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


Version info:
FragPipe version 19.1
MSFragger version 3.7
IonQuant version 1.8.10
Philosopher version 4.8.1


LCMS files:
  Experiment/Group: 230329HN02AdipositeKRNpepNtermC1_05TFA
  - D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN02AdipositeKRNpepNtermC1_05TFA.raw	DDA
  Experiment/Group: 230329HN03AdipositeKRNpepNtermC2_05TFA
  - D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN03AdipositeKRNpepNtermC2_05TFA.raw	DDA
  Experiment/Group: 230329HN04AdipositeKRNpepNtermC3_05TFA
  - D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN04AdipositeKRNpepNtermC3_05TFA.raw	DDA
  Experiment/Group: 230329HN06AdipositeKRNpepNtermP1_05TFA
  - D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN06AdipositeKRNpepNtermP1_05TFA.raw	DDA
  Experiment/Group: 230329HN07AdipositeKRNpepNtermP2_05TFA
  - D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN07AdipositeKRNpepNtermP2_05TFA.raw	DDA
  Experiment/Group: 230329HN08AdipositeKRNpepNtermP3_05TFA
  - D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN08AdipositeKRNpepNtermP3_05TFA.raw	DDA


81 commands to execute:
CheckCentroid
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -Xmx219G -cp "D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\batmass-io-1.28.9.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN02AdipositeKRNpepNtermC1_05TFA.raw 33
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\81e1a381-d1a8-4b0d-aa52-d84dfd4e0926
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\21a32455-0036-41a0-b678-b77ccf6fb06d
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\8c1af717-af95-4e34-ad2c-2947ce2ef7a7
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\01fe5729-ddee-4a57-8ec1-63ec1f63625d
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\68b05448-6e5d-4084-a073-fc8c346edb49
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\4755a4a8-08b2-4e7f-99b8-79772e05bddc
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\2a815ba0-775e-43eb-9695-795ba8fbbe66
MSFragger [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx219G D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\MSFragger-3.7\MSFragger-3.7.jar D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\fragger.params D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN02AdipositeKRNpepNtermC1_05TFA.raw D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN03AdipositeKRNpepNtermC2_05TFA.raw D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN04AdipositeKRNpepNtermC3_05TFA.raw D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN06AdipositeKRNpepNtermP1_05TFA.raw D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN07AdipositeKRNpepNtermP2_05TFA.raw D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN08AdipositeKRNpepNtermP3_05TFA.raw
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN02AdipositeKRNpepNtermC1_05TFA.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\230329HN02AdipositeKRNpepNtermC1_05TFA.pepXML
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN02AdipositeKRNpepNtermC1_05TFA.pin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\230329HN02AdipositeKRNpepNtermC1_05TFA.pin
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN03AdipositeKRNpepNtermC2_05TFA.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\230329HN03AdipositeKRNpepNtermC2_05TFA.pepXML
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN03AdipositeKRNpepNtermC2_05TFA.pin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\230329HN03AdipositeKRNpepNtermC2_05TFA.pin
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN04AdipositeKRNpepNtermC3_05TFA.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\230329HN04AdipositeKRNpepNtermC3_05TFA.pepXML
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN04AdipositeKRNpepNtermC3_05TFA.pin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\230329HN04AdipositeKRNpepNtermC3_05TFA.pin
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN06AdipositeKRNpepNtermP1_05TFA.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\230329HN06AdipositeKRNpepNtermP1_05TFA.pepXML
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN06AdipositeKRNpepNtermP1_05TFA.pin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\230329HN06AdipositeKRNpepNtermP1_05TFA.pin
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN07AdipositeKRNpepNtermP2_05TFA.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\230329HN07AdipositeKRNpepNtermP2_05TFA.pepXML
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN07AdipositeKRNpepNtermP2_05TFA.pin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\230329HN07AdipositeKRNpepNtermP2_05TFA.pin
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN08AdipositeKRNpepNtermP3_05TFA.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\230329HN08AdipositeKRNpepNtermP3_05TFA.pepXML
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN08AdipositeKRNpepNtermP3_05TFA.pin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\230329HN08AdipositeKRNpepNtermP3_05TFA.pin
MSBooster [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -Xmx219G -cp "D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\msbooster-1.1.11.jar;D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\batmass-io-1.28.9.jar" Features.MainClass --paramsList D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\msbooster_params.txt
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_decoy_psms.tsv 230329HN08AdipositeKRNpepNtermP3_05TFA_edited.pin
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_decoy_psms.tsv 230329HN02AdipositeKRNpepNtermC1_05TFA_edited.pin
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_decoy_psms.tsv 230329HN03AdipositeKRNpepNtermC2_05TFA_edited.pin
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_decoy_psms.tsv 230329HN04AdipositeKRNpepNtermC3_05TFA_edited.pin
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_decoy_psms.tsv 230329HN06AdipositeKRNpepNtermP1_05TFA_edited.pin
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_decoy_psms.tsv 230329HN07AdipositeKRNpepNtermP2_05TFA_edited.pin
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230329HN08AdipositeKRNpepNtermP3_05TFA.pin 230329HN08AdipositeKRNpepNtermP3_05TFA 230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_target_psms.tsv 230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_decoy_psms.tsv interact-230329HN08AdipositeKRNpepNtermP3_05TFA DDA 0.5
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_target_psms.tsv
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230329HN02AdipositeKRNpepNtermC1_05TFA.pin 230329HN02AdipositeKRNpepNtermC1_05TFA 230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_target_psms.tsv 230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_decoy_psms.tsv interact-230329HN02AdipositeKRNpepNtermC1_05TFA DDA 0.5
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_target_psms.tsv
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230329HN03AdipositeKRNpepNtermC2_05TFA.pin 230329HN03AdipositeKRNpepNtermC2_05TFA 230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_target_psms.tsv 230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_decoy_psms.tsv interact-230329HN03AdipositeKRNpepNtermC2_05TFA DDA 0.5
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_target_psms.tsv
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230329HN04AdipositeKRNpepNtermC3_05TFA.pin 230329HN04AdipositeKRNpepNtermC3_05TFA 230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_target_psms.tsv 230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_decoy_psms.tsv interact-230329HN04AdipositeKRNpepNtermC3_05TFA DDA 0.5
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_target_psms.tsv
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230329HN06AdipositeKRNpepNtermP1_05TFA.pin 230329HN06AdipositeKRNpepNtermP1_05TFA 230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_target_psms.tsv 230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_decoy_psms.tsv interact-230329HN06AdipositeKRNpepNtermP1_05TFA DDA 0.5
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_target_psms.tsv
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230329HN07AdipositeKRNpepNtermP2_05TFA.pin 230329HN07AdipositeKRNpepNtermP2_05TFA 230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_target_psms.tsv 230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_decoy_psms.tsv interact-230329HN07AdipositeKRNpepNtermP2_05TFA DDA 0.5
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_target_psms.tsv
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_decoy_psms.tsv
ProteinProphet [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA --protxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\combined.prot.xml --razor
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA --protxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\combined.prot.xml --razorbin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA --protxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\combined.prot.xml --razorbin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA --protxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\combined.prot.xml --razorbin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA --protxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\combined.prot.xml --razorbin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA --protxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\combined.prot.xml --razorbin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
IonQuant [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -Xmx219G -Dlibs.bruker.dir="D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\MSFragger-3.7\ext\bruker" -Dlibs.thermo.dir="D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\MSFragger-3.7\ext\thermo" -cp "D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\jfreechart-1.5.3.jar;D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\batmass-io-1.28.9.jar;D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\IonQuant-1.8.10.jar" ionquant.IonQuant --threads 33 --ionmobility 0 --minexps 1 --mbr 0 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\filelist_ionquant.txt --modlist D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\modmasses_ionquant.txt
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
    Cmd: [CheckCentroid], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
    Cmd: [MSFragger], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
    Cmd: [MSBooster], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
    Cmd: [Percolator], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
    Cmd: [ProteinProphet], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
    Cmd: [PhilosopherFilter], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
    Cmd: [PhilosopherReport], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
    Cmd: [WorkspaceClean], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
    Cmd: [WorkspaceClean], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
    Cmd: [WorkspaceClean], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
    Cmd: [WorkspaceClean], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
    Cmd: [WorkspaceClean], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
    Cmd: [WorkspaceClean], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
    Cmd: [WorkspaceClean], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
    Cmd: [IonQuant], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]

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

~~~~~~Sample of D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas~~~~~~~
>rev_sp|A0A087WPF7-2|AUTS2_MOUSE Isoform 2 of Autism susceptibility gene 2 protein homolog OS=Mus musculus OX=10090 GN=Auts2
>rev_sp|Q5UKY4-4|MO2R3_MOUSE Isoform 4 of Cell surface glycoprotein CD200 receptor 3 OS=Mus musculus OX=10090 GN=Cd200r3
>rev_sp|Q91YK0|LRC49_MOUSE Leucine-rich repeat-containing protein 49 OS=Mus musculus OX=10090 GN=Lrrc49 PE=1 SV=1
>rev_tr|A0A0G2JFU4|A0A0G2JFU4_MOUSE Checkpoint with forkhead and ring finger domains OS=Mus musculus OX=10090 GN=Chfr PE=1 SV=1
>rev_tr|A0A3B2W3L2|A0A3B2W3L2_MOUSE Vomeronasal 2, receptor 79 OS=Mus musculus OX=10090 GN=Vmn2r79 PE=4 SV=1
>rev_tr|C0IQA7|C0IQA7_MOUSE Testis specific expressed protein 5 OS=Mus musculus OX=10090 GN=4930544G11Rik PE=2 SV=1
>rev_tr|F6U8V3|F6U8V3_MOUSE Histocompatibility 2, M region locus 11 (Fragment) OS=Mus musculus OX=10090 GN=H2-M11 PE=3 SV=1
>rev_tr|Q3TCL6|Q3TCL6_MOUSE Anthrax toxin receptor OS=Mus musculus OX=10090 GN=Antxr2 PE=1 SV=1
>rev_tr|Q548K2|Q548K2_MOUSE Alcohol dehydrogenase class 4 OS=Mus musculus OX=10090 GN=Adh7 PE=2 SV=1
>rev_tr|Q8C980|Q8C980_MOUSE Uncharacterized protein OS=Mus musculus OX=10090 GN=Gm10006 PE=2 SV=1
>rev_tr|Z4YN74|Z4YN74_MOUSE Transmembrane protein 11 (Fragment) OS=Mus musculus OX=10090 GN=Tmem11 PE=1 SV=1
>sp|Q5U901|CBPA6_MOUSE Carboxypeptidase A6 OS=Mus musculus OX=10090 GN=Cpa6 PE=2 SV=1
>sp|Q91YI4-2|ARRB2_MOUSE Isoform 2 of Beta-arrestin-2 OS=Mus musculus OX=10090 GN=Arrb2
>tr|A0A0G2JFT4|A0A0G2JFT4_MOUSE Microtubule-associated protein (Fragment) OS=Mus musculus OX=10090 GN=Map4 PE=1 SV=1
