229 INFO  [main] Q3 = true
2024-02-21 11:19:01,229 INFO  [main] 
2024-02-21 11:19:01,229 INFO  [main] #Signal extraction: mass accuracy and resolution
2024-02-21 11:19:01,229 INFO  [main] # resolution parameter matters only for data generated in profile mode
2024-02-21 11:19:01,229 INFO  [main] SE.MS1PPM = 10
2024-02-21 11:19:01,229 INFO  [main] SE.MS2PPM = 20
2024-02-21 11:19:01,229 INFO  [main] SE.Resolution = 60000
2024-02-21 11:19:01,229 INFO  [main] 
2024-02-21 11:19:01,229 INFO  [main] #Signal extraction: signal to noise filter
2024-02-21 11:19:01,229 INFO  [main] SE.SN = 1.1
2024-02-21 11:19:01,229 INFO  [main] SE.MS2SN = 1.1
2024-02-21 11:19:01,229 INFO  [main] 
2024-02-21 11:19:01,229 INFO  [main] #Signal extraction: minimum signal intensity filter
2024-02-21 11:19:01,229 INFO  [main] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2024-02-21 11:19:01,229 INFO  [main] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2024-02-21 11:19:01,229 INFO  [main] SE.EstimateBG = false
2024-02-21 11:19:01,229 INFO  [main] SE.MinMSIntensity = 1
2024-02-21 11:19:01,229 INFO  [main] SE.MinMSMSIntensity = 1
2024-02-21 11:19:01,229 INFO  [main] 
2024-02-21 11:19:01,229 INFO  [main] #Signal extraction: peak curve detection and isotope grouping
2024-02-21 11:19:01,229 INFO  [main] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2024-02-21 11:19:01,239 INFO  [main] SE.NoMissedScan = 1
2024-02-21 11:19:01,239 INFO  [main] SE.MaxCurveRTRange = 2
2024-02-21 11:19:01,239 INFO  [main] SE.RemoveGroupedPeaks = true
2024-02-21 11:19:01,239 INFO  [main] SE.RemoveGroupedPeaksRTOverlap = 0.3
2024-02-21 11:19:01,239 INFO  [main] SE.RemoveGroupedPeaksCorr = 0.3
2024-02-21 11:19:01,239 INFO  [main] SE.MinNoPeakCluster = 2
2024-02-21 11:19:01,239 INFO  [main] SE.MaxNoPeakCluster = 4
2024-02-21 11:19:01,239 INFO  [main] 
2024-02-21 11:19:01,438 INFO  [main] #Signal extraction: filtering of MS1 features
2024-02-21 11:19:01,438 INFO  [main] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2024-02-21 11:19:01,438 INFO  [main] SE.IsoPattern = 0.3
2024-02-21 11:19:01,438 INFO  [main] SE.MassDefectFilter = true
2024-02-21 11:19:01,438 INFO  [main] SE.MassDefectOffset = 0.1
2024-02-21 11:19:01,438 INFO  [main] 
2024-02-21 11:19:01,438 INFO  [main] #Signal extraction: other
2024-02-21 11:19:01,438 INFO  [main] SE.StartCharge = 1
2024-02-21 11:19:01,438 INFO  [main] SE.EndCharge = 5
2024-02-21 11:19:01,438 INFO  [main] SE.MS2StartCharge = 2
2024-02-21 11:19:01,438 INFO  [main] SE.MS2EndCharge = 5
2024-02-21 11:19:01,438 INFO  [main] SE.MinFrag = 10
2024-02-21 11:19:01,438 INFO  [main] SE.StartRT = 0
2024-02-21 11:19:01,438 INFO  [main] SE.EndRT = 9999
2024-02-21 11:19:01,438 INFO  [main] SE.MinMZ = 200
2024-02-21 11:19:01,438 INFO  [main] SE.MinPrecursorMass = 600
2024-02-21 11:19:01,438 INFO  [main] SE.MaxPrecursorMass = 5000
2024-02-21 11:19:01,438 INFO  [main] 
2024-02-21 11:19:01,438 INFO  [main] 
2024-02-21 11:19:01,438 INFO  [main] #Isolation window setting
2024-02-21 11:19:01,438 INFO  [main] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2024-02-21 11:19:01,438 INFO  [main] WindowType = SWATH
2024-02-21 11:19:01,438 INFO  [main] 
2024-02-21 11:19:01,438 INFO  [main] #Fix window size (For SWATH)
2024-02-21 11:19:01,438 INFO  [main] # for Thermo data, this will be determined from raw data automatically
2024-02-21 11:19:01,438 INFO  [main] WindowSize = 10
2024-02-21 11:19:01,438 INFO  [main] 
2024-02-21 11:19:01,438 INFO  [main] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2024-02-21 11:19:01,438 INFO  [main] # for Thermo data, this will be determined from raw data automatically
2024-02-21 11:19:01,438 INFO  [main] ==window setting begin
2024-02-21 11:19:01,438 INFO  [main] 
2024-02-21 11:19:01,438 INFO  [main] =================================================================================================
2024-02-21 11:19:01,438 INFO  [main] Processing D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01.raw....
