System OS: Windows 11, Architecture: AMD64
Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium
.NET Core Info: N/A


Version info:
FragPipe version 22.0
MSFragger version 4.1
IonQuant version 1.10.27
diaTracer version 1.1.5
Philosopher version 5.1.1


LCMS files:
  Experiment/Group: Aerabic_1
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.d	DDA
  Experiment/Group: Aerabic_2
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.d	DDA
  Experiment/Group: Aerabic_3
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.d	DDA
  Experiment/Group: Anaerabic_1
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.d	DDA
  Experiment/Group: Anaerabic_2
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.d	DDA
  Experiment/Group: Anaerabic_3
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.d	DDA


81 commands to execute:
CheckCentroid
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -Xmx54G -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.d 20
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\981b17f7-e9c8-4eda-a57e-e3958608ab45
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\2bb32b39-f780-4fd7-85e5-7099ae49e7e0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\b33bdce1-b5f5-43ac-a50e-efcfea3e797d
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\964a4738-2a3d-417f-a160-8b3a5600e182
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\a08d488a-22fd-4429-8e27-68a8a1783980
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\fb2d0c7f-d77f-4eb9-ba60-bcf357b3442f
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\3b3f049f-5bbe-4b2c-9a85-51ac48ba7548
MSFragger [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx54G C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\fragger.params D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.d D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.d D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.d D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.d D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.d D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.d
MSFragger move pepxml
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pepXML D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pepXML
MSFragger move pin
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pin
MSFragger move pepxml
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pepXML D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pepXML
MSFragger move pin
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pin
MSFragger move pepxml
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pepXML D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pepXML
MSFragger move pin
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pin
MSFragger move pepxml
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pepXML D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pepXML
MSFragger move pin
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pin
MSFragger move pepxml
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pepXML D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pepXML
MSFragger move pin
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pin
MSFragger move pepxml
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pepXML D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pepXML
MSFragger move pin
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pin
Percolator [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pin
Percolator [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pin
Percolator [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pin
Percolator [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pin
Percolator [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pin
Percolator [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pin
Percolator: Convert to pepxml [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pin PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350 PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_target_psms.tsv PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_decoy_psms.tsv interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350 DDA 0.5 D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_calibrated.mzML
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_target_psms.tsv
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pin PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354 PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_target_psms.tsv PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_decoy_psms.tsv interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354 DDA 0.5 D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_calibrated.mzML
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_target_psms.tsv
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pin PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356 PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_target_psms.tsv PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_decoy_psms.tsv interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356 DDA 0.5 D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_calibrated.mzML
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_target_psms.tsv
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pin PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348 PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_target_psms.tsv PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_decoy_psms.tsv interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348 DDA 0.5 D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_calibrated.mzML
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_target_psms.tsv
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pin PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346 PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_target_psms.tsv PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_decoy_psms.tsv interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346 DDA 0.5 D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_calibrated.mzML
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_target_psms.tsv
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pin PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352 PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_target_psms.tsv PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_decoy_psms.tsv interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352 DDA 0.5 D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_calibrated.mzML
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_target_psms.tsv
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_decoy_psms.tsv
PTMProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,K:114.04293 MINPROB=0.5 MAXTHREADS=1 interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pep.xml interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.mod.pep.xml
PTMProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,K:114.04293 MINPROB=0.5 MAXTHREADS=1 interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pep.xml interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.mod.pep.xml
PTMProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,K:114.04293 MINPROB=0.5 MAXTHREADS=1 interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pep.xml interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.mod.pep.xml
PTMProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,K:114.04293 MINPROB=0.5 MAXTHREADS=1 interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pep.xml interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.mod.pep.xml
PTMProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,K:114.04293 MINPROB=0.5 MAXTHREADS=1 interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pep.xml interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.mod.pep.xml
PTMProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,K:114.04293 MINPROB=0.5 MAXTHREADS=1 interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pep.xml interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.mod.pep.xml
ProteinProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --output combined D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe database --annotate D:\fasta_SpecLib\DAINN19\2024-09-14-decoys-Eglacilis.isoseq.cdhit95-transdecoder-longest.fasta.fas --prefix rev_
PhilosopherFilter [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --protxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\combined.prot.xml --razor
PhilosopherFilter [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2 --dbbin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --protxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\combined.prot.xml --probin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --razor
PhilosopherFilter [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3 --dbbin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --protxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\combined.prot.xml --probin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --razor
PhilosopherFilter [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1 --dbbin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --protxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\combined.prot.xml --probin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --razor
PhilosopherFilter [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2 --dbbin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --protxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\combined.prot.xml --probin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --razor
PhilosopherFilter [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3 --dbbin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --protxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\combined.prot.xml --probin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --razor
PhilosopherReport [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
PhilosopherReport [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
PhilosopherReport [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
PhilosopherReport [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
PhilosopherReport [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
PhilosopherReport [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
IonQuant [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -Xmx54G -Dlibs.bruker.dir=C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\..\tools\MSFragger-4.1\ext\bruker -Dlibs.thermo.dir=C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\jfreechart-1.5.3.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\IonQuant-1.10.27.jar ionquant.IonQuant --threads 20 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 1 --site-reports 1 --msstats 1 --minexps 1 --mbr 1 --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 1 --locprob 0.75 --uniqueness 0 --multidir . --filelist D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\filelist_ionquant.txt --modlist D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\modmasses_ionquant.txt
Skyline [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -Xmx54G -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\commons-lang3-3.14.0.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\maven-artifact-3.9.6.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.skyline.Skyline C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\SkylineDailyRunner.exe D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result 24.0.9.184 0 0
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
    Cmd: [CheckCentroid], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
    Cmd: [MSFragger], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
    Cmd: [Percolator], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
    Cmd: [PTMProphet], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
    Cmd: [ProteinProphet], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
    Cmd: [PhilosopherFilter], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
    Cmd: [PhilosopherReport], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
    Cmd: [WorkspaceClean], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
    Cmd: [WorkspaceClean], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
    Cmd: [WorkspaceClean], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
    Cmd: [WorkspaceClean], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
    Cmd: [WorkspaceClean], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
    Cmd: [WorkspaceClean], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
    Cmd: [WorkspaceClean], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
    Cmd: [IonQuant], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
    Cmd: [Skyline], Work dir: [D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]

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

~~~~~~Sample of D:\fasta_SpecLib\DAINN19\2024-09-14-decoys-Eglacilis.isoseq.cdhit95-transdecoder-longest.fasta.fas~~~~~~~
>rev_transcript/0.p1 type:complete len:1877 gc:universal transcript/0:2015-7645(+)
>rev_transcript/11752.p7 type:complete len:116 gc:universal transcript/11752:3602-3255(-)
>rev_transcript/136324.p3 type:5prime_partial len:110 gc:universal transcript/136324:1-330(+)
>rev_transcript/1577.p4 type:complete len:294 gc:universal transcript/1577:5016-4135(-)
>rev_transcript/184822.p1 type:complete len:121 gc:universal transcript/184822:148-510(+)
>rev_transcript/29339.p3 type:5prime_partial len:144 gc:universal transcript/29339:1-432(+)
>rev_transcript/41746.p1 type:complete len:775 gc:universal transcript/41746:53-2377(+)
>rev_transcript/55405.p2 type:complete len:474 gc:universal transcript/55405:1687-266(-)
>rev_transcript/69349.p5 type:complete len:107 gc:universal transcript/69349:356-36(-)
>rev_transcript/84191.p2 type:5prime_partial len:164 gc:universal transcript/84191:1870-1379(-)
>rev_transcript/99998.p1 type:3prime_partial len:446 gc:universal transcript/99998:1337-3(-)
>transcript/11752.p3 type:complete len:263 gc:universal transcript/11752:2274-3062(+)
>transcript/136322.p2 type:5prime_partial len:275 gc:universal transcript/136322:1316-492(-)
>transcript/157699.p2 type:complete len:101 gc:universal transcript/157699:606-304(-)
>transcript/18482.p6 type:3prime_partial len:133 gc:universal transcript/18482:2865-3260(+)
>transcript/29334.p3 type:complete len:227 gc:universal transcript/29334:2625-1945(-)
>transcript/41738.p3 type:complete len:212 gc:universal transcript/41738:2196-1561(-)
>transcript/55402.p4 type:5prime_partial len:111 gc:universal transcript/55402:1-333(+)
>transcript/69349.p1 type:complete len:403 gc:universal transcript/69349:318-1526(+)
>transcript/84186.p1 type:5prime_partial len:454 gc:universal transcript/84186:3-1364(+)
>transcript/99991.p2 type:complete len:161 gc:universal transcript/99991:1112-630(-)
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v22.0ui state cache


# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\fasta_SpecLib\\DAINN19\\2024-09-14-decoys-Eglacilis.isoseq.cdhit95-transdecoder-longest.fasta.fas

Table.editor=15.9949
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
diann.quantification-strategy-2=QuantUMS (high accuracy)
diann.run-dia-nn=false
diann.run-dia-plex=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=true
diatracer.corr-threshold=0.3
diatracer.delta-apex-im=0.01
diatracer.delta-apex-rt=3