>tr|A0A3B2W3G7|A0A3B2W3G7_MOUSE Peroxisomal, testis specific 1 OS=Mus musculus OX=10090 GN=Pxt1 PE=4 SV=1
>tr|C0H5Y0|C0H5Y0_MOUSE Asb7 protein OS=Mus musculus OX=10090 GN=Asb7 PE=2 SV=1
>tr|F6U786|F6U786_MOUSE Rho guanine nucleotide exchange factor (GEF) 38 OS=Mus musculus OX=10090 GN=Arhgef38 PE=4 SV=1
>tr|Q3TCI1|Q3TCI1_MOUSE EF-hand domain-containing protein (Fragment) OS=Mus musculus OX=10090 GN=Nucb1 PE=2 SV=1
>tr|Q547S9|Q547S9_MOUSE cAMP response element binding protein OS=Mus musculus OX=10090 GN=Creb1 PE=2 SV=1
>tr|Q8C961|Q8C961_MOUSE Uncharacterized protein (Fragment) OS=Mus musculus OX=10090 GN=Ncoa2 PE=2 SV=1
>tr|Z4YN17|Z4YN17_MOUSE XIAP associated factor 1 (Fragment) OS=Mus musculus OX=10090 GN=Xaf1 PE=1 SV=1
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v19.1ui state cache


# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\Personal\\Nishida\\Adiposite\\230413_AdipositeTMT\\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas

Table.editor=[^
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=3
diann.run-dia-nn=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=true
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=false
fragpipe-config.bin-ionquant=D\:\\Personal\\Nishida\\FragPipe-jre-19.1\\fragpipe\\tools\\IonQuant-1.8.10.jar
fragpipe-config.bin-msfragger=D\:\\Personal\\Nishida\\FragPipe-jre-19.1\\fragpipe\\tools\\MSFragger-3.7\\MSFragger-3.7.jar
fragpipe-config.bin-philosopher=D\:\\Personal\\Nishida\\FragPipe-jre-19.1\\fragpipe\\tools\\philosopher_v4.8.1_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\massUser\\anaconda3\\python
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=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
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.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.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=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2/3
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
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=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
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=500
msfragger.misc.fragger.enzyme-dropdown-1=lysn_promisc
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=3
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
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=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=lysn_promisc
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=N
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),true,-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,3; 42.0106,n^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 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_topN_peaks=150
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.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.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 --picked --prot 0.01
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.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=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
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.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
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=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=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.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\:\\Personal\\Nishida\\Adiposite\\230817_Re\\Label1\\Result
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=33

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -Xmx219G -cp "D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\batmass-io-1.28.9.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN02AdipositeKRNpepNtermC1_05TFA.raw 33
Done in 0 ms.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[21:51:33] Executing Workspace  v4.8.1                  
INFO[21:51:33] Removing workspace                           
WARN[21:51:33] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[21:51:33] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\81e1a381-d1a8-4b0d-aa52-d84dfd4e0926
INFO[21:51:33] Executing Workspace  v4.8.1                  
INFO[21:51:33] Creating workspace                           
INFO[21:51:33] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[21:51:34] Executing Workspace  v4.8.1                  
INFO[21:51:34] Removing workspace                           
WARN[21:51:34] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[21:51:34] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\21a32455-0036-41a0-b678-b77ccf6fb06d
INFO[21:51:34] Executing Workspace  v4.8.1                  
INFO[21:51:34] Creating workspace                           
INFO[21:51:34] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[21:51:35] Executing Workspace  v4.8.1                  
INFO[21:51:35] Removing workspace                           
WARN[21:51:35] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[21:51:35] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\8c1af717-af95-4e34-ad2c-2947ce2ef7a7
INFO[21:51:35] Executing Workspace  v4.8.1                  
INFO[21:51:35] Creating workspace                           
INFO[21:51:35] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[21:51:35] Executing Workspace  v4.8.1                  
INFO[21:51:36] Removing workspace                           
WARN[21:51:36] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[21:51:36] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\01fe5729-ddee-4a57-8ec1-63ec1f63625d
INFO[21:51:36] Executing Workspace  v4.8.1                  
INFO[21:51:36] Creating workspace                           
INFO[21:51:36] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[21:51:36] Executing Workspace  v4.8.1                  
INFO[21:51:36] Removing workspace                           
WARN[21:51:36] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[21:51:36] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\68b05448-6e5d-4084-a073-fc8c346edb49
INFO[21:51:37] Executing Workspace  v4.8.1                  
INFO[21:51:37] Creating workspace                           
INFO[21:51:37] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[21:51:37] Executing Workspace  v4.8.1                  
INFO[21:51:37] Removing workspace                           
WARN[21:51:37] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[21:51:37] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\4755a4a8-08b2-4e7f-99b8-79772e05bddc
INFO[21:51:38] Executing Workspace  v4.8.1                  
INFO[21:51:38] Creating workspace                           
INFO[21:51:38] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[21:51:38] Executing Workspace  v4.8.1                  
INFO[21:51:38] Removing workspace                           
WARN[21:51:38] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[21:51:38] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\2a815ba0-775e-43eb-9695-795ba8fbbe66
INFO[21:51:38] Executing Workspace  v4.8.1                  
INFO[21:51:38] Creating workspace                           
INFO[21:51:38] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx219G D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\MSFragger-3.7\MSFragger-3.7.jar D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\fragger.params D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN02AdipositeKRNpepNtermC1_05TFA.raw D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN03AdipositeKRNpepNtermC2_05TFA.raw D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN04AdipositeKRNpepNtermC3_05TFA.raw D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN06AdipositeKRNpepNtermP1_05TFA.raw D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN07AdipositeKRNpepNtermP2_05TFA.raw D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN08AdipositeKRNpepNtermP3_05TFA.raw
MSFragger version MSFragger-3.7
Batmass-IO version 1.28.9
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved.
System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
JVM started with 219 GB memory
Checking database...
Checking spectral files...
D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN06AdipositeKRNpepNtermP1_05TFA.raw: Scans = 82144
D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN07AdipositeKRNpepNtermP2_05TFA.raw: Scans = 85461
D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN08AdipositeKRNpepNtermP3_05TFA.raw: Scans = 85910
D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN02AdipositeKRNpepNtermC1_05TFA.raw: Scans = 87763
D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN03AdipositeKRNpepNtermC2_05TFA.raw: Scans = 86270
D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN04AdipositeKRNpepNtermC3_05TFA.raw: Scans = 88649
The data appears to be low resolution MS/MS. Switching to 300 ppm fragment tolerance.
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 33
database_name = D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas
decoy_prefix = rev_
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 300.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = false
write_calibrated_mzml = 0
write_uncalibrated_mgf = false
isotope_error = 0/1
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = lysn_promisc
search_enzyme_sense_1 = N
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 3
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = false
override_charge = false
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 2
deisotope = 0
deneutralloss = false
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
activation_types = all
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = true
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 n^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 1.50 Da.
7585331714 fragments to be searched in 1 slices (113.03 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 92.40 s
	001. 230329HN02AdipositeKRNpepNtermC1_05TFA.raw 47.0 s
		[progress: 87325/87325 (100%) - 5651 spectra/s] 15.5s | postprocessing 0.7 s
	002. 230329HN03AdipositeKRNpepNtermC2_05TFA.raw 36.2 s
		[progress: 85749/85749 (100%) - 7538 spectra/s] 11.4s | postprocessing 0.3 s
	003. 230329HN04AdipositeKRNpepNtermC3_05TFA.raw 37.4 s
		[progress: 88079/88079 (100%) - 7047 spectra/s] 12.5s | postprocessing 0.6 s
	004. 230329HN06AdipositeKRNpepNtermP1_05TFA.raw 33.3 s
		[progress: 81697/81697 (100%) - 7541 spectra/s] 10.8s | postprocessing 0.3 s
	005. 230329HN07AdipositeKRNpepNtermP2_05TFA.raw 35.9 s
		[progress: 84918/84918 (100%) - 8083 spectra/s] 10.5s | postprocessing 0.3 s
	006. 230329HN08AdipositeKRNpepNtermP3_05TFA.raw 34.6 s
		[progress: 85469/85469 (100%) - 7725 spectra/s] 11.1s | postprocessing 0.3 s
***************************FIRST SEARCH DONE IN 7.035 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |   2.70   0.50 |   0.10   0.52 |  -28.20  95.36 |  -1.53  87.24  
 002 |   2.73   0.49 |   0.01   0.50 |  -27.25  92.96 |  -2.28  86.57  
 003 |   3.07   0.53 |  -0.00   0.49 |  -27.95  90.27 |  -1.82  84.81  
 004 |   3.23   0.49 |   0.15   0.43 |  -55.52  92.55 |  -8.72  88.33  
 005 |   3.00   0.46 |   0.07   0.45 |  -54.07  94.90 |  -10.47  90.07  
 006 |   2.98   0.49 |   0.02   0.48 |  -59.02  95.31 |  -7.65  89.01  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |  150  |  200  |  250  |  300  |  350  |  400  |  450  |  500  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count | skip  |   2443|   1825| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------
 Peaks | 150_1 | 125_1 | 100_1 |  75_1 
-------|-------|-------|-------|-------
 Count |   2443|   2517|   2672|   2811
-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |   2200
-------|-------
-------|-------
 Rm P. |    0  
-------|-------
 Count |   1941
-------|-------
-------|-------
FragChg|    1  
-------|-------
 Count |   3724
-------|-------
New fragment_mass_tolerance = 200 PPM
New use_topN_peaks = 75
New minimum_ratio = 0.010000
New intensity_transform = 0
New remove_precursor_peak = 1
New max_fragment_charge = 1
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 13.287 MIN*********

************************************MAIN SEARCH************************************
Checking database...
Parameters:
num_threads = 33
database_name = D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas
decoy_prefix = rev_
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 200.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = false
write_calibrated_mzml = 0
write_uncalibrated_mgf = false
isotope_error = 0/1/2/3
mass_offsets = 0.0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = lysn_promisc
search_enzyme_sense_1 = N
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 3
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = true
override_charge = false
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 0
deneutralloss = false
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 75
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
activation_types = all
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = true
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 n^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 1.00 Da.