2024-02-21 11:19:01,438 INFO  [main] Writing DIA setting to file:D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01_diasetting.ser...
2024-02-21 11:19:01,448 INFO  [main] Writing parameter to file:D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01_params.ser...
2024-02-21 11:19:01,448 INFO  [main] Module A: Signal extraction
Batmass-IO version 1.30.0
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.nustaq.serialization.FSTClazzInfo (file:/C:/DATA/FragPipe-jre-21.1/fragpipe/tools/DIA_Umpire_SE-2.3.2.jar) to field java.lang.String.value
WARNING: Please consider reporting this to the maintainers of org.nustaq.serialization.FSTClazzInfo
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2024-02-21 11:19:12,116 INFO  [main] Writing DIA setting to file:D:\Nicolas\Drug_treatments\Class1\raw_files\20230825_INT001-02674-HLAIp_R01_diasetting.ser...
2024-02-21 11:19:13,125 INFO  [main] Processing MS1 peak detection
2024-02-21 11:19:13,125 INFO  [main] MS1 average cycle time : 2.2910988 seconds
2024-02-21 11:19:15,175 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:15,175 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:23,292 INFO  [main] 1752266 Peak curves found (Memory usage:1331MB)
2024-02-21 11:19:23,292 INFO  [main] Inclusion mz values found: 0/0
2024-02-21 11:19:23,292 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:23,292 INFO  [main] Building PeakCurve Mass-RT KD tree
2024-02-21 11:19:32,450 INFO  [main] No of ion clusters:93026 (Memory usage:1566MB)
2024-02-21 11:19:32,500 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_PeakCluster.serFS...
2024-02-21 11:19:33,360 INFO  [main] ==================================================================================
2024-02-21 11:19:33,360 INFO  [main] Processing DIA MS2 (mz range):1630.292_1631.492( 1/37495 )
2024-02-21 11:19:33,370 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:33,370 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:33,570 INFO  [main] 7 Peak curves found (Memory usage:1607MB)
2024-02-21 11:19:33,570 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:33,730 INFO  [main] No of ion clusters:0 (Memory usage:1607MB)
2024-02-21 11:19:33,730 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1630_1631_PeakCluster.serFS...
2024-02-21 11:19:33,730 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:33,730 INFO  [main] No. of fragment peaks: 7
2024-02-21 11:19:33,730 INFO  [main] No. of remaining fragment peaks: 4
2024-02-21 11:19:33,730 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:33,810 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:34,020 INFO  [main] ==================================================================================
2024-02-21 11:19:34,020 INFO  [main] Processing DIA MS2 (mz range):1629.9976_1631.1975( 2/37495 )
2024-02-21 11:19:34,020 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:34,020 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:34,179 INFO  [main] 7 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:34,179 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:34,329 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:34,329 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1629_1631_PeakCluster.serFS...
2024-02-21 11:19:34,329 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:34,329 INFO  [main] No. of fragment peaks: 7
2024-02-21 11:19:34,329 INFO  [main] No. of remaining fragment peaks: 7
2024-02-21 11:19:34,329 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:34,349 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:34,509 INFO  [main] ==================================================================================
2024-02-21 11:19:34,509 INFO  [main] Processing DIA MS2 (mz range):1628.1133_1629.3132( 3/37495 )
2024-02-21 11:19:34,509 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:34,509 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:34,659 INFO  [main] 9 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:34,659 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:34,809 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:34,809 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1628_1629_PeakCluster.serFS...