diatracer.mass-defect-filter=true
diatracer.mass-defect-offset=0.1
diatracer.rf-max=500
diatracer.run-diatracer=false
diatracer.write-intermediate-files=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fpop.fpop-tmt=false
fpop.label_control=
fpop.label_fpop=
fpop.region_size=1
fpop.run-fpop=false
fpop.subtract-control=false
fragpipe-config.bin-diann=C\:\\Users\\tokus\\OneDrive\\\u30C7\u30B9\u30AF\u30C8\u30C3\u30D7\\FragPipe-jre-21.1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=C\:\\Users\\tokus\\OneDrive\\\u30C7\u30B9\u30AF\u30C8\u30C3\u30D7\\FragPipe-jre-21.1\\fragpipe\\tools\\IonQuant-1.10.27.jar
fragpipe-config.bin-msfragger=C\:\\Users\\tokus\\OneDrive\\\u30C7\u30B9\u30AF\u30C8\u30C3\u30D7\\FragPipe-jre-21.1\\fragpipe\\tools\\MSFragger-4.1\\MSFragger-4.1.jar
fragpipe-config.bin-philosopher=C\:\\Users\\tokus\\OneDrive\\\u30C7\u30B9\u30AF\u30C8\u30C3\u30D7\\FragPipe-jre-21.1\\fragpipe\\tools\\philosopher_v5.1.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\tokus\\AppData\\Local\\Programs\\Python\\Python39\\python
fragpipe-config.tools-folder=C\:\\Users\\tokus\\OneDrive\\\u30C7\u30B9\u30AF\u30C8\u30C3\u30D7\\FragPipe-jre-22.0\\fragpipe\\lib\\..\\tools
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=1
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.find-best-rt-model=false
msbooster.find-best-spectra-model=false
msbooster.koina-url=
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.rt-model=DIA-NN
msbooster.run-msbooster=false
msbooster.spectra-model=DIA-NN
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.analyzer_types=all
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.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=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=stricttrypsin
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=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
msfragger.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.require_precursor=true
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),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,[^,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; 114.04293,K,true,2; 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=true
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mzml=true
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=4
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=true
phi-report.print-decoys=false
phi-report.prot-level-summary=false
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106,K\:114.04293 MINPROB\=0.5
ptmprophet.run-ptmprophet=true
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.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_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
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_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.iterloc_maxEpoch=100
ptmshepherd.iterloc_mode=false
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.print_full_glyco_params=false
ptmshepherd.prob_dhexOx=2,0.5,0.1
ptmshepherd.prob_dhexY=2,0.5
ptmshepherd.prob_mass=0.5
ptmshepherd.prob_neuacOx=2,0.05,0.2
ptmshepherd.prob_neugcOx=2,0.05,0.2
ptmshepherd.prob_phosphoOx=2,0.05,0.2
ptmshepherd.prob_regY=5,0.5
ptmshepherd.prob_sulfoOx=2,0.05,0.2
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=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
skyline.run-skyline=true
skyline.skyline=false
skyline.skyline-custom=false
skyline.skyline-custom-path=
skyline.skyline-daily=true
skyline.skyline-mode=0
skyline.skyline-mods-mode=Default
speclibgen.convert-pepxml=true
speclibgen.convert-psm=false
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.max_glycan_qval=1
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.ignore_unannotated=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.labile_mode=Regular (not glyco)
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.philosopher-msstats=false
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\:\\timsTOF_HT\\PJ1314_Tamaki_Kgg_DDA\\result
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.misc.save-sdrf=true
workflow.ram=0
workflow.threads=20

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -Xmx54G -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.d 20
Done in 0.0 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:37:57" level=info msg="Executing Workspace  v5.1.1"
time="18:37:57" level=info msg="Removing workspace"
time="18:37:57" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\981b17f7-e9c8-4eda-a57e-e3958608ab45
time="18:37:58" level=info msg="Executing Workspace  v5.1.1"
time="18:37:58" level=info msg="Creating workspace"
time="18:37:58" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:37:58" level=info msg="Executing Workspace  v5.1.1"
time="18:37:58" level=info msg="Removing workspace"
time="18:37:58" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\2bb32b39-f780-4fd7-85e5-7099ae49e7e0
time="18:37:59" level=info msg="Executing Workspace  v5.1.1"
time="18:37:59" level=info msg="Creating workspace"
time="18:37:59" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:38:00" level=info msg="Executing Workspace  v5.1.1"
time="18:38:00" level=info msg="Removing workspace"
time="18:38:00" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\b33bdce1-b5f5-43ac-a50e-efcfea3e797d
time="18:38:00" level=info msg="Executing Workspace  v5.1.1"
time="18:38:00" level=info msg="Creating workspace"
time="18:38:00" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:38:01" level=info msg="Executing Workspace  v5.1.1"
time="18:38:01" level=info msg="Removing workspace"
time="18:38:01" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\964a4738-2a3d-417f-a160-8b3a5600e182
time="18:38:01" level=info msg="Executing Workspace  v5.1.1"
time="18:38:01" level=info msg="Creating workspace"
time="18:38:01" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:38:02" level=info msg="Executing Workspace  v5.1.1"
time="18:38:02" level=info msg="Removing workspace"
time="18:38:02" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\a08d488a-22fd-4429-8e27-68a8a1783980
time="18:38:03" level=info msg="Executing Workspace  v5.1.1"
time="18:38:03" level=info msg="Creating workspace"
time="18:38:03" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:38:03" level=info msg="Executing Workspace  v5.1.1"
time="18:38:03" level=info msg="Removing workspace"
time="18:38:03" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\fb2d0c7f-d77f-4eb9-ba60-bcf357b3442f
time="18:38:04" level=info msg="Executing Workspace  v5.1.1"
time="18:38:04" level=info msg="Creating workspace"
time="18:38:04" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:38:05" level=info msg="Executing Workspace  v5.1.1"
time="18:38:05" level=info msg="Removing workspace"
time="18:38:05" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\tokus\AppData\Local\Temp\3b3f049f-5bbe-4b2c-9a85-51ac48ba7548
time="18:38:05" level=info msg="Executing Workspace  v5.1.1"
time="18:38:05" level=info msg="Creating workspace"
time="18:38:05" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx54G C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\fragger.params D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.d D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.d D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.d D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.d D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.d D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.d
MSFragger version MSFragger-4.1
Batmass-IO version 1.33.4
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 11, Architecture: AMD64
Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium
JVM started with 54 GB memory
Checking database...
Checking spectral files...