7585331714 fragments to be searched in 1 slices (113.03 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 50.19 s
	001. 230329HN02AdipositeKRNpepNtermC1_05TFA.mzBIN_calibrated 3.1 s
		[progress: 87311/87311 (100%) - 10507 spectra/s] 8.3s | remapping alternative proteins and postprocessing 18.6 s
	002. 230329HN03AdipositeKRNpepNtermC2_05TFA.mzBIN_calibrated 3.0 s
		[progress: 85736/85736 (100%) - 11017 spectra/s] 7.8s | remapping alternative proteins and postprocessing 19.6 s
	003. 230329HN04AdipositeKRNpepNtermC3_05TFA.mzBIN_calibrated 6.1 s
		[progress: 88071/88071 (100%) - 9887 spectra/s] 8.9s | remapping alternative proteins and postprocessing 14.8 s
	004. 230329HN06AdipositeKRNpepNtermP1_05TFA.mzBIN_calibrated 2.7 s
		[progress: 81672/81672 (100%) - 11895 spectra/s] 6.9s | remapping alternative proteins and postprocessing 17.3 s
	005. 230329HN07AdipositeKRNpepNtermP2_05TFA.mzBIN_calibrated 2.7 s
		[progress: 84896/84896 (100%) - 12184 spectra/s] 7.0s | remapping alternative proteins and postprocessing 14.0 s
	006. 230329HN08AdipositeKRNpepNtermP3_05TFA.mzBIN_calibrated 2.9 s
		[progress: 85454/85454 (100%) - 11814 spectra/s] 7.2s | remapping alternative proteins and postprocessing 13.8 s
***************************MAIN SEARCH DONE IN 3.865 MIN***************************

*******************************TOTAL TIME 24.186 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN02AdipositeKRNpepNtermC1_05TFA.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\230329HN02AdipositeKRNpepNtermC1_05TFA.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN02AdipositeKRNpepNtermC1_05TFA.pin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\230329HN02AdipositeKRNpepNtermC1_05TFA.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN03AdipositeKRNpepNtermC2_05TFA.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\230329HN03AdipositeKRNpepNtermC2_05TFA.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN03AdipositeKRNpepNtermC2_05TFA.pin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\230329HN03AdipositeKRNpepNtermC2_05TFA.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN04AdipositeKRNpepNtermC3_05TFA.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\230329HN04AdipositeKRNpepNtermC3_05TFA.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN04AdipositeKRNpepNtermC3_05TFA.pin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\230329HN04AdipositeKRNpepNtermC3_05TFA.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN06AdipositeKRNpepNtermP1_05TFA.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\230329HN06AdipositeKRNpepNtermP1_05TFA.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN06AdipositeKRNpepNtermP1_05TFA.pin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\230329HN06AdipositeKRNpepNtermP1_05TFA.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN07AdipositeKRNpepNtermP2_05TFA.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\230329HN07AdipositeKRNpepNtermP2_05TFA.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN07AdipositeKRNpepNtermP2_05TFA.pin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\230329HN07AdipositeKRNpepNtermP2_05TFA.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN08AdipositeKRNpepNtermP3_05TFA.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\230329HN08AdipositeKRNpepNtermP3_05TFA.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN08AdipositeKRNpepNtermP3_05TFA.pin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\230329HN08AdipositeKRNpepNtermP3_05TFA.pin
Process 'MSFragger move pin' finished, exit code: 0
MSBooster [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -Xmx219G -cp "D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\msbooster-1.1.11.jar;D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\batmass-io-1.28.9.jar" Features.MainClass --paramsList D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\msbooster_params.txt
MSBooster v1.1.11
Using 33 threads
Generating input file for DIA-NN
351664 unique peptides from 428793 PSMs
Writing DIA-NN input file
Diann input file generation took 2602 milliseconds
Input file at  D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\spectraRT.tsv
351664 unique peptides from 428793 PSMs
createFull input file generation took 2230 milliseconds
Input file at  D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\spectraRT_full.tsv
Generating DIA-NN predictions
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\spectraRT.tsv --predict --threads 33 --strip-unknown-mods --mod TMT,229.1629 --predict-n-frag 100
DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks)
Compiled on Sep 15 2022 18:28:57
Current date and time: Mon Aug 21 22:16:05 2023
CPU: GenuineIntel Intel(R) Core(TM) i9-10980XE CPU @ 3.00GHz
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 36
Predicted spectra will be saved in a binary format
Thread number set to 33
DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option
Modification TMT with mass delta 229.163 added to the list of recognised modifications for spectral library-based search
Deep learning predictor will predict 100 fragments
Cannot find a UniMod modification match for TMT: 73.0618 minimal mass discrepancy; using the original modificaiton name

0 files will be processed
[0:00] Loading spectral library D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\spectraRT.tsv
[0:01] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:01] Spectral library loaded: 0 protein isoforms, 0 protein groups and 351664 precursors in 349197 elution groups.
[0:01] Encoding peptides for spectra and RTs prediction
[0:02] Predicting spectra and IMs
[0:39] Predicting RTs
[0:54] Decoding predicted spectra and IMs
[1:00] Decoding RTs
[1:00] Saving the list of predictions to D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\spectraRT.predicted.bin
Finished
Done generating DIA-NN predictions
Model running took 62139 milliseconds
Generating edited pin with following features: [unweightedSpectralEntropy, deltaRTLOESS]
Loading predicted spectra
Processing 230329HN02AdipositeKRNpepNtermC1_05TFA_uncalibrated.mzML
RT regression using 786 PSMs
Edited pin file at D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\230329HN02AdipositeKRNpepNtermC1_05TFA_edited.pin
Processing 230329HN03AdipositeKRNpepNtermC2_05TFA_uncalibrated.mzML
RT regression using 707 PSMs
Edited pin file at D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\230329HN03AdipositeKRNpepNtermC2_05TFA_edited.pin
Processing 230329HN04AdipositeKRNpepNtermC3_05TFA_uncalibrated.mzML
RT regression using 854 PSMs
Edited pin file at D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\230329HN04AdipositeKRNpepNtermC3_05TFA_edited.pin
Processing 230329HN06AdipositeKRNpepNtermP1_05TFA_uncalibrated.mzML
RT regression using 631 PSMs
Edited pin file at D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\230329HN06AdipositeKRNpepNtermP1_05TFA_edited.pin
Processing 230329HN07AdipositeKRNpepNtermP2_05TFA_uncalibrated.mzML
RT regression using 592 PSMs
Edited pin file at D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\230329HN07AdipositeKRNpepNtermP2_05TFA_edited.pin
Processing 230329HN08AdipositeKRNpepNtermP3_05TFA_uncalibrated.mzML
RT regression using 670 PSMs
Edited pin file at D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\230329HN08AdipositeKRNpepNtermP3_05TFA_edited.pin
Done in 41195 ms
Process 'MSBooster' finished, exit code: 0
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_decoy_psms.tsv 230329HN08AdipositeKRNpepNtermP3_05TFA_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_decoy_psms.tsv 230329HN08AdipositeKRNpepNtermP3_05TFA_edited.pin
Started Mon Aug 21 22:17:48 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230329HN08AdipositeKRNpepNtermP3_05TFA_edited.pin
Features:
retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more 15.9949M 42.0106n^ unweighted_spectral_entropy delta_RT_loess 
Found 69564 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 37971 positives and 31593 negatives, size ratio=1.20188 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 5 as initial direction. Could separate 1681 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 5 as initial direction. Could separate 1545 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 24 as initial direction. Could separate 1808 training set positives with q<0.01 in that direction.
Found 2026 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 1.227 cpu seconds or 2 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 5114 PSMs with q<0.01
Iteration 2:	Estimated 5949 PSMs with q<0.01
Iteration 3:	Estimated 6164 PSMs with q<0.01
Iteration 4:	Estimated 6222 PSMs with q<0.01
Iteration 5:	Estimated 6242 PSMs with q<0.01
Iteration 6:	Estimated 6238 PSMs with q<0.01
Iteration 7:	Estimated 6244 PSMs with q<0.01
Iteration 8:	Estimated 6242 PSMs with q<0.01
Iteration 9:	Estimated 6246 PSMs with q<0.01
Iteration 10:	Estimated 6247 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0268	 0.0653	 0.0193	retentiontime
 0.0000	 0.0000	 0.0000	rank
-0.8501	-0.7611	-0.8181	abs_ppm
-0.7495	-0.5073	-0.7648	isotope_errors
-0.6369	-0.4881	-0.6323	log10_evalue
 0.2357	 0.1988	 0.4192	hyperscore
 0.3731	 0.2143	 0.3538	delta_hyperscore
-0.3966	-0.2710	-0.4217	matched_ion_num
-0.1791	-0.1015	-0.1209	complementary_ions
 0.0862	 0.0430	 0.0226	ion_series
-0.0307	-0.0896	-0.0626	weighted_average_abs_fragment_ppm
 0.7083	 0.4157	 0.6539	peptide_length
 0.0388	 0.1206	 0.0359	ntt
 0.0054	 0.0417	 0.0508	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.0521	 0.0475	 0.0283	charge_2
 0.0027	-0.0377	 0.0248	charge_3
-0.1932	-0.0323	-0.1982	charge_4
-0.0191	-0.0352	 0.0275	charge_5
 0.0735	 0.0362	 0.0644	charge_6
 0.0228	 0.0440	 0.0192	charge_7_or_more
 0.2351	 0.1281	 0.1517	15.9949M
-0.1553	-0.1092	-0.1756	42.0106n^
 2.8851	 1.7180	 2.7866	unweighted_spectral_entropy
-2.7899	-1.1536	-2.1594	delta_RT_loess
-7.6958	-4.3887	-7.0895	m0
Found 6158 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 37971 target PSMs and 31593 decoy PSMs.
Calculating q values.
Final list yields 6163 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 4.955 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_decoy_psms.tsv 230329HN02AdipositeKRNpepNtermC1_05TFA_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_decoy_psms.tsv 230329HN02AdipositeKRNpepNtermC1_05TFA_edited.pin
Started Mon Aug 21 22:17:55 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230329HN02AdipositeKRNpepNtermC1_05TFA_edited.pin
Features:
retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more 15.9949M 42.0106n^ unweighted_spectral_entropy delta_RT_loess 
Found 74337 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 40895 positives and 33442 negatives, size ratio=1.22286 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 5 as initial direction. Could separate 1881 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 5 as initial direction. Could separate 1960 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 5 as initial direction. Could separate 2133 training set positives with q<0.01 in that direction.
Found 2867 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 1.236 cpu seconds or 1 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 5546 PSMs with q<0.01
Iteration 2:	Estimated 6553 PSMs with q<0.01
Iteration 3:	Estimated 6852 PSMs with q<0.01
Iteration 4:	Estimated 6912 PSMs with q<0.01
Iteration 5:	Estimated 6930 PSMs with q<0.01
Iteration 6:	Estimated 6939 PSMs with q<0.01
Iteration 7:	Estimated 6952 PSMs with q<0.01
Iteration 8:	Estimated 6953 PSMs with q<0.01
Iteration 9:	Estimated 6959 PSMs with q<0.01
Iteration 10:	Estimated 6969 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0914	 0.0100	 0.0589	retentiontime
 0.0000	 0.0000	 0.0000	rank
-1.3356	-1.1820	-1.3734	abs_ppm
-0.8575	-0.5968	-0.7733	isotope_errors
-0.5538	-0.4085	-0.7546	log10_evalue
 0.6731	 0.4045	 0.0511	hyperscore
 0.2446	 0.4162	 0.3153	delta_hyperscore
-0.2122	-0.1524	 0.4116	matched_ion_num
-0.2361	-0.1931	-0.4281	complementary_ions
-0.2370	-0.0272	-0.1264	ion_series
-0.0822	-0.0455	-0.1175	weighted_average_abs_fragment_ppm
 0.6991	 0.6969	 0.6895	peptide_length
 0.1756	 0.1072	 0.0167	ntt
-0.0366	-0.0166	-0.1142	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.0837	 0.1140	 0.0695	charge_2
-0.0658	-0.0707	-0.0058	charge_3
-0.0704	-0.1611	-0.2166	charge_4
-0.0367	 0.0160	-0.0527	charge_5
 0.0456	 0.0285	 0.0566	charge_6
 0.1356	 0.0070	 0.0211	charge_7_or_more
 0.1346	 0.1608	 0.1272	15.9949M
-0.0553	-0.0941	-0.0679	42.0106n^
 2.8550	 2.4676	 3.2335	unweighted_spectral_entropy
-2.6745	-2.3329	-3.1110	delta_RT_loess
-7.8594	-6.4101	-8.5101	m0
Found 6872 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 40895 target PSMs and 33442 decoy PSMs.