2024-02-21 11:19:34,809 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:34,809 INFO  [main] No. of fragment peaks: 9
2024-02-21 11:19:34,809 INFO  [main] No. of remaining fragment peaks: 6
2024-02-21 11:19:34,809 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:34,829 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:34,999 INFO  [main] ==================================================================================
2024-02-21 11:19:34,999 INFO  [main] Processing DIA MS2 (mz range):1627.6342_1628.8341( 4/37495 )
2024-02-21 11:19:34,999 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:34,999 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:35,139 INFO  [main] 8 Peak curves found (Memory usage:1544MB)
2024-02-21 11:19:35,139 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:35,279 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:35,279 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1627_1628_PeakCluster.serFS...
2024-02-21 11:19:35,279 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:35,279 INFO  [main] No. of fragment peaks: 8
2024-02-21 11:19:35,279 INFO  [main] No. of remaining fragment peaks: 3
2024-02-21 11:19:35,279 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:35,289 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:35,429 INFO  [main] ==================================================================================
2024-02-21 11:19:35,429 INFO  [main] Processing DIA MS2 (mz range):1624.77_1625.97( 5/37495 )
2024-02-21 11:19:35,429 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:35,429 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:35,579 INFO  [main] 11 Peak curves found (Memory usage:1544MB)
2024-02-21 11:19:35,579 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:35,739 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:35,739 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1624_1625_PeakCluster.serFS...
2024-02-21 11:19:35,739 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:35,739 INFO  [main] No. of fragment peaks: 11
2024-02-21 11:19:35,739 INFO  [main] No. of remaining fragment peaks: 4
2024-02-21 11:19:35,739 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:35,749 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:35,889 INFO  [main] ==================================================================================
2024-02-21 11:19:35,889 INFO  [main] Processing DIA MS2 (mz range):1622.8365_1624.0365( 6/37495 )
2024-02-21 11:19:35,889 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:35,889 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:36,029 INFO  [main] 7 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:36,029 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:36,159 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:36,159 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1622_1624_PeakCluster.serFS...
2024-02-21 11:19:36,159 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:36,159 INFO  [main] No. of fragment peaks: 7
2024-02-21 11:19:36,159 INFO  [main] No. of remaining fragment peaks: 4
2024-02-21 11:19:36,159 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:36,169 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:36,309 INFO  [main] ==================================================================================
2024-02-21 11:19:36,309 INFO  [main] Processing DIA MS2 (mz range):1621.8092_1623.0092( 7/37495 )
2024-02-21 11:19:36,319 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:36,319 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:36,459 INFO  [main] 10 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:36,459 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:36,589 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:36,589 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1621_1623_PeakCluster.serFS...
2024-02-21 11:19:36,589 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:36,589 INFO  [main] No. of fragment peaks: 10
2024-02-21 11:19:36,589 INFO  [main] No. of remaining fragment peaks: 6
2024-02-21 11:19:36,589 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:36,599 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:36,739 INFO  [main] ==================================================================================
2024-02-21 11:19:36,739 INFO  [main] Processing DIA MS2 (mz range):1618.4862_1619.6862( 8/37495 )
2024-02-21 11:19:36,749 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:36,749 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:36,899 INFO  [main] 12 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:36,899 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:37,029 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:37,029 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1618_1619_PeakCluster.serFS...
2024-02-21 11:19:37,029 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:37,029 INFO  [main] No. of fragment peaks: 12
2024-02-21 11:19:37,029 INFO  [main] No. of remaining fragment peaks: 9
2024-02-21 11:19:37,029 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:37,039 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:37,169 INFO  [main] ==================================================================================
2024-02-21 11:19:37,169 INFO  [main] Processing DIA MS2 (mz range):1616.7262_1617.9261( 9/37495 )
2024-02-21 11:19:37,169 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:37,169 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:37,299 INFO  [main] 8 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:37,309 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:37,459 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:37,459 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1616_1617_PeakCluster.serFS...
2024-02-21 11:19:37,459 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:37,459 INFO  [main] No. of fragment peaks: 8
2024-02-21 11:19:37,459 INFO  [main] No. of remaining fragment peaks: 3
2024-02-21 11:19:37,459 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:37,469 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:37,609 INFO  [main] ==================================================================================
2024-02-21 11:19:37,609 INFO  [main] Processing DIA MS2 (mz range):1615.9564_1617.1564( 10/37495 )
2024-02-21 11:19:37,609 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:37,609 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:37,748 INFO  [main] 11 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:37,748 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:37,878 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:37,878 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1615_1617_PeakCluster.serFS...