D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.d: Scans = 33581; ITMS: false; FTMS: false; Isolation sizes = []
D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.d: Scans = 33571; ITMS: false; FTMS: false; Isolation sizes = []
D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.d: Scans = 33485; ITMS: false; FTMS: false; Isolation sizes = []
D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.d: Scans = 33568; ITMS: false; FTMS: false; Isolation sizes = []
D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.d: Scans = 33582; ITMS: false; FTMS: false; Isolation sizes = []
D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.d: Scans = 33576; ITMS: false; FTMS: false; Isolation sizes = []
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 20
database_name = D:\fasta_SpecLib\DAINN19\2024-09-14-decoys-Eglacilis.isoseq.cdhit95-transdecoder-longest.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 = 20.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 1
write_calibrated_mzml = 1
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
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 = 0
override_charge = 0
precursor_charge_low = 2
precursor_charge_high = 3
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 = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
activation_types = all
analyzer_types = all
group_variable = 0
require_precursor = 1
reuse_dia_fragment_peaks = 0
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 = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
variable_mod_10 = 114.04293 K 2
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
Number of unique peptides
	of length 7: 796431
	of length 8: 834826
	of length 9: 806686
	of length 10: 784569
	of length 11: 750311
	of length 12: 714030
	of length 13: 673668
	of length 14: 638330
	of length 15: 603182
	of length 16: 569338
	of length 17: 535261
	of length 18: 501971
	of length 19: 472353
	of length 20: 443367
	of length 21: 416672
	of length 22: 388825
	of length 23: 362272
	of length 24: 337081
	of length 25: 315661
	of length 26: 295470
	of length 27: 274011
	of length 28: 258251
	of length 29: 237080
	of length 30: 220157
	of length 31: 205416
	of length 32: 190133
	of length 33: 177378
	of length 34: 164096
	of length 35: 155362
	of length 36: 141700
	of length 37: 132508
	of length 38: 122994
	of length 39: 114074
	of length 40: 106352
	of length 41: 97139
	of length 42: 91177
	of length 43: 82038
	of length 44: 72183
	of length 45: 60783
	of length 46: 48178
	of length 47: 34772
	of length 48: 23830
	of length 49: 14970
	of length 50: 8839
In total 14273725 peptides.
Generated 33150283 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.10 Da.
1346355814 fragments to be searched in 1 slices (20.06 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 6.25 s
	001. PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.d loading 99% 58.4 s | deisotoping 1.8 s
		[progress: 66535/66535 (100%) - 19615 spectra/s] 3.4s | postprocessing 0.2 s
	002. PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.d loading 99% 55.2 s | deisotoping 1.9 s
		[progress: 65292/65292 (100%) - 32777 spectra/s] 2.0s | postprocessing 0.1 s
	003. PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.d loading 99% 66.7 s | deisotoping 2.6 s
		[progress: 79908/79908 (100%) - 30120 spectra/s] 2.7s | postprocessing 0.2 s
	004. PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.d loading 99% 61.8 s | deisotoping 1.3 s
		[progress: 76153/76153 (100%) - 32796 spectra/s] 2.3s | postprocessing 0.2 s
	005. PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.d loading 99% 52.3 s | deisotoping 1.7 s
		[progress: 64209/64209 (100%) - 34172 spectra/s] 1.9s | postprocessing 0.2 s
	006. PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.d loading 99% 73.9 s | deisotoping 3.1 s
		[progress: 83144/83144 (100%) - 34258 spectra/s] 2.4s | postprocessing 0.3 s
***************************FIRST SEARCH DONE IN 6.899 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |  -1.79   3.83 |   0.04   3.02 |  -2.52   5.57 |  -0.31   5.30  
 002 |  -2.15   3.53 |   0.13   2.98 |  -2.59   5.74 |  -0.40   5.54  
 003 |  -1.58   3.73 |   0.15   3.10 |  -2.27   5.67 |  -0.26   5.45  
 004 |  -1.10   3.26 |  -0.13   3.01 |  -1.41   5.92 |  -0.31   5.74  
 005 |  -1.69   3.31 |   0.21   3.01 |  -2.03   5.88 |  -0.38   5.65  
 006 |  -1.57   4.04 |   0.07   3.26 |  -2.70   5.39 |  -0.42   5.12  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count | skip  | skip  | skip  |  17907|  17831| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |  18035|  18044|  18019| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |  17864
-------|-------
-------|-------
 Rm P. |    0  
-------|-------
 Count |  17446
-------|-------
New fragment_mass_tolerance = 15.000000 PPM
New use_topN_peaks = 200
New minimum_ratio = 0.000000
New intensity_transform = 0
New remove_precursor_peak = 1
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 2.507 MIN*********

************************************MAIN SEARCH************************************
Checking database...
Parameters:
num_threads = 20
database_name = D:\fasta_SpecLib\DAINN19\2024-09-14-decoys-Eglacilis.isoseq.cdhit95-transdecoder-longest.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 = 15.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 1
write_calibrated_mzml = 1
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1/2
mass_offsets = 0.0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
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 = 1
override_charge = 0
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 = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
minimum_peaks = 15
use_topN_peaks = 200
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.0
intensity_transform = 0
activation_types = all
analyzer_types = all
group_variable = 0
require_precursor = 1
reuse_dia_fragment_peaks = 0
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 = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
variable_mod_10 = 114.04293 K 2
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
Number of unique peptides
	of length 7: 796431
	of length 8: 834826
	of length 9: 806686
	of length 10: 784569
	of length 11: 750311
	of length 12: 714030
	of length 13: 673668
	of length 14: 638330
	of length 15: 603182
	of length 16: 569338
	of length 17: 535261
	of length 18: 501971
	of length 19: 472353
	of length 20: 443367
	of length 21: 416672
	of length 22: 388825
	of length 23: 362272
	of length 24: 337081
	of length 25: 315661
	of length 26: 295470
	of length 27: 274011
	of length 28: 258251
	of length 29: 237080
	of length 30: 220157
	of length 31: 205416
	of length 32: 190133
	of length 33: 177378
	of length 34: 164096
	of length 35: 155362
	of length 36: 141700
	of length 37: 132508
	of length 38: 122994
	of length 39: 114074
	of length 40: 106352
	of length 41: 97139
	of length 42: 91177
	of length 43: 82038
	of length 44: 72183
	of length 45: 60783
	of length 46: 48178
	of length 47: 34772
	of length 48: 23830
	of length 49: 14970
	of length 50: 8839
In total 14273725 peptides.