Calculating q values.
Final list yields 6876 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 6.112 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_decoy_psms.tsv 230329HN03AdipositeKRNpepNtermC2_05TFA_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_decoy_psms.tsv 230329HN03AdipositeKRNpepNtermC2_05TFA_edited.pin
Started Mon Aug 21 22:18:03 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230329HN03AdipositeKRNpepNtermC2_05TFA_edited.pin
Features:
retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more 15.9949M 42.0106n^ unweighted_spectral_entropy delta_RT_loess 
Found 71809 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 39184 positives and 32625 negatives, size ratio=1.20104 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 24 as initial direction. Could separate 1953 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 5 as initial direction. Could separate 1576 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 24 as initial direction. Could separate 1921 training set positives with q<0.01 in that direction.
Found 2281 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 1.208 cpu seconds or 1 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 5598 PSMs with q<0.01
Iteration 2:	Estimated 6149 PSMs with q<0.01
Iteration 3:	Estimated 6296 PSMs with q<0.01
Iteration 4:	Estimated 6313 PSMs with q<0.01
Iteration 5:	Estimated 6326 PSMs with q<0.01
Iteration 6:	Estimated 6322 PSMs with q<0.01
Iteration 7:	Estimated 6330 PSMs with q<0.01
Iteration 8:	Estimated 6334 PSMs with q<0.01
Iteration 9:	Estimated 6329 PSMs with q<0.01
Iteration 10:	Estimated 6331 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
-0.0294	-0.1112	-0.0216	retentiontime
 0.0000	 0.0000	 0.0000	rank
-1.1708	-0.6791	-1.1587	abs_ppm
-0.6504	-0.5021	-0.8053	isotope_errors
-0.6428	-0.3659	-0.5796	log10_evalue
 0.3166	 0.1700	 0.3311	hyperscore
 0.3739	 0.1979	 0.3957	delta_hyperscore
-0.2278	-0.0521	-0.2021	matched_ion_num
-0.1250	-0.1056	-0.1133	complementary_ions
-0.1195	-0.0466	-0.0883	ion_series
-0.0616	-0.0585	-0.1567	weighted_average_abs_fragment_ppm
 0.3528	 0.3608	 0.4089	peptide_length
-0.0199	 0.0004	 0.0059	ntt
-0.0041	 0.0091	-0.0922	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0050	-0.0060	-0.0577	charge_2
 0.0176	 0.0093	 0.0798	charge_3
-0.0740	-0.0219	-0.1114	charge_4
 0.0623	 0.0218	 0.0824	charge_5
 0.0823	 0.0262	 0.0697	charge_6
 0.0748	 0.0348	 0.1012	charge_7_or_more
 0.1869	 0.0936	 0.2166	15.9949M
-0.0904	-0.0909	-0.2010	42.0106n^
 2.7814	 1.9086	 3.5848	unweighted_spectral_entropy
-1.8482	-1.2387	-2.7256	delta_RT_loess
-6.6775	-4.6657	-9.1276	m0
Found 6267 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 39184 target PSMs and 32625 decoy PSMs.
Calculating q values.
Final list yields 6267 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.033 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_decoy_psms.tsv 230329HN04AdipositeKRNpepNtermC3_05TFA_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_decoy_psms.tsv 230329HN04AdipositeKRNpepNtermC3_05TFA_edited.pin
Started Mon Aug 21 22:18:10 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230329HN04AdipositeKRNpepNtermC3_05TFA_edited.pin
Features:
retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more 15.9949M 42.0106n^ unweighted_spectral_entropy delta_RT_loess 
Found 74980 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 41538 positives and 33442 negatives, size ratio=1.24209 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 5 as initial direction. Could separate 2375 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 5 as initial direction. Could separate 2402 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 5 as initial direction. Could separate 2321 training set positives with q<0.01 in that direction.
Found 3491 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 1.3 cpu seconds or 1 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 5786 PSMs with q<0.01
Iteration 2:	Estimated 6908 PSMs with q<0.01
Iteration 3:	Estimated 7204 PSMs with q<0.01
Iteration 4:	Estimated 7279 PSMs with q<0.01
Iteration 5:	Estimated 7302 PSMs with q<0.01
Iteration 6:	Estimated 7325 PSMs with q<0.01
Iteration 7:	Estimated 7338 PSMs with q<0.01
Iteration 8:	Estimated 7349 PSMs with q<0.01
Iteration 9:	Estimated 7353 PSMs with q<0.01
Iteration 10:	Estimated 7344 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.1789	 0.1857	 0.2530	retentiontime
 0.0000	 0.0000	 0.0000	rank
-1.1141	-1.1900	-1.2255	abs_ppm
-0.6768	-0.7182	-0.6535	isotope_errors
-0.8056	-0.7706	-0.8923	log10_evalue
 0.4651	 0.2621	 0.5456	hyperscore
 0.4365	 0.2909	 0.3732	delta_hyperscore
-0.3937	-0.0707	-0.3779	matched_ion_num
-0.1558	-0.3055	-0.2971	complementary_ions
-0.0158	-0.0481	-0.0914	ion_series
-0.0264	-0.0176	-0.1303	weighted_average_abs_fragment_ppm
 0.6318	 0.5398	 0.5475	peptide_length
-0.0408	-0.0111	 0.0692	ntt
 0.1037	 0.0480	 0.1639	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.0790	 0.0652	 0.0610	charge_2
-0.0562	-0.0098	-0.0206	charge_3
-0.0879	-0.2131	-0.1737	charge_4
-0.0141	 0.0258	 0.0436	charge_5
 0.0704	 0.0733	 0.1227	charge_6
-0.0065	 0.0102	 0.0098	charge_7_or_more
 0.0561	 0.1356	 0.1378	15.9949M
-0.1277	-0.1013	-0.2489	42.0106n^
 3.0079	 2.9599	 3.6137	unweighted_spectral_entropy
-1.6448	-2.0044	-2.1285	delta_RT_loess
-6.4130	-7.1736	-7.8891	m0
Found 7190 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 41538 target PSMs and 33442 decoy PSMs.
Calculating q values.
Final list yields 7191 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.316 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_decoy_psms.tsv 230329HN06AdipositeKRNpepNtermP1_05TFA_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_decoy_psms.tsv 230329HN06AdipositeKRNpepNtermP1_05TFA_edited.pin
Started Mon Aug 21 22:18:18 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230329HN06AdipositeKRNpepNtermP1_05TFA_edited.pin
Features:
retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more 15.9949M 42.0106n^ unweighted_spectral_entropy delta_RT_loess 
Found 68431 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 37228 positives and 31203 negatives, size ratio=1.19309 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 5 as initial direction. Could separate 1506 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 5 as initial direction. Could separate 1565 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 5 as initial direction. Could separate 1474 training set positives with q<0.01 in that direction.
Found 2179 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 1.224 cpu seconds or 1 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 4503 PSMs with q<0.01
Iteration 2:	Estimated 5514 PSMs with q<0.01
Iteration 3:	Estimated 5713 PSMs with q<0.01
Iteration 4:	Estimated 5787 PSMs with q<0.01
Iteration 5:	Estimated 5809 PSMs with q<0.01
Iteration 6:	Estimated 5815 PSMs with q<0.01
Iteration 7:	Estimated 5828 PSMs with q<0.01
Iteration 8:	Estimated 5833 PSMs with q<0.01
Iteration 9:	Estimated 5842 PSMs with q<0.01
Iteration 10:	Estimated 5843 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0152	-0.1323	-0.0366	retentiontime
 0.0000	 0.0000	 0.0000	rank
-0.6583	-1.1253	-1.4718	abs_ppm
-0.6438	-1.1968	-1.1987	isotope_errors
-0.3612	-0.4721	-0.6503	log10_evalue
 0.1704	-0.2405	-0.0741	hyperscore
 0.2935	 0.5167	 0.5785	delta_hyperscore
-0.1734	 0.3721	 0.2639	matched_ion_num
-0.0746	-0.3226	-0.2343	complementary_ions
 0.0371	 0.0257	 0.0202	ion_series
-0.1630	-0.3171	-0.2918	weighted_average_abs_fragment_ppm
 0.4080	 0.7866	 0.6438	peptide_length
 0.0707	 0.0338	 0.0842	ntt
-0.0288	-0.0525	-0.1328	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.0039	 0.0189	-0.0126	charge_2
 0.0258	 0.0113	 0.0289	charge_3
-0.1007	-0.1077	-0.0534	charge_4
-0.0364	-0.0336	-0.0551	charge_5
 0.0660	 0.1106	 0.1152	charge_6
 0.0398	 0.0366	 0.0353	charge_7_or_more
 0.1511	 0.2149	 0.3095	15.9949M
-0.1081	-0.1318	-0.1480	42.0106n^
 1.8763	 3.1258	 3.3728	unweighted_spectral_entropy
-1.4442	-2.9803	-2.5119	delta_RT_loess
-5.2076	-8.7205	-9.0873	m0
Found 5740 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 37228 target PSMs and 31203 decoy PSMs.
Calculating q values.
Final list yields 5763 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.014 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_decoy_psms.tsv 230329HN07AdipositeKRNpepNtermP2_05TFA_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_target_psms.tsv --decoy-results-psms 230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_decoy_psms.tsv 230329HN07AdipositeKRNpepNtermP2_05TFA_edited.pin
Started Mon Aug 21 22:18:24 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230329HN07AdipositeKRNpepNtermP2_05TFA_edited.pin
Features:
retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more 15.9949M 42.0106n^ unweighted_spectral_entropy delta_RT_loess 
Found 69672 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 37643 positives and 32029 negatives, size ratio=1.17528 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 5 as initial direction. Could separate 1427 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 5 as initial direction. Could separate 1509 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 5 as initial direction. Could separate 1469 training set positives with q<0.01 in that direction.