2024-02-21 11:19:37,878 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:37,878 INFO  [main] No. of fragment peaks: 11
2024-02-21 11:19:37,878 INFO  [main] No. of remaining fragment peaks: 5
2024-02-21 11:19:37,878 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:37,888 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:38,028 INFO  [main] ==================================================================================
2024-02-21 11:19:38,028 INFO  [main] Processing DIA MS2 (mz range):1615.8507_1617.0507( 11/37495 )
2024-02-21 11:19:38,028 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:38,028 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:38,168 INFO  [main] 9 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:38,168 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:38,338 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:38,338 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1615_1617_PeakCluster.serFS...
2024-02-21 11:19:38,348 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:38,348 INFO  [main] No. of fragment peaks: 9
2024-02-21 11:19:38,348 INFO  [main] No. of remaining fragment peaks: 6
2024-02-21 11:19:38,348 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:38,358 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:38,498 INFO  [main] ==================================================================================
2024-02-21 11:19:38,498 INFO  [main] Processing DIA MS2 (mz range):1613.4197_1614.6196( 12/37495 )
2024-02-21 11:19:38,498 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:38,498 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:38,658 INFO  [main] 10 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:38,658 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:38,808 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:38,808 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1613_1614_PeakCluster.serFS...
2024-02-21 11:19:38,808 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:38,808 INFO  [main] No. of fragment peaks: 10
2024-02-21 11:19:38,808 INFO  [main] No. of remaining fragment peaks: 5
2024-02-21 11:19:38,808 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:38,818 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:38,968 INFO  [main] ==================================================================================
2024-02-21 11:19:38,968 INFO  [main] Processing DIA MS2 (mz range):1613.0239_1614.2239( 13/37495 )
2024-02-21 11:19:38,968 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:38,968 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:39,108 INFO  [main] 9 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:39,108 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:39,248 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:39,248 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1613_1614_PeakCluster.serFS...
2024-02-21 11:19:39,258 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:39,258 INFO  [main] No. of fragment peaks: 9
2024-02-21 11:19:39,258 INFO  [main] No. of remaining fragment peaks: 5
2024-02-21 11:19:39,258 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:39,268 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:39,408 INFO  [main] ==================================================================================
2024-02-21 11:19:39,408 INFO  [main] Processing DIA MS2 (mz range):1610.8248_1612.0248( 14/37495 )
2024-02-21 11:19:39,408 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:39,408 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:39,548 INFO  [main] 18 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:39,548 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:39,698 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:39,698 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1610_1612_PeakCluster.serFS...
2024-02-21 11:19:39,698 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:39,698 INFO  [main] No. of fragment peaks: 18
2024-02-21 11:19:39,698 INFO  [main] No. of remaining fragment peaks: 10
2024-02-21 11:19:39,698 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:39,718 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:39,858 INFO  [main] ==================================================================================
2024-02-21 11:19:39,858 INFO  [main] Processing DIA MS2 (mz range):1610.7758_1611.9757( 15/37495 )
2024-02-21 11:19:39,858 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:39,858 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:39,988 INFO  [main] 11 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:39,998 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:40,128 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:40,128 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1610_1611_PeakCluster.serFS...
2024-02-21 11:19:40,128 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:40,128 INFO  [main] No. of fragment peaks: 11
2024-02-21 11:19:40,128 INFO  [main] No. of remaining fragment peaks: 7
2024-02-21 11:19:40,128 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:40,148 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:40,288 INFO  [main] ==================================================================================
2024-02-21 11:19:40,288 INFO  [main] Processing DIA MS2 (mz range):1607.4424_1608.6423( 16/37495 )
2024-02-21 11:19:40,288 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:40,288 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:40,448 INFO  [main] 11 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:40,458 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:40,588 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:40,588 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1607_1608_PeakCluster.serFS...
2024-02-21 11:19:40,588 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:40,588 INFO  [main] No. of fragment peaks: 11
2024-02-21 11:19:40,588 INFO  [main] No. of remaining fragment peaks: 6
2024-02-21 11:19:40,588 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:40,598 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:40,738 INFO  [main] ==================================================================================
2024-02-21 11:19:40,738 INFO  [main] Processing DIA MS2 (mz range):1607.3809_1608.5808( 17/37495 )
2024-02-21 11:19:40,738 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:40,738 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:40,868 INFO  [main] 8 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:40,878 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:41,008 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:41,008 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1607_1608_PeakCluster.serFS...