Generated 33150283 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.08 Da.
1346355814 fragments to be searched in 1 slices (20.06 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 5.60 s
	001. PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.mzBIN_calibrated 0.6 s
		[progress: 66535/66535 (100%) - 22927 spectra/s] 2.9s | remapping alternative proteins and postprocessing 4.7 s
	002. PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.mzBIN_calibrated 0.6 s
		[progress: 65292/65292 (100%) - 24564 spectra/s] 2.7s | remapping alternative proteins and postprocessing 4.0 s
	003. PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.mzBIN_calibrated 0.7 s
		[progress: 79908/79908 (100%) - 23229 spectra/s] 3.4s | remapping alternative proteins and postprocessing 4.2 s
	004. PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.mzBIN_calibrated 0.6 s
		[progress: 76153/76153 (100%) - 23577 spectra/s] 3.2s | remapping alternative proteins and postprocessing 4.2 s
	005. PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.mzBIN_calibrated 0.5 s
		[progress: 64209/64209 (100%) - 25239 spectra/s] 2.5s | remapping alternative proteins and postprocessing 3.7 s
	006. PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.mzBIN_calibrated 0.7 s
		[progress: 83144/83144 (100%) - 23520 spectra/s] 3.5s | remapping alternative proteins and postprocessing 4.3 s
***************************MAIN SEARCH DONE IN 1.048 MIN***************************

*******************************TOTAL TIME 10.454 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pepXML D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pepXML D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pepXML D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pepXML D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pepXML D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pepXML D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/tokus/OneDrive/%e3%83%87%e3%82%b9%e3%82%af%e3%83%88%e3%83%83%e3%83%97/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pin
Process 'MSFragger move pin' finished, exit code: 0
Percolator [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
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:
C:\Users\tokus\OneDrive\�f�X�N�g�b�v\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pin
Started Sat Sep 14 18:48:36 2024
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 114.04293K 15.9949M 
Found 51308 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 36945 positives and 14363 negatives, size ratio=2.57223 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 12104 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 11972 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 12015 training set positives with q<0.01 in that direction.
Found 18018 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.5300 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 19310 PSMs with q<0.01
Iteration 2:	Estimated 19535 PSMs with q<0.01
Iteration 3:	Estimated 19638 PSMs with q<0.01
Iteration 4:	Estimated 19672 PSMs with q<0.01
Iteration 5:	Estimated 19696 PSMs with q<0.01
Iteration 6:	Estimated 19701 PSMs with q<0.01
Iteration 7:	Estimated 19699 PSMs with q<0.01
Iteration 8:	Estimated 19700 PSMs with q<0.01
Iteration 9:	Estimated 19704 PSMs with q<0.01
Iteration 10:	Estimated 19706 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.9301	-0.6697	-0.8137	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.2982	 0.2229	 0.2427	isotope_error_0
 0.0554	 0.0271	 0.0565	isotope_error_1
-0.4559	-0.3248	-0.3838	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-2.3230	-2.0060	-2.5313	log10_evalue
 0.8071	 0.9781	 0.7771	hyperscore
 1.4531	 1.2243	 1.5408	delta_hyperscore
 1.7651	 1.3795	 1.9346	matched_ion_num
-1.3568	-1.2280	-1.5085	complementary_ions
 0.6453	 0.6169	 0.5574	ion_series
-0.3066	-0.3446	-0.4772	weighted_average_abs_fragment_ppm
 0.0367	 0.0226	 0.0146	length_7
 0.0295	 0.0283	 0.0248	length_8
-0.0605	-0.0391	-0.0503	length_9_30
 0.0418	 0.0239	 0.0400	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.2894	-0.2306	-0.2771	nmc
-0.0274	-0.0284	 0.0079	charge_1
-0.1593	-0.1324	-0.1610	charge_2
 0.1821	 0.1218	 0.1459	charge_3
 0.1281	 0.1138	 0.1556	charge_4
-0.1839	-0.1176	-0.1645	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
 0.0882	 0.1327	 0.1112	114.04293K
 0.1182	 0.1436	 0.1135	15.9949M
 0.7115	 0.7383	 0.8245	m0
Found 19638 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 36945 target PSMs and 14363 decoy PSMs.
Calculating q values.
Final list yields 19648 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 3.7470 cpu seconds or 4 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
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:
C:\Users\tokus\OneDrive\�f�X�N�g�b�v\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pin
Started Sat Sep 14 18:48:41 2024
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 114.04293K 15.9949M 
Found 39010 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 28408 positives and 10602 negatives, size ratio=2.67949 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 9526 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 9403 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 9387 training set positives with q<0.01 in that direction.