Found 2101 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 1.141 cpu seconds or 1 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 4285 PSMs with q<0.01
Iteration 2:	Estimated 5134 PSMs with q<0.01
Iteration 3:	Estimated 5488 PSMs with q<0.01
Iteration 4:	Estimated 5534 PSMs with q<0.01
Iteration 5:	Estimated 5538 PSMs with q<0.01
Iteration 6:	Estimated 5548 PSMs with q<0.01
Iteration 7:	Estimated 5552 PSMs with q<0.01
Iteration 8:	Estimated 5552 PSMs with q<0.01
Iteration 9:	Estimated 5545 PSMs with q<0.01
Iteration 10:	Estimated 5555 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
-0.1986	-0.0709	-0.0745	retentiontime
 0.0000	 0.0000	 0.0000	rank
-1.3200	-0.7153	-0.7437	abs_ppm
-0.7504	-0.4194	-0.3865	isotope_errors
-0.4736	-0.2767	-0.3176	log10_evalue
 0.1193	 0.1725	 0.1633	hyperscore
 0.4409	 0.2300	 0.1879	delta_hyperscore
 0.0398	-0.1407	-0.0680	matched_ion_num
-0.2254	-0.0522	-0.0723	complementary_ions
-0.0576	 0.0734	 0.0380	ion_series
-0.0718	-0.0602	-0.0521	weighted_average_abs_fragment_ppm
 1.0363	 0.4090	 0.4010	peptide_length
 0.0430	-0.0011	 0.0180	ntt
 0.1068	 0.0340	 0.0118	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.1241	 0.0138	 0.0307	charge_2
-0.0834	 0.0039	-0.0167	charge_3
-0.1645	-0.0618	-0.0589	charge_4
-0.0127	-0.0230	-0.0053	charge_5
 0.0348	 0.0056	 0.0441	charge_6
 0.0638	-0.0066	-0.0065	charge_7_or_more
 0.1263	 0.0702	 0.0814	15.9949M
-0.2763	-0.0700	-0.0676	42.0106n^
 3.2062	 1.5638	 1.4985	unweighted_spectral_entropy
-2.0572	-0.9412	-0.9482	delta_RT_loess
-8.4238	-3.7357	-3.7306	m0
Found 5494 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 37643 target PSMs and 32029 decoy PSMs.
Calculating q values.
Final list yields 5512 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.418 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230329HN08AdipositeKRNpepNtermP3_05TFA.pin 230329HN08AdipositeKRNpepNtermP3_05TFA 230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_target_psms.tsv 230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_decoy_psms.tsv interact-230329HN08AdipositeKRNpepNtermP3_05TFA DDA 0.5
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\230329HN08AdipositeKRNpepNtermP3_05TFA_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230329HN02AdipositeKRNpepNtermC1_05TFA.pin 230329HN02AdipositeKRNpepNtermC1_05TFA 230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_target_psms.tsv 230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_decoy_psms.tsv interact-230329HN02AdipositeKRNpepNtermC1_05TFA DDA 0.5
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\230329HN02AdipositeKRNpepNtermC1_05TFA_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230329HN03AdipositeKRNpepNtermC2_05TFA.pin 230329HN03AdipositeKRNpepNtermC2_05TFA 230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_target_psms.tsv 230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_decoy_psms.tsv interact-230329HN03AdipositeKRNpepNtermC2_05TFA DDA 0.5
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\230329HN03AdipositeKRNpepNtermC2_05TFA_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230329HN04AdipositeKRNpepNtermC3_05TFA.pin 230329HN04AdipositeKRNpepNtermC3_05TFA 230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_target_psms.tsv 230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_decoy_psms.tsv interact-230329HN04AdipositeKRNpepNtermC3_05TFA DDA 0.5
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\230329HN04AdipositeKRNpepNtermC3_05TFA_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230329HN06AdipositeKRNpepNtermP1_05TFA.pin 230329HN06AdipositeKRNpepNtermP1_05TFA 230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_target_psms.tsv 230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_decoy_psms.tsv interact-230329HN06AdipositeKRNpepNtermP1_05TFA DDA 0.5
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\230329HN06AdipositeKRNpepNtermP1_05TFA_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230329HN07AdipositeKRNpepNtermP2_05TFA.pin 230329HN07AdipositeKRNpepNtermP2_05TFA 230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_target_psms.tsv 230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_decoy_psms.tsv interact-230329HN07AdipositeKRNpepNtermP2_05TFA DDA 0.5
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\230329HN07AdipositeKRNpepNtermP2_05TFA_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
ProteinProphet [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\filelist_proteinprophet.txt
INFO[22:18:50] Executing ProteinProphet  v4.8.1             
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64))
 (no FPKM) (no groups) (using degen pep info)
Reading in D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\interact-230329HN02AdipositeKRNpepNtermC1_05TFA.pep.xml...
...read in 0 1+, 5048 2+, 2859 3+, 348 4+, 21 5+, 3 6+, 5 7+ spectra with min prob 0.05

Reading in D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\interact-230329HN03AdipositeKRNpepNtermC2_05TFA.pep.xml...
...read in 0 1+, 4760 2+, 2486 3+, 289 4+, 14 5+, 4 6+, 1 7+ spectra with min prob 0.05

Reading in D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\interact-230329HN04AdipositeKRNpepNtermC3_05TFA.pep.xml...
...read in 0 1+, 5191 2+, 3043 3+, 361 4+, 26 5+, 7 6+, 1 7+ spectra with min prob 0.05

Reading in D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\interact-230329HN06AdipositeKRNpepNtermP1_05TFA.pep.xml...
...read in 0 1+, 4232 2+, 2295 3+, 298 4+, 8 5+, 3 6+, 2 7+ spectra with min prob 0.05

Reading in D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\interact-230329HN07AdipositeKRNpepNtermP2_05TFA.pep.xml...
...read in 0 1+, 4205 2+, 2221 3+, 244 4+, 11 5+, 4 6+, 3 7+ spectra with min prob 0.05

Reading in D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\interact-230329HN08AdipositeKRNpepNtermP3_05TFA.pep.xml...
...read in 0 1+, 4566 2+, 2522 3+, 330 4+, 15 5+, 3 6+, 4 7+ spectra with min prob 0.05

Initializing 11766 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry rev_sp|Q3UQA7|SELH_MOUSE : U
MSLYKKLEEVVEQPEPFKLKRPPGKKIGTWLEVRSNDSRLLTVEFSGRRPKSPNVQVPLEPAELQLAQSLAAAHRGYVRUSTCHEIVVTAGEALKERKDVTEMPAAGAKRKRGHPA
...:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9DBC0|SELO_MOUSE : U
MSSUTVCLEAAWLPPRNSYSSQEETSRAVAEPGTAEEESHYPSELLKLVRRVESFDGNEAAEIAKQAIYNRLVYKPNNARMVRVREAQWAATDGVGEKEKDLRDRYEQLWAEWHDRNKRQLDSPSLQELRSQHEVRELEKTVNAQTGILAFLQPNSQALMLMMSLQRPDMQPRFALRLEELSACQSTLRSLFEASDSLDAPFSSLVCFTNTFDAGTLHMTELLKAVLTGDEEKEVRILGLKKRMKQLYHRQFETDFEEKLIAEALALPLEPELAEALKQLNWKCVQPQKSYTYRGANDSANCIHDPDYRDLFGFPGYDITLGVISMNDTNLVGCHFGVCQWEAVMRATRQTVERFFAANRQINDTDCTHAAQIEPYFSSIVYDLLQVRIDDRGVSPGARGTHEDPPKFIEFSGFRIFTPAIRLVVTCKEYKPNGDYFVDRMVTSESTVCAGARTTPIGLHFMAESCLFERISSRLVKRGDAQRSFPTPGAGKLQLEWREGAATCVEGLYMAAGDGLQGAFQGFQHGCYCHAAPETGPLLANGSFFLAAEAEVEAEESAELGLLALAPESLAVLRPRRLPAPRARSFCAGPVPRPTALSDEPGPPPTEVPLERLARNDFRLGALWRPTPEMAAAWASRPASSPLALGVCRPRTRAVALSAGVAARVSA
...:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9JLT4-2|TRXR2_MOUSE : U
MGUCGTVTPELGSRKSIHLKVVEESCTPHIGVTQMVQAYSAGCKIGLAFGQTVEGANPGLFHLGLVLQPPERMCVMKIYCQSADRDAVTFELPKYYAHYVEVHEQGHLAVAEEESLGVCGYELPTFVTTPVNSYDMLTSSKGFLRQALLKGAKIATPTLEPRGEAVDGIAYIHPVSTAEQADVIIKQNKPNTSIGAKELNLTRTEPVRGIAWLVTDFTGTDEKGSAHDEWTVQLQNTPLKKIHSPCVGKLFQTGHSEMHETVLSSMQQDFGRLPISRMMVTTDLGIGTLFGACELAVYSAGVVLTKGPSEKLWFIDDSTIGYELAGKVQTPYRPRGGTAIVIHEASLLTAKGGKDVGRVTHEDVFSAKINFYKVKRDQLQVRHGWNLSKVHNQVAEAMTKWNHQVPQAVEWGYHHADRIMGGLLAAQHMLKKPICGVNVCTGGLGWKTGRPSPEVYDAVAVKKGLQAAEKACALGGSGGGIVLLDFSQQGE
WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9JLT4-4|TRXR2_MOUSE : U
MGUCGTVTPELGSRKSIHLKVVEESCTPHIGVTQMVQAYSAGCKIGLAFGQTVEGANPGLFHLGLVLQPPERMCVMKIYCQSADRDAVTFELPKYYAHYVNSYDMLTSSKGFLRQALLKGAKIATPTLEPRGEAVDGIAYIHPVSTAEQADVIIKQNKPNTSIGAKELNLTRTEPVRGIAWLVTDFTGTDEKGSAHDEWTVQLQNTPLKKIHSPVCGKLFQTGHSEMHETVLSSMQQDFGRLPISRMMVTTDLGIGTLFGACELAVYSAGVVLTKGPSEKLWFIDDSTIGYELAGKVQTPYRPRGGTAIVIHEASLLTAKGGKDVGRVTHEDVFSAKINFYKVKRDQLQVRHGWNLSKVHNQVAEAMTKWNHQVPQAVEWGYHHADRIMGGLLAAQHMLKKPICGVNVCTGGLGWKTGRPSPEVYDAVAVKKGLQAAEKACALGGSGGGIVLLDFSQQGGAASAAGRTGRTLARTRPRFRRSPGRLAAVMAAV
WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9JLT4|TRXR2_MOUSE : U
MGUCGTVTPELGSRKSIHLKVVEESCTPHIGVTQMVQAYSAGCKIGLAFGQTVEGANPGLFHLGLVLQPPERMCVMKIYCQSADRDAVTFELPKYYAHYVEVHEQGHLAVAEEESLGVCGYELPTFVTTPVNSYDMLTSSKGFLRQALLKGAKIATPTLEPRGEAVDGIAYIHPVSTAEQADVIIKQNKPNTSIGAKELNLTRTEPVRGIAWLVTDFTGTDEKGSAHDEWTVQLQNTPLKKIHSPVCGKLFQTGHSEMHETVLSSMQQDFGRLPISRMMVTTDLGIGTLFGACELAVYSAGVVLTKGPSEKLWFIDDSTIGYELAGKVQTPYRPRGGTAIVIHEASLLTAKGGKDVGRVTHEDVFSAKINFYKVKRDQLQVRHGWNLSKVHNQVAEAMTKWNHQVPQAVEWGYHHADRIMGGLLAAQHMLKKPICGVNVCTGGLGWKTGRPSPEVYDAVAVKKGLQAAEKACALGGSGGGIVLLDFSQQGGAASAAGRTGRTLARTRPRFRRSPGRLAAVMAAV
.....24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........43000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........44000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........45000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........46000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........47000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........48000
.........:.........:.........WARNING: Found the following zero-mass residues in protein entry rev_tr|B9EJ24|B9EJ24_MOUSE : U
MSSUTVCLEAAWLPPRNSYSSQEETSRAVAEPGTAEEESHYPSELLKLVRRVESFDGNEAAEIAKQAIYNRLVYKPNNARMVRVREAQWAATDGVGEKEKDLRDRYEQLWAEWHDRNKRQLDSPSLQELRSQHEVRELEKTVNAQTGILAFLQPNSQALMLMMSLQRPDMQPRFALRLEELSACQSTLRSLFEASDSLDAPFSSLVCFTNTFDAGTLHMTELLKAVLTGDEEKEVRILGLKKRMKQLYHRQFETDFEEKLIAEAAALPLEPELAEALKQLNWKCVQPQKSYTYRGANDSANCIHDPDYRDLFGFPGYDITLGVISMNDTNLVGCHFGVCQWEAVMRATRQTVERFFAANRQINDTDCTHAAQIEPYFSSIVYDLLQVRIDDRGVSPGARGTHEDPPKFIEFSGFRIFTPAIRLVVTCKEYKPNGDYFVDRMVTSESTVCAGARTTPIGLHFMAESCLFERISSRLVKRGDAQRSFPTPGAGKLQLEWREGAATCVEGLYMAAGDGLQGAFQGFQHGCYCHAAPETGPLLANGSFFLAAEAEVEAEESAELGLLALAPESLAVLRPRRLPAPRARSFCAGPVPRPTALSDEPGPPPTEVPLERLARNDFRLGALWRPTPEMAAAWASRPASSPLALGVCRPRTRAVALSAGVAARVSA
:.........:.........:.........:.........:.........:.........:.........49000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........50000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........51000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........52000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........53000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........54000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........55000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........56000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........57000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........58000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........59000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........60000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........61000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........62000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........63000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........64000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........65000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........66000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........67000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........68000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........78000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........82000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........85000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........86000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........87000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........88000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........89000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........90000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........91000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........92000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........93000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........94000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........95000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........96000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........97000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........98000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........99000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........100000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........101000
.........:.........:.........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry sp|P46412|GPX3_MOUSE : U
MARILRASCLLSLLLAGFVPPGRGQEKSKTDCHGGMSGTIYEYGALTIDGEEYIPFKQYAGKYILFVNVASYUGLTDQYLELNALQEELGPFGLVILGFPSNQFGKQEPGENSEILPSLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTAELLGSPGRLFWEPMKIHDIRWNFEKFLVGPDGIPVMRWYHRTTVSNVKMDILSYMRRQAALSARGK