2024-02-21 11:19:41,008 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:41,008 INFO  [main] No. of fragment peaks: 8
2024-02-21 11:19:41,008 INFO  [main] No. of remaining fragment peaks: 3
2024-02-21 11:19:41,008 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:41,018 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:41,148 INFO  [main] ==================================================================================
2024-02-21 11:19:41,148 INFO  [main] Processing DIA MS2 (mz range):1603.8033_1605.0033( 18/37495 )
2024-02-21 11:19:41,158 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:41,158 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:41,287 INFO  [main] 8 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:41,287 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:41,417 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:41,417 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1603_1605_PeakCluster.serFS...
2024-02-21 11:19:41,417 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:41,417 INFO  [main] No. of fragment peaks: 8
2024-02-21 11:19:41,417 INFO  [main] No. of remaining fragment peaks: 3
2024-02-21 11:19:41,417 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:41,427 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:41,567 INFO  [main] ==================================================================================
2024-02-21 11:19:41,567 INFO  [main] Processing DIA MS2 (mz range):1603.7378_1604.9377( 19/37495 )
2024-02-21 11:19:41,567 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:41,567 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:41,697 INFO  [main] 7 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:41,707 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:41,837 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:41,837 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1603_1604_PeakCluster.serFS...
2024-02-21 11:19:41,837 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:41,837 INFO  [main] No. of fragment peaks: 7
2024-02-21 11:19:41,837 INFO  [main] No. of remaining fragment peaks: 3
2024-02-21 11:19:41,837 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:41,847 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:41,987 INFO  [main] ==================================================================================
2024-02-21 11:19:41,987 INFO  [main] Processing DIA MS2 (mz range):1603.6365_1604.8364( 20/37495 )
2024-02-21 11:19:41,987 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:41,987 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:42,127 INFO  [main] 12 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:42,127 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:42,257 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:42,257 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1603_1604_PeakCluster.serFS...
2024-02-21 11:19:42,257 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:42,257 INFO  [main] No. of fragment peaks: 12
2024-02-21 11:19:42,257 INFO  [main] No. of remaining fragment peaks: 6
2024-02-21 11:19:42,257 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:42,267 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:42,407 INFO  [main] ==================================================================================
2024-02-21 11:19:42,407 INFO  [main] Processing DIA MS2 (mz range):1603.3059_1604.5059( 21/37495 )
2024-02-21 11:19:42,417 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:42,417 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:42,547 INFO  [main] 13 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:42,547 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:42,677 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:42,677 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1603_1604_PeakCluster.serFS...
2024-02-21 11:19:42,677 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:42,677 INFO  [main] No. of fragment peaks: 13
2024-02-21 11:19:42,677 INFO  [main] No. of remaining fragment peaks: 10
2024-02-21 11:19:42,677 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:42,687 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:42,827 INFO  [main] ==================================================================================
2024-02-21 11:19:42,827 INFO  [main] Processing DIA MS2 (mz range):1602.6926_1603.8926( 22/37495 )
2024-02-21 11:19:42,827 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:42,827 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:42,967 INFO  [main] 8 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:42,967 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:43,107 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:43,107 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1602_1603_PeakCluster.serFS...
2024-02-21 11:19:43,107 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:43,107 INFO  [main] No. of fragment peaks: 8
2024-02-21 11:19:43,107 INFO  [main] No. of remaining fragment peaks: 3
2024-02-21 11:19:43,107 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:43,117 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:43,257 INFO  [main] ==================================================================================
2024-02-21 11:19:43,257 INFO  [main] Processing DIA MS2 (mz range):1602.6787_1603.8787( 23/37495 )
2024-02-21 11:19:43,257 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:43,257 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:43,387 INFO  [main] 13 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:43,387 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:43,517 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:43,517 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1602_1603_PeakCluster.serFS...
2024-02-21 11:19:43,517 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:43,517 INFO  [main] No. of fragment peaks: 13
2024-02-21 11:19:43,517 INFO  [main] No. of remaining fragment peaks: 10
2024-02-21 11:19:43,517 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:43,527 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:43,677 INFO  [main] ==================================================================================
2024-02-21 11:19:43,677 INFO  [main] Processing DIA MS2 (mz range):1601.3041_1602.504( 24/37495 )
2024-02-21 11:19:43,677 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:43,677 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:43,817 INFO  [main] 6 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:43,817 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:43,947 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:43,947 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1601_1602_PeakCluster.serFS...