Found 14136 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3720 cpu seconds or 0 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 15293 PSMs with q<0.01
Iteration 2:	Estimated 15505 PSMs with q<0.01
Iteration 3:	Estimated 15568 PSMs with q<0.01
Iteration 4:	Estimated 15569 PSMs with q<0.01
Iteration 5:	Estimated 15588 PSMs with q<0.01
Iteration 6:	Estimated 15592 PSMs with q<0.01
Iteration 7:	Estimated 15597 PSMs with q<0.01
Iteration 8:	Estimated 15583 PSMs with q<0.01
Iteration 9:	Estimated 15596 PSMs with q<0.01
Iteration 10:	Estimated 15597 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.6618	-0.5793	-0.5941	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.3028	 0.2560	 0.1941	isotope_error_0
 0.0659	 0.0666	 0.0092	isotope_error_1
-0.4817	-0.4197	-0.2713	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-2.1389	-2.1029	-1.8099	log10_evalue
 1.7342	 1.4706	 1.4210	hyperscore
 0.8582	 0.8280	 0.8354	delta_hyperscore
 1.2111	 0.9554	 0.9920	matched_ion_num
-1.3454	-1.1831	-1.1114	complementary_ions
 0.5928	 0.4592	 0.4788	ion_series
-0.4423	-0.3533	-0.2882	weighted_average_abs_fragment_ppm
 0.0304	 0.0113	 0.0139	length_7
 0.0768	 0.1043	 0.0883	length_8
-0.0021	-0.0279	-0.0113	length_9_30
-0.0404	-0.0167	-0.0292	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.1823	-0.1249	-0.1585	nmc
-0.0505	-0.0505	-0.0301	charge_1
-0.2190	-0.1360	-0.1164	charge_2
 0.1115	 0.0928	 0.0780	charge_3
 0.1086	 0.0667	 0.0934	charge_4
 0.0365	-0.0142	-0.0583	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
 0.1257	 0.1533	 0.1374	114.04293K
 0.1585	 0.0398	 0.0969	15.9949M
 0.8460	 0.4661	 0.7671	m0
Found 15482 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 28408 target PSMs and 10602 decoy PSMs.
Calculating q values.
Final list yields 15495 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.3990 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
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:
C:\Users\tokus\OneDrive\�f�X�N�g�b�v\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pin
Started Sat Sep 14 18:48:47 2024
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 114.04293K 15.9949M 
Found 49347 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 36039 positives and 13308 negatives, size ratio=2.70807 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 12216 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 12353 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 12044 training set positives with q<0.01 in that direction.
Found 18326 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4640 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 19762 PSMs with q<0.01
Iteration 2:	Estimated 20032 PSMs with q<0.01
Iteration 3:	Estimated 20086 PSMs with q<0.01
Iteration 4:	Estimated 20106 PSMs with q<0.01
Iteration 5:	Estimated 20119 PSMs with q<0.01
Iteration 6:	Estimated 20130 PSMs with q<0.01
Iteration 7:	Estimated 20135 PSMs with q<0.01
Iteration 8:	Estimated 20129 PSMs with q<0.01
Iteration 9:	Estimated 20133 PSMs with q<0.01
Iteration 10:	Estimated 20146 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.4892	-0.6007	-0.4492	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.3246	 0.2913	 0.2636	isotope_error_0
-0.0592	-0.0197	 0.0294	isotope_error_1
-0.3691	-0.3690	-0.3875	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-2.1141	-2.3003	-1.5981	log10_evalue
 1.2420	 1.3474	 0.9540	hyperscore
 1.2839	 1.0921	 0.7399	delta_hyperscore
 1.6207	 1.0635	 1.0544	matched_ion_num
-1.2842	-1.3266	-0.9857	complementary_ions
 0.4839	 0.8108	 0.3341	ion_series
-0.3978	-0.3613	-0.2253	weighted_average_abs_fragment_ppm
 0.0138	-0.0173	 0.0227	length_7
 0.0665	 0.0334	 0.0158	length_8
-0.0270	-0.0089	-0.0128	length_9_30
-0.0074	 0.0013	-0.0027	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.3308	-0.2842	-0.1710	nmc
-0.0418	-0.0453	-0.0162	charge_1
-0.1714	-0.1363	-0.1265	charge_2
 0.1328	 0.1314	 0.1252	charge_3
 0.0967	 0.0533	 0.0434	charge_4
-0.0425	-0.0476	-0.0460	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
-0.0564	-0.0809	-0.0803	114.04293K
 0.1220	 0.1043	 0.1097	15.9949M
 1.0365	 0.9890	-0.0152	m0
Found 20033 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 36039 target PSMs and 13308 decoy PSMs.
Calculating q values.
Final list yields 20040 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 3.1790 cpu seconds or 3 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
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:
C:\Users\tokus\OneDrive\�f�X�N�g�b�v\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pin
Started Sat Sep 14 18:48:51 2024
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 114.04293K 15.9949M 
Found 36328 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 25416 positives and 10912 negatives, size ratio=2.32918 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 7644 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 7641 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 7512 training set positives with q<0.01 in that direction.