........:.........102000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........103000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........104000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........105000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........106000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........107000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........108000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........109000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........110000
.WARNING: Found the following zero-mass residues in protein entry sp|Q80TA1|EPT1_MOUSE : U
MAGYEYVSPEQLSGFDKYKYSALDTNPLSLYIMHPFWNTIVKVFPTWLAPNLITFSGFMLLVFNFLLLTYFDPDFYASAPGHKHVPDWVWIVVGILNFAAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGPTGVSVFVLYLLLWVVLFSFILSHWEKYNTGVLFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKSNTLKHKSVYEAMVPFFSPCLLFTLCTVWILWSPSDILEIHPRIFYFMVGTAFANITCQLIVCQMSSTRCPTLNWLLLPLLLVVAAVIVGAATSRLESALLYTLTAAFTLAHIHYGVQVVKQLSRHFQIYPFSLRKPNSDULGMEEQNIGL
........:.........:.........:.........:.........:.........:.........:.........:.........:.........111000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........112000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........113000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........114000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........115000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........116000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........117000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........118000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........119000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........120000
.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|Q9ERR7|SEP15_MOUSE : U
MAAGQGGWLRPALGLRLLLATAFQAVSALGAEFASEACRELGFSSNLLCSSCDLLGQFNLLPLDPVCRGCCQEEAQFETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEELSILKWNTDSVEEFLSEKLERI
.........:.........:.........:.........:.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|Q9JLT4-4|TRXR2_MOUSE : U
MVAAMVAALRGPSRRFRPRTRALTRGTRGAASAAGGQQSFDLLVIGGGSGGLACAKEAAQLGKKVAVADYVEPSPRGTKWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAHHYGWEVAQPVQHNWKTMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVRGVDKGGKATLLSAEHIVIATGGRPRYPTQVKGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTVMMRSIPLRGFDQQMSSLVTEHMESHGTQFLKGCVPSHIKKLPTNQLQVTWEDHASGKEDTGTFDTVLWAIGRVPETRTLNLEKAGISTNPKNQKIIVDAQEATSVPHIYAIGDVAEGRPELTPTAIKAGKLLAQRLFGKSSTLMDYSNVYHAYYKPLEFTVADRDASQCYIKMVCMREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMQTVGIHPTCSEEVVKLHISKRSGLEPTVTGCUG
WARNING: Found the following zero-mass residues in protein entry sp|Q9JLT4|TRXR2_MOUSE : U
MVAAMVAALRGPSRRFRPRTRALTRGTRGAASAAGGQQSFDLLVIGGGSGGLACAKEAAQLGKKVAVADYVEPSPRGTKWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAHHYGWEVAQPVQHNWKTMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVRGVDKGGKATLLSAEHIVIATGGRPRYPTQVKGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTVMMRSIPLRGFDQQMSSLVTEHMESHGTQFLKGCVPSHIKKLPTNQLQVTWEDHASGKEDTGTFDTVLWAIGRVPETRTLNLEKAGISTNPKNQKIIVDAQEATSVPHIYAIGDVAEGRPELTPTAIKAGKLLAQRLFGKSSTLMDYSNVPTTVFTPLEYGCVGLSEEEAVALHGQEHVEVYHAYYKPLEFTVADRDASQCYIKMVCMREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMQTVGIHPTCSEEVVKLHISKRSGLEPTVTGCUG
......121000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........122000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........123000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........124000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........125000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........126000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........127000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........128000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........129000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........130000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........131000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........132000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........133000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........134000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........135000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........136000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........137000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........138000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........139000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........140000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........141000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........142000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........143000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........144000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........145000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........146000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........147000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........148000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........149000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........150000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........151000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........152000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........153000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........154000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........155000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........156000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........157000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........158000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........159000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........160000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........161000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........162000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........163000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........164000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........165000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........166000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........167000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........168000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........169000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........170000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........171000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........172000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........173000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........174000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........175000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........176000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........177000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........178000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........179000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........180000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........181000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........182000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........183000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........184000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........185000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........186000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........187000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........188000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........189000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........190000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........191000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........192000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........193000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.......  Total: 193978
Computing degenerate peptides for 21853 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 26734 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 26734 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 26734 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 26734 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 26734 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=1.33891e-05, db_size=162072768
Computing MU for 26734 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO[22:19:01] Done                                         
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
INFO[22:19:01] Executing Database  v4.8.1                   
INFO[22:19:01] Annotating the database                      
INFO[22:19:23] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
INFO[22:19:23] Executing Database  v4.8.1                   
INFO[22:19:23] Annotating the database                      
INFO[22:19:46] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
INFO[22:19:46] Executing Database  v4.8.1                   
INFO[22:19:46] Annotating the database                      
INFO[22:20:08] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
INFO[22:20:09] Executing Database  v4.8.1                   
INFO[22:20:09] Annotating the database                      
INFO[22:20:31] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
INFO[22:20:31] Executing Database  v4.8.1                   
INFO[22:20:31] Annotating the database                      
INFO[22:20:53] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
INFO[22:20:53] Executing Database  v4.8.1                   
INFO[22:20:53] Annotating the database                      
INFO[22:21:15] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
INFO[22:21:15] Executing Database  v4.8.1                   
INFO[22:21:15] Annotating the database                      
INFO[22:21:38] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA --protxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\combined.prot.xml --razor
INFO[22:21:38] Executing Filter  v4.8.1                     
INFO[22:21:38] Processing peptide identification files      
INFO[22:21:38] Parsing D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\interact-230329HN02AdipositeKRNpepNtermC1_05TFA.pep.xml 
INFO[22:21:40] 1+ Charge profile                             decoy=0 target=0
INFO[22:21:40] 2+ Charge profile                             decoy=301 target=4747
INFO[22:21:40] 3+ Charge profile                             decoy=122 target=2737
INFO[22:21:40] 4+ Charge profile                             decoy=10 target=338
INFO[22:21:40] 5+ Charge profile                             decoy=4 target=17
INFO[22:21:40] 6+ Charge profile                             decoy=2 target=1
INFO[22:21:40] Database search results                       ions=5605 peptides=4879 psms=8284
INFO[22:21:40] Converged to 0.99 % FDR with 6881 PSMs        decoy=68 threshold=0.844517 total=6949
INFO[22:21:40] Converged to 1.00 % FDR with 3510 Peptides    decoy=35 threshold=0.907497 total=3545
INFO[22:21:40] Converged to 0.99 % FDR with 4241 Ions        decoy=42 threshold=0.887803 total=4283
INFO[22:21:43] Protein inference results                     decoy=1989 target=5692
INFO[22:21:43] Converged to 0.96 % FDR with 1982 Proteins    decoy=19 threshold=0.9705 total=2001
INFO[22:21:44] Applying sequential FDR estimation            ions=4249 peptides=3578 psms=6699
INFO[22:21:44] Converged to 0.22 % FDR with 6684 PSMs        decoy=15 threshold=0.844517 total=6699
INFO[22:21:44] Converged to 0.34 % FDR with 3566 Peptides    decoy=12 threshold=0.845274 total=3578
INFO[22:21:44] Converged to 0.28 % FDR with 4237 Ions        decoy=12 threshold=0.845274 total=4249
INFO[22:21:44] Post processing identifications              
INFO[22:21:47] Assigning protein identifications to layers  
INFO[22:21:49] Processing protein inference                 
INFO[22:22:23] Synchronizing PSMs and proteins              
INFO[22:22:24] Final report numbers after FDR filtering, and post-processing  ions=4237 peptides=3566 proteins=1689 psms=6684
INFO[22:22:24] Saving                                       
INFO[22:22:24] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA --protxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\combined.prot.xml --razorbin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin
INFO[22:22:24] Executing Filter  v4.8.1                     
INFO[22:22:24] Fetching razor assignment from: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin: 10435 razor groups imported. 