2024-02-21 11:19:43,947 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:43,947 INFO  [main] No. of fragment peaks: 6
2024-02-21 11:19:43,947 INFO  [main] No. of remaining fragment peaks: 4
2024-02-21 11:19:43,947 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:43,967 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:44,097 INFO  [main] ==================================================================================
2024-02-21 11:19:44,097 INFO  [main] Processing DIA MS2 (mz range):1600.7432_1601.9431( 25/37495 )
2024-02-21 11:19:44,097 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:44,097 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:44,227 INFO  [main] 8 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:44,227 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:44,377 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:44,377 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1600_1601_PeakCluster.serFS...
2024-02-21 11:19:44,377 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:44,377 INFO  [main] No. of fragment peaks: 8
2024-02-21 11:19:44,377 INFO  [main] No. of remaining fragment peaks: 5
2024-02-21 11:19:44,377 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:44,387 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:44,537 INFO  [main] ==================================================================================
2024-02-21 11:19:44,537 INFO  [main] Processing DIA MS2 (mz range):1599.1812_1600.3811( 26/37495 )
2024-02-21 11:19:44,537 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:44,537 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:44,677 INFO  [main] 15 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:44,677 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:44,807 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:44,807 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1599_1600_PeakCluster.serFS...
2024-02-21 11:19:44,807 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:44,807 INFO  [main] No. of fragment peaks: 15
2024-02-21 11:19:44,807 INFO  [main] No. of remaining fragment peaks: 9
2024-02-21 11:19:44,807 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:44,817 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:44,946 INFO  [main] ==================================================================================
2024-02-21 11:19:44,946 INFO  [main] Processing DIA MS2 (mz range):1599.103_1600.303( 27/37495 )
2024-02-21 11:19:44,946 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:44,946 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:45,086 INFO  [main] 7 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:45,086 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:45,216 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:45,216 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1599_1600_PeakCluster.serFS...
2024-02-21 11:19:45,216 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:45,216 INFO  [main] No. of fragment peaks: 7
2024-02-21 11:19:45,216 INFO  [main] No. of remaining fragment peaks: 4
2024-02-21 11:19:45,216 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:45,226 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:45,356 INFO  [main] ==================================================================================
2024-02-21 11:19:45,356 INFO  [main] Processing DIA MS2 (mz range):1599.0664_1600.2664( 28/37495 )
2024-02-21 11:19:45,366 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:45,366 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:45,516 INFO  [main] 10 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:45,516 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:45,646 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:45,646 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1599_1600_PeakCluster.serFS...
2024-02-21 11:19:45,646 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:45,646 INFO  [main] No. of fragment peaks: 10
2024-02-21 11:19:45,646 INFO  [main] No. of remaining fragment peaks: 8
2024-02-21 11:19:45,646 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:45,656 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:45,796 INFO  [main] ==================================================================================
2024-02-21 11:19:45,796 INFO  [main] Processing DIA MS2 (mz range):1598.6715_1599.8715( 29/37495 )
2024-02-21 11:19:45,796 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:45,796 INFO  [main] Smoothing detected signals......
2024-02-21 11:19:45,946 INFO  [main] 12 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:45,946 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:46,066 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:46,066 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1598_1599_PeakCluster.serFS...
2024-02-21 11:19:46,066 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:46,066 INFO  [main] No. of fragment peaks: 12
2024-02-21 11:19:46,066 INFO  [main] No. of remaining fragment peaks: 6
2024-02-21 11:19:46,066 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:46,086 INFO  [main] Building precursor-fragment pairs for unfragmented ions....
2024-02-21 11:19:46,216 INFO  [main] ==================================================================================
2024-02-21 11:19:46,216 INFO  [main] Processing DIA MS2 (mz range):1598.6547_1599.8546( 30/37495 )
2024-02-21 11:19:46,216 INFO  [main] Processing all scans to detect possible m/z peak curves and
2024-02-21 11:19:46,216 INFO  [main] Smoothing detected signals......