Found 11381 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3480 cpu seconds or 0 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 12533 PSMs with q<0.01
Iteration 2:	Estimated 12723 PSMs with q<0.01
Iteration 3:	Estimated 12765 PSMs with q<0.01
Iteration 4:	Estimated 12761 PSMs with q<0.01
Iteration 5:	Estimated 12788 PSMs with q<0.01
Iteration 6:	Estimated 12790 PSMs with q<0.01
Iteration 7:	Estimated 12796 PSMs with q<0.01
Iteration 8:	Estimated 12797 PSMs with q<0.01
Iteration 9:	Estimated 12801 PSMs with q<0.01
Iteration 10:	Estimated 12798 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.5296	-0.7774	-0.6104	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.2025	 0.3713	 0.2530	isotope_error_0
 0.0830	 0.1045	-0.0206	isotope_error_1
-0.3618	-0.6096	-0.3118	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-1.5155	-1.9048	-1.7020	log10_evalue
 1.1435	 1.7226	 1.2764	hyperscore
 0.8535	 1.0448	 1.0353	delta_hyperscore
 0.5557	 0.7653	 0.9448	matched_ion_num
-0.8708	-1.3207	-1.1210	complementary_ions
 0.4511	 0.6104	 0.5661	ion_series
-0.2666	-0.3936	-0.2586	weighted_average_abs_fragment_ppm
-0.0487	 0.0089	 0.0187	length_7
 0.0196	 0.0113	 0.0410	length_8
-0.0547	-0.0536	-0.0093	length_9_30
 0.0731	 0.0518	-0.0161	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.2194	-0.2447	-0.3085	nmc
 0.0120	-0.0062	-0.0182	charge_1
-0.0526	-0.0445	-0.1115	charge_2
 0.1142	 0.1788	 0.1478	charge_3
 0.0051	 0.0954	 0.0849	charge_4
-0.1245	-0.3810	-0.1838	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
 0.0632	 0.0471	 0.0865	114.04293K
 0.0707	 0.1539	 0.0673	15.9949M
-0.4543	-0.0591	 0.1794	m0
Found 12716 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 25416 target PSMs and 10912 decoy PSMs.
Calculating q values.
Final list yields 12725 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.6230 cpu seconds or 3 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
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:
C:\Users\tokus\OneDrive\�f�X�N�g�b�v\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pin
Started Sat Sep 14 18:48:54 2024
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 114.04293K 15.9949M 
Found 47319 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 34490 positives and 12829 negatives, size ratio=2.68844 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 11352 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 11601 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 11528 training set positives with q<0.01 in that direction.
Found 17205 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4490 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 18608 PSMs with q<0.01
Iteration 2:	Estimated 18877 PSMs with q<0.01
Iteration 3:	Estimated 18935 PSMs with q<0.01
Iteration 4:	Estimated 18966 PSMs with q<0.01
Iteration 5:	Estimated 18966 PSMs with q<0.01
Iteration 6:	Estimated 18971 PSMs with q<0.01
Iteration 7:	Estimated 18972 PSMs with q<0.01
Iteration 8:	Estimated 18967 PSMs with q<0.01
Iteration 9:	Estimated 18971 PSMs with q<0.01
Iteration 10:	Estimated 18970 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.6049	-0.7521	-0.7396	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.2199	 0.2396	 0.2500	isotope_error_0
 0.0464	 0.0474	 0.0563	isotope_error_1
-0.3497	-0.3773	-0.4016	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-1.7901	-2.4610	-2.7099	log10_evalue
 1.0244	 1.0114	 0.6409	hyperscore
 1.2400	 1.4906	 1.4077	delta_hyperscore
 1.0930	 1.0547	 1.5738	matched_ion_num
-1.0411	-1.2417	-1.2949	complementary_ions
 0.5163	 0.6765	 0.3025	ion_series
-0.3082	-0.4247	-0.3731	weighted_average_abs_fragment_ppm
 0.0268	 0.0354	 0.0281	length_7
 0.0239	 0.0325	 0.0674	length_8
-0.0360	 0.0233	-0.0465	length_9_30
 0.0195	-0.0533	 0.0114	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.2189	-0.1606	-0.2771	nmc
-0.0116	-0.0093	 0.0341	charge_1
-0.0748	-0.0679	-0.0910	charge_2
 0.1531	 0.1455	 0.1118	charge_3
 0.0893	 0.0967	 0.1048	charge_4
-0.2589	-0.2674	-0.1821	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
 0.1918	 0.1766	 0.2901	114.04293K
 0.0421	 0.0185	 0.0271	15.9949M
 0.3073	 0.8445	 0.7663	m0
Found 18844 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 34490 target PSMs and 12829 decoy PSMs.
Calculating q values.
Final list yields 18844 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 3.1710 cpu seconds or 3 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
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:
C:\Users\tokus\OneDrive\�f�X�N�g�b�v\FragPipe-jre-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_target_psms.tsv --decoy-results-psms PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pin
Started Sat Sep 14 18:48:58 2024
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 114.04293K 15.9949M 
Found 38386 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 27354 positives and 11032 negatives, size ratio=2.47951 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 8573 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 8503 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 8405 training set positives with q<0.01 in that direction.