INFO[22:22:24] Processing peptide identification files      
INFO[22:22:24] Parsing D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\interact-230329HN03AdipositeKRNpepNtermC2_05TFA.pep.xml 
INFO[22:22:27] 1+ Charge profile                             decoy=0 target=0
INFO[22:22:27] 2+ Charge profile                             decoy=317 target=4443
INFO[22:22:27] 3+ Charge profile                             decoy=98 target=2388
INFO[22:22:27] 4+ Charge profile                             decoy=11 target=278
INFO[22:22:27] 5+ Charge profile                             decoy=3 target=11
INFO[22:22:27] 6+ Charge profile                             decoy=1 target=3
INFO[22:22:27] Database search results                       ions=5060 peptides=4391 psms=7554
INFO[22:22:27] Converged to 0.99 % FDR with 6268 PSMs        decoy=62 threshold=0.84799 total=6330
INFO[22:22:27] Converged to 0.98 % FDR with 3276 Peptides    decoy=32 threshold=0.884773 total=3308
INFO[22:22:27] Converged to 0.99 % FDR with 3924 Ions        decoy=39 threshold=0.873223 total=3963
INFO[22:22:29] Protein inference results                     decoy=1989 target=5692
INFO[22:22:30] Converged to 0.96 % FDR with 1982 Proteins    decoy=19 threshold=0.9705 total=2001
INFO[22:22:30] Applying sequential FDR estimation            ions=3870 peptides=3257 psms=6097
INFO[22:22:30] Converged to 0.10 % FDR with 6091 PSMs        decoy=6 threshold=0.84799 total=6097
INFO[22:22:30] Converged to 0.12 % FDR with 3253 Peptides    decoy=4 threshold=0.84799 total=3257
INFO[22:22:30] Converged to 0.10 % FDR with 3866 Ions        decoy=4 threshold=0.84799 total=3870
INFO[22:22:30] Post processing identifications              
INFO[22:22:33] Assigning protein identifications to layers  
INFO[22:22:35] Processing protein inference                 
INFO[22:23:09] Synchronizing PSMs and proteins              
INFO[22:23:09] Final report numbers after FDR filtering, and post-processing  ions=3866 peptides=3253 proteins=1590 psms=6091
INFO[22:23:09] Saving                                       
INFO[22:23:09] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA --protxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\combined.prot.xml --razorbin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin
INFO[22:23:09] Executing Filter  v4.8.1                     
INFO[22:23:10] Fetching razor assignment from: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin: 10435 razor groups imported. 
INFO[22:23:10] Processing peptide identification files      
INFO[22:23:10] Parsing D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\interact-230329HN04AdipositeKRNpepNtermC3_05TFA.pep.xml 
INFO[22:23:12] 1+ Charge profile                             decoy=0 target=0
INFO[22:23:12] 2+ Charge profile                             decoy=286 target=4905
INFO[22:23:12] 3+ Charge profile                             decoy=142 target=2901
INFO[22:23:12] 4+ Charge profile                             decoy=9 target=352
INFO[22:23:12] 5+ Charge profile                             decoy=4 target=22
INFO[22:23:12] 6+ Charge profile                             decoy=2 target=5
INFO[22:23:12] Database search results                       ions=5750 peptides=4958 psms=8629
INFO[22:23:12] Converged to 1.00 % FDR with 7201 PSMs        decoy=72 threshold=0.837086 total=7273
INFO[22:23:12] Converged to 0.99 % FDR with 3727 Peptides    decoy=37 threshold=0.872248 total=3764
INFO[22:23:12] Converged to 0.98 % FDR with 4485 Ions        decoy=44 threshold=0.865393 total=4529
INFO[22:23:15] Protein inference results                     decoy=1989 target=5692
INFO[22:23:15] Converged to 0.96 % FDR with 1982 Proteins    decoy=19 threshold=0.9705 total=2001
INFO[22:23:16] Applying sequential FDR estimation            ions=4391 peptides=3651 psms=6997
INFO[22:23:16] Converged to 0.10 % FDR with 6990 PSMs        decoy=7 threshold=0.837307 total=6997
INFO[22:23:16] Converged to 0.11 % FDR with 3647 Peptides    decoy=4 threshold=0.837307 total=3651
INFO[22:23:16] Converged to 0.09 % FDR with 4387 Ions        decoy=4 threshold=0.837307 total=4391
INFO[22:23:16] Post processing identifications              
INFO[22:23:19] Assigning protein identifications to layers  
INFO[22:23:20] Processing protein inference                 
INFO[22:23:54] Synchronizing PSMs and proteins              
INFO[22:23:55] Final report numbers after FDR filtering, and post-processing  ions=4387 peptides=3647 proteins=1699 psms=6990
INFO[22:23:55] Saving                                       
INFO[22:23:55] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA --protxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\combined.prot.xml --razorbin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin
INFO[22:23:55] Executing Filter  v4.8.1                     
INFO[22:23:55] Fetching razor assignment from: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin: 10435 razor groups imported. 
INFO[22:23:55] Processing peptide identification files      
INFO[22:23:55] Parsing D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\interact-230329HN06AdipositeKRNpepNtermP1_05TFA.pep.xml 
INFO[22:23:57] 1+ Charge profile                             decoy=0 target=0
INFO[22:23:57] 2+ Charge profile                             decoy=248 target=3984
INFO[22:23:57] 3+ Charge profile                             decoy=92 target=2203
INFO[22:23:57] 4+ Charge profile                             decoy=12 target=286
INFO[22:23:57] 5+ Charge profile                             decoy=1 target=7
INFO[22:23:57] 6+ Charge profile                             decoy=1 target=2
INFO[22:23:58] Database search results                       ions=4569 peptides=4003 psms=6838
INFO[22:23:58] Converged to 0.99 % FDR with 5765 PSMs        decoy=57 threshold=0.819155 total=5822
INFO[22:23:58] Converged to 0.98 % FDR with 3052 Peptides    decoy=30 threshold=0.863115 total=3082
INFO[22:23:58] Converged to 1.00 % FDR with 3607 Ions        decoy=36 threshold=0.850594 total=3643
INFO[22:24:00] Protein inference results                     decoy=1989 target=5692
INFO[22:24:01] Converged to 0.96 % FDR with 1982 Proteins    decoy=19 threshold=0.9705 total=2001
INFO[22:24:01] Applying sequential FDR estimation            ions=3520 peptides=2997 psms=5587
INFO[22:24:01] Converged to 0.09 % FDR with 5582 PSMs        decoy=5 threshold=0.819433 total=5587
INFO[22:24:01] Converged to 0.13 % FDR with 2993 Peptides    decoy=4 threshold=0.819433 total=2997
INFO[22:24:01] Converged to 0.11 % FDR with 3516 Ions        decoy=4 threshold=0.819433 total=3520
INFO[22:24:01] Post processing identifications              
INFO[22:24:04] Assigning protein identifications to layers  
INFO[22:24:05] Processing protein inference                 
INFO[22:24:41] Synchronizing PSMs and proteins              
INFO[22:24:41] Final report numbers after FDR filtering, and post-processing  ions=3516 peptides=2993 proteins=1494 psms=5582
INFO[22:24:41] Saving                                       
INFO[22:24:41] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA --protxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\combined.prot.xml --razorbin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin
INFO[22:24:41] Executing Filter  v4.8.1                     
INFO[22:24:42] Fetching razor assignment from: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin: 10435 razor groups imported. 
INFO[22:24:42] Processing peptide identification files      
INFO[22:24:42] Parsing D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\interact-230329HN07AdipositeKRNpepNtermP2_05TFA.pep.xml 
INFO[22:24:44] 1+ Charge profile                             decoy=0 target=0
INFO[22:24:44] 2+ Charge profile                             decoy=268 target=3937
INFO[22:24:44] 3+ Charge profile                             decoy=100 target=2121
INFO[22:24:44] 4+ Charge profile                             decoy=12 target=232
INFO[22:24:44] 5+ Charge profile                             decoy=2 target=9
INFO[22:24:44] 6+ Charge profile                             decoy=1 target=3
INFO[22:24:44] Database search results                       ions=4499 peptides=3959 psms=6688
INFO[22:24:44] Converged to 1.00 % FDR with 5515 PSMs        decoy=55 threshold=0.84246 total=5570
INFO[22:24:44] Converged to 0.99 % FDR with 2821 Peptides    decoy=28 threshold=0.903569 total=2849
INFO[22:24:44] Converged to 1.00 % FDR with 3417 Ions        decoy=34 threshold=0.875984 total=3451
INFO[22:24:47] Protein inference results                     decoy=1989 target=5692
INFO[22:24:47] Converged to 0.96 % FDR with 1982 Proteins    decoy=19 threshold=0.9705 total=2001
INFO[22:24:47] Applying sequential FDR estimation            ions=3394 peptides=2887 psms=5383
INFO[22:24:47] Converged to 0.13 % FDR with 5376 PSMs        decoy=7 threshold=0.84252 total=5383
INFO[22:24:47] Converged to 0.14 % FDR with 2883 Peptides    decoy=4 threshold=0.84252 total=2887
INFO[22:24:47] Converged to 0.15 % FDR with 3389 Ions        decoy=5 threshold=0.84252 total=3394
INFO[22:24:47] Post processing identifications              
INFO[22:24:50] Assigning protein identifications to layers  
INFO[22:24:52] Processing protein inference                 
INFO[22:25:26] Synchronizing PSMs and proteins              
INFO[22:25:26] Final report numbers after FDR filtering, and post-processing  ions=3389 peptides=2883 proteins=1471 psms=5376
INFO[22:25:26] Saving                                       
INFO[22:25:26] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA --protxml D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\combined.prot.xml --razorbin D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin
INFO[22:25:26] Executing Filter  v4.8.1                     
INFO[22:25:26] Fetching razor assignment from: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\.meta\razor.bin: 10435 razor groups imported. 