Exception in thread "main" java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException
	at MSUmpire.PeptidePeakClusterDetection.PDHandlerDIAMS2.PrecursorFragmentPairBuildingForMS1(PDHandlerDIAMS2.java:186)
	at MSUmpire.PeptidePeakClusterDetection.PDHandlerDIAMS2.FragmentGrouping(PDHandlerDIAMS2.java:100)
	at MSUmpire.LCMSPeakStructure.LCMSPeakDIAMS2.PeakDetectionPFGrouping(LCMSPeakDIAMS2.java:140)
	at MSUmpire.DIA.DIAPack.DIAMS2PeakDetection(DIAPack.java:1029)
	at MSUmpire.DIA.DIAPack.process(DIAPack.java:179)
	at dia_umpire_se.DIA_Umpire_SE.main(DIA_Umpire_SE.java:379)
Caused by: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException
	at java.base/java.util.concurrent.ForkJoinTask.get(Unknown Source)
	at MSUmpire.PeptidePeakClusterDetection.PDHandlerDIAMS2.PrecursorFragmentPairBuildingForMS1(PDHandlerDIAMS2.java:185)
	... 5 more
Caused by: java.lang.ArrayIndexOutOfBoundsException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.base/java.lang.reflect.Constructor.newInstance(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(Unknown Source)
	... 7 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
	at ExternalPackages.SortedListLib.SortedList.get(SortedList.java:483)
	at MSUmpire.DIA.CorrCalcCluster2CurveUnit.run(CorrCalcCluster2CurveUnit.java:65)
	at java.base/java.util.concurrent.ForkJoinTask$AdaptedRunnable.exec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool.scan(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinWorkerThread.run(Unknown Source)
2024-02-21 11:19:46,366 INFO  [main] 1 Peak curves found (Memory usage:1543MB)
2024-02-21 11:19:46,366 INFO  [main] Grouping isotopic peak curves........
2024-02-21 11:19:46,506 INFO  [main] No of ion clusters:0 (Memory usage:1543MB)
2024-02-21 11:19:46,506 INFO  [main] Writing PeakCluster serialization to file:20230825_INT001-02674-HLAIp_R01_1598_1599_PeakCluster.serFS...
2024-02-21 11:19:46,506 INFO  [main] Performing mass defect filter on fragment peaks
2024-02-21 11:19:46,506 INFO  [main] No. of fragment peaks: 1
2024-02-21 11:19:46,506 INFO  [main] No. of remaining fragment peaks: 0
2024-02-21 11:19:46,506 INFO  [main] Building precursor-fragment pairs for MS1 features....
2024-02-21 11:19:46,516 ERROR [main] java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException
	at MSUmpire.PeptidePeakClusterDetection.PDHandlerDIAMS2.PrecursorFragmentPairBuildingForMS1(PDHandlerDIAMS2.java:186)
	at MSUmpire.PeptidePeakClusterDetection.PDHandlerDIAMS2.FragmentGrouping(PDHandlerDIAMS2.java:100)
	at MSUmpire.LCMSPeakStructure.LCMSPeakDIAMS2.PeakDetectionPFGrouping(LCMSPeakDIAMS2.java:140)
	at MSUmpire.DIA.DIAPack.DIAMS2PeakDetection(DIAPack.java:1029)
	at MSUmpire.DIA.DIAPack.process(DIAPack.java:179)
	at dia_umpire_se.DIA_Umpire_SE.main(DIA_Umpire_SE.java:379)
Caused by: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException
	at java.base/java.util.concurrent.ForkJoinTask.get(Unknown Source)
	at MSUmpire.PeptidePeakClusterDetection.PDHandlerDIAMS2.PrecursorFragmentPairBuildingForMS1(PDHandlerDIAMS2.java:185)
	... 5 more
Caused by: java.lang.ArrayIndexOutOfBoundsException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.base/java.lang.reflect.Constructor.newInstance(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(Unknown Source)
	... 7 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
	at ExternalPackages.SortedListLib.SortedList.get(SortedList.java:483)
	at MSUmpire.DIA.CorrCalcCluster2CurveUnit.run(CorrCalcCluster2CurveUnit.java:65)
	at java.base/java.util.concurrent.ForkJoinTask$AdaptedRunnable.exec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool.scan(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinWorkerThread.run(Unknown Source)

Process 'UmpireSe' finished, exit code: 1
Process returned non-zero exit code, stopping

~~~~~~~~~~~~~~~~~~~~
Cancelling 5008 remaining tasks