Found 12693 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3640 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 13678 PSMs with q<0.01
Iteration 2:	Estimated 13882 PSMs with q<0.01
Iteration 3:	Estimated 13967 PSMs with q<0.01
Iteration 4:	Estimated 14008 PSMs with q<0.01
Iteration 5:	Estimated 14041 PSMs with q<0.01
Iteration 6:	Estimated 14044 PSMs with q<0.01
Iteration 7:	Estimated 14035 PSMs with q<0.01
Iteration 8:	Estimated 14037 PSMs with q<0.01
Iteration 9:	Estimated 14025 PSMs with q<0.01
Iteration 10:	Estimated 14043 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.7093	-0.5217	-0.5185	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.2468	 0.2277	 0.2568	isotope_error_0
-0.0214	 0.0160	 0.0289	isotope_error_1
-0.3010	-0.3181	-0.3712	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-1.8622	-1.7810	-1.5286	log10_evalue
 1.0267	 1.5760	 1.2378	hyperscore
 1.0593	 0.8718	 0.9174	delta_hyperscore
 1.3727	 0.8456	 1.2885	matched_ion_num
-1.0332	-1.0872	-0.9622	complementary_ions
 0.5541	 0.4354	 0.5597	ion_series
-0.3325	-0.3839	-0.4082	weighted_average_abs_fragment_ppm
 0.0060	 0.0236	 0.0123	length_7
 0.0404	 0.0892	 0.0051	length_8
-0.0399	 0.0333	 0.0102	length_9_30
 0.0255	-0.0782	-0.0173	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.3179	-0.3162	-0.2414	nmc
-0.0758	-0.0091	-0.0589	charge_1
-0.1473	-0.1854	-0.1438	charge_2
 0.1386	 0.0937	 0.0533	charge_3
 0.1728	 0.1001	 0.1441	charge_4
-0.1766	 0.0184	-0.0279	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
-0.1093	-0.0370	-0.0761	114.04293K
 0.1609	 0.1342	 0.1311	15.9949M
 0.4380	 0.2240	 0.1356	m0
Found 13885 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 27354 target PSMs and 11032 decoy PSMs.
Calculating q values.
Final list yields 13893 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 3.1590 cpu seconds or 3 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pin PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350 PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_target_psms.tsv PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_decoy_psms.tsv interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350 DDA 0.5 D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_calibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pin PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354 PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_target_psms.tsv PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_decoy_psms.tsv interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354 DDA 0.5 D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_calibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pin PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356 PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_target_psms.tsv PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_decoy_psms.tsv interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356 DDA 0.5 D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_calibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pin PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348 PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_target_psms.tsv PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_decoy_psms.tsv interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348 DDA 0.5 D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_calibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pin PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346 PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_target_psms.tsv PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_decoy_psms.tsv interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346 DDA 0.5 D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_calibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pin PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352 PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_target_psms.tsv PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_decoy_psms.tsv interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352 DDA 0.5 D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_calibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
PTMProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,K:114.04293 MINPROB=0.5 MAXTHREADS=1 interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pep.xml interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.mod.pep.xml
PTMProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,K:114.04293 MINPROB=0.5 MAXTHREADS=1 interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pep.xml interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.mod.pep.xml
PTMProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,K:114.04293 MINPROB=0.5 MAXTHREADS=1 interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pep.xml interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.mod.pep.xml
PTMProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,K:114.04293 MINPROB=0.5 MAXTHREADS=1 interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pep.xml interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.mod.pep.xml
PTMProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,K:114.04293 MINPROB=0.5 MAXTHREADS=1 interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pep.xml interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.mod.pep.xml
PTMProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,K:114.04293 MINPROB=0.5 MAXTHREADS=1 interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pep.xml interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.mod.pep.xml
Please wait. PTMProphet is running. It can take a long time.
Please wait. PTMProphet is running. It can take a long time.
Please wait. PTMProphet is running. It can take a long time.
Please wait. PTMProphet is running. It can take a long time.
Please wait. PTMProphet is running. It can take a long time.
Please wait. PTMProphet is running. It can take a long time.
[INFO:] Using statically set 15 PPM tolerance ... 
[INFO:] Writing file interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pep.xml.tmp.a18392 ...

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pep.xml ...
​
[INFO:] processed 14000/14350 spectrum_queries		 
[INFO:] done ... 
[INFO:] Computing EM Models ... 
[INFO:] Iterating PTM Model: ....5...done
[INFO:] done ... 
[INFO:] done ... 

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pep.xml ...
​
[INFO:] written 14000/14350 spectrum_queries		 
[INFO:] done ... 
[INFO:] Writing file interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.mod.pep.xml ...
'chmod' �́A�����R�}���h�܂��͊O���R�}���h�A
����\�ȃv���O�����܂��̓o�b�` �t�@�C���Ƃ��ĔF������Ă��܂���B
[INFO:] done ... 

command "chmod 664 interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.mod.pep.xml" failed: Operation not permitted
Process 'PTMProphet' finished, exit code: 0
[INFO:] Using statically set 15 PPM tolerance ... 
[INFO:] Writing file interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pep.xml.tmp.a07696 ...

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pep.xml ...
​
[INFO:] processed 15000/15847 spectrum_queries		 
[INFO:] done ... 
[INFO:] Computing EM Models ... 
[INFO:] Iterating PTM Model: ....5...done
[INFO:] done ... 
[INFO:] done ... 

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pep.xml ...
​
[INFO:] written 15000/15847 spectrum_queries		 
[INFO:] done ... 
[INFO:] Writing file interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.mod.pep.xml ...
'chmod' �́A�����R�}���h�܂��͊O���R�}���h�A
����\�ȃv���O�����܂��̓o�b�` �t�@�C���Ƃ��ĔF������Ă��܂���B
[INFO:] done ... 

command "chmod 664 interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.mod.pep.xml" failed: Operation not permitted
Process 'PTMProphet' finished