INFO[22:25:26] Processing peptide identification files      
INFO[22:25:26] Parsing D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\interact-230329HN08AdipositeKRNpepNtermP3_05TFA.pep.xml 
INFO[22:25:29] 1+ Charge profile                             decoy=0 target=0
INFO[22:25:29] 2+ Charge profile                             decoy=281 target=4285
INFO[22:25:29] 3+ Charge profile                             decoy=105 target=2417
INFO[22:25:29] 4+ Charge profile                             decoy=14 target=316
INFO[22:25:29] 5+ Charge profile                             decoy=2 target=13
INFO[22:25:29] 6+ Charge profile                             decoy=1 target=2
INFO[22:25:29] Database search results                       ions=4990 peptides=4319 psms=7440
INFO[22:25:29] Converged to 0.99 % FDR with 6170 PSMs        decoy=61 threshold=0.835853 total=6231
INFO[22:25:29] Converged to 1.00 % FDR with 3113 Peptides    decoy=31 threshold=0.8967 total=3144
INFO[22:25:29] Converged to 0.98 % FDR with 3790 Ions        decoy=37 threshold=0.879113 total=3827
INFO[22:25:31] Protein inference results                     decoy=1989 target=5692
INFO[22:25:32] Converged to 0.96 % FDR with 1982 Proteins    decoy=19 threshold=0.9705 total=2001
INFO[22:25:32] Applying sequential FDR estimation            ions=3771 peptides=3151 psms=6004
INFO[22:25:32] Converged to 0.08 % FDR with 5999 PSMs        decoy=5 threshold=0.835853 total=6004
INFO[22:25:32] Converged to 0.16 % FDR with 3146 Peptides    decoy=5 threshold=0.835853 total=3151
INFO[22:25:32] Converged to 0.13 % FDR with 3766 Ions        decoy=5 threshold=0.835853 total=3771
INFO[22:25:32] Post processing identifications              
INFO[22:25:35] Assigning protein identifications to layers  
INFO[22:25:36] Processing protein inference                 
INFO[22:26:10] Synchronizing PSMs and proteins              
INFO[22:26:10] Final report numbers after FDR filtering, and post-processing  ions=3766 peptides=3146 proteins=1557 psms=5999
INFO[22:26:10] Saving                                       
INFO[22:26:10] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
INFO[22:26:10] Executing Report  v4.8.1                     
INFO[22:26:10] Creating reports                             
INFO[22:26:12] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
INFO[22:26:12] Executing Report  v4.8.1                     
INFO[22:26:12] Creating reports                             
INFO[22:26:13] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
INFO[22:26:13] Executing Report  v4.8.1                     
INFO[22:26:13] Creating reports                             
INFO[22:26:14] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
INFO[22:26:14] Executing Report  v4.8.1                     
INFO[22:26:14] Creating reports                             
INFO[22:26:15] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
INFO[22:26:16] Executing Report  v4.8.1                     
INFO[22:26:16] Creating reports                             
INFO[22:26:17] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
INFO[22:26:17] Executing Report  v4.8.1                     
INFO[22:26:17] Creating reports                             
INFO[22:26:18] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[22:26:18] Executing Workspace  v4.8.1                  
INFO[22:26:18] Removing workspace                           
INFO[22:26:18] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[22:26:19] Executing Workspace  v4.8.1                  
INFO[22:26:19] Removing workspace                           
INFO[22:26:19] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[22:26:19] Executing Workspace  v4.8.1                  
INFO[22:26:19] Removing workspace                           
INFO[22:26:19] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[22:26:19] Executing Workspace  v4.8.1                  
INFO[22:26:19] Removing workspace                           
INFO[22:26:19] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[22:26:20] Executing Workspace  v4.8.1                  
INFO[22:26:20] Removing workspace                           
INFO[22:26:20] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[22:26:20] Executing Workspace  v4.8.1                  
INFO[22:26:20] Removing workspace                           
INFO[22:26:20] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[22:26:21] Executing Workspace  v4.8.1                  
INFO[22:26:21] Removing workspace                           
INFO[22:26:21] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
IonQuant [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -Xmx219G -Dlibs.bruker.dir="D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\MSFragger-3.7\ext\bruker" -Dlibs.thermo.dir="D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\MSFragger-3.7\ext\thermo" -cp "D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\jfreechart-1.5.3.jar;D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\batmass-io-1.28.9.jar;D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\IonQuant-1.8.10.jar" ionquant.IonQuant --threads 33 --ionmobility 0 --minexps 1 --mbr 0 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\filelist_ionquant.txt --modlist D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\modmasses_ionquant.txt
IonQuant version IonQuant-1.8.10
Batmass-IO version 1.28.9
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
JVM started with 219 GB memory
2023-08-21 22:26:22 [INFO] - Collecting variable modifications from all psm.tsv files...
2023-08-21 22:26:22 [INFO] - Collecting run names from all psm.tsv files...
2023-08-21 22:26:23 [INFO] - Parameters:
2023-08-21 22:26:23 [INFO] - threads = 33
2023-08-21 22:26:23 [INFO] - mztol = 10.0
2023-08-21 22:26:23 [INFO] - rttol = 0.4
2023-08-21 22:26:23 [INFO] - imtol = 0.05
2023-08-21 22:26:23 [INFO] - minisotopes = 2
2023-08-21 22:26:23 [INFO] - minscans = 3
2023-08-21 22:26:23 [INFO] - psm = D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\psm.tsv
2023-08-21 22:26:23 [INFO] - psm = D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\psm.tsv
2023-08-21 22:26:23 [INFO] - psm = D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\psm.tsv
2023-08-21 22:26:23 [INFO] - psm = D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\psm.tsv
2023-08-21 22:26:23 [INFO] - psm = D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\psm.tsv
2023-08-21 22:26:23 [INFO] - psm = D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\psm.tsv
2023-08-21 22:26:23 [INFO] - multidir = D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\.\
2023-08-21 22:26:23 [INFO] - excludemods = 
2023-08-21 22:26:23 [INFO] - minions = 2
2023-08-21 22:26:23 [INFO] - maxlfq = 1
2023-08-21 22:26:23 [INFO] - ibaq = 0
2023-08-21 22:26:23 [INFO] - normalization = 1
2023-08-21 22:26:23 [INFO] - minexps = 1
2023-08-21 22:26:23 [INFO] - minfreq = 0.0
2023-08-21 22:26:23 [INFO] - tp = 0
2023-08-21 22:26:23 [INFO] - mbr = 0
2023-08-21 22:26:23 [INFO] - mbrrttol = 1.0
2023-08-21 22:26:23 [INFO] - mbrimtol = 0.05
2023-08-21 22:26:23 [INFO] - mbrtoprun = 10
2023-08-21 22:26:23 [INFO] - mbrmincorr = 0.0
2023-08-21 22:26:23 [INFO] - ionmobility = 0
2023-08-21 22:26:23 [INFO] - ionfdr = 0.01
2023-08-21 22:26:23 [INFO] - peptidefdr = 1.0
2023-08-21 22:26:23 [INFO] - proteinfdr = 1.0
2023-08-21 22:26:23 [INFO] - light = 
2023-08-21 22:26:23 [INFO] - medium = 
2023-08-21 22:26:23 [INFO] - heavy = 
2023-08-21 22:26:23 [INFO] - requantify = 0
2023-08-21 22:26:23 [INFO] - writeindex = 0
2023-08-21 22:26:23 [INFO] - locprob = 0.75
2023-08-21 22:26:23 [INFO] - uniqueness = 0
2023-08-21 22:26:23 [INFO] - filelist = D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\filelist_ionquant.txt
2023-08-21 22:26:23 [INFO] - specdir = D:\Personal\Nishida\Adiposite\230817_Re\Label1
2023-08-21 22:26:23 [INFO] - modlist = D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\modmasses_ionquant.txt
2023-08-21 22:26:23 [INFO] - mod masses:
2023-08-21 22:26:23 [INFO] - 15.9949
2023-08-21 22:26:23 [INFO] - 42.0106
2023-08-21 22:26:23 [INFO] - 57.02146
2023-08-21 22:26:23 [INFO] - Checking D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN07AdipositeKRNpepNtermP2_05TFA.raw...
2023-08-21 22:26:33 [INFO] - Checking D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN03AdipositeKRNpepNtermC2_05TFA.raw...
2023-08-21 22:26:43 [INFO] - Checking D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN06AdipositeKRNpepNtermP1_05TFA.raw...
2023-08-21 22:26:52 [INFO] - Checking D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN02AdipositeKRNpepNtermC1_05TFA.raw...
2023-08-21 22:27:02 [INFO] - Checking D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN04AdipositeKRNpepNtermC3_05TFA.raw...
2023-08-21 22:27:11 [INFO] - Checking D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN08AdipositeKRNpepNtermP3_05TFA.raw...
2023-08-21 22:27:21 [INFO] - Loading D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN07AdipositeKRNpepNtermP2_05TFA.raw...
2023-08-21 22:27:39 [INFO] - 230329HN07AdipositeKRNpepNtermP2_05TFA has 3 compensation voltages: -80.0, -60.0, -40.0
2023-08-21 22:27:39 [INFO] - Building index...
2023-08-21 22:27:40 [INFO] - Loading D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN07AdipositeKRNpepNtermP2_05TFA\psm.tsv....
2023-08-21 22:27:40 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2023-08-21 22:27:40 [INFO] - Quantifying...
2023-08-21 22:27:40 [INFO] - Loading D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN03AdipositeKRNpepNtermC2_05TFA.raw...
2023-08-21 22:27:57 [INFO] - 230329HN03AdipositeKRNpepNtermC2_05TFA has 3 compensation voltages: -80.0, -60.0, -40.0
2023-08-21 22:27:57 [INFO] - Building index...
2023-08-21 22:27:58 [INFO] - Loading D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN03AdipositeKRNpepNtermC2_05TFA\psm.tsv....
2023-08-21 22:27:58 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2023-08-21 22:27:58 [INFO] - Quantifying...
2023-08-21 22:27:58 [INFO] - Loading D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN06AdipositeKRNpepNtermP1_05TFA.raw...
2023-08-21 22:28:13 [INFO] - 230329HN06AdipositeKRNpepNtermP1_05TFA has 3 compensation voltages: -80.0, -60.0, -40.0
2023-08-21 22:28:13 [INFO] - Building index...
2023-08-21 22:28:14 [INFO] - Loading D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN06AdipositeKRNpepNtermP1_05TFA\psm.tsv....
2023-08-21 22:28:14 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2023-08-21 22:28:14 [INFO] - Quantifying...
2023-08-21 22:28:14 [INFO] - Loading D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN02AdipositeKRNpepNtermC1_05TFA.raw...
2023-08-21 22:28:31 [INFO] - 230329HN02AdipositeKRNpepNtermC1_05TFA has 3 compensation voltages: -80.0, -60.0, -40.0
2023-08-21 22:28:31 [INFO] - Building index...
2023-08-21 22:28:32 [INFO] - Loading D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN02AdipositeKRNpepNtermC1_05TFA\psm.tsv....
2023-08-21 22:28:32 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2023-08-21 22:28:32 [INFO] - Quantifying...
2023-08-21 22:28:32 [INFO] - Loading D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN04AdipositeKRNpepNtermC3_05TFA.raw...
2023-08-21 22:28:50 [INFO] - 230329HN04AdipositeKRNpepNtermC3_05TFA has 3 compensation voltages: -80.0, -60.0, -40.0
2023-08-21 22:28:50 [INFO] - Building index...
2023-08-21 22:28:50 [INFO] - Loading D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN04AdipositeKRNpepNtermC3_05TFA\psm.tsv....
2023-08-21 22:28:50 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2023-08-21 22:28:50 [INFO] - Quantifying...
2023-08-21 22:28:50 [INFO] - Loading D:\Personal\Nishida\Adiposite\230817_Re\Label1\230329HN08AdipositeKRNpepNtermP3_05TFA.raw...
2023-08-21 22:29:08 [INFO] - 230329HN08AdipositeKRNpepNtermP3_05TFA has 3 compensation voltages: -80.0, -60.0, -40.0
2023-08-21 22:29:08 [INFO] - Building index...
2023-08-21 22:29:08 [INFO] - Loading D:\Personal\Nishida\Adiposite\230817_Re\Label1\Result\230329HN08AdipositeKRNpepNtermP3_05TFA\psm.tsv....
2023-08-21 22:29:08 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2023-08-21 22:29:08 [INFO] - Quantifying...
2023-08-21 22:29:08 [INFO] - Updating Philosopher's tables...
2023-08-21 22:29:10 [INFO] - Combining experiments and estimating protein intensity...
2023-08-21 22:29:13 [INFO] - Done!
Process 'IonQuant' finished, exit code: 0

Please cite:
(Any searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017)
(Any searches) Fast deisotoping algorithm and its implementation in the MSFragger search engine. J. Proteome Res. 20:498 (2021)
(Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020)
(Glyco/labile search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125 (2020)
(timsTOF PASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19:1575 (2020)
(PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923 (2007)
(Protein inference with ProteinProphet)A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75:4646 (2003)
(FDR filtering and reporting) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020)
(Label-free/isotopic-labeling quantification) IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics 20:100077 (2021)
(Visualization with FP-PDV) PDV: an integrative proteomics data viewer. Bioinformatics. 35(7):1249 (2019)

=============================================================ALL JOBS DONE IN 37.7 MINUTES=============================================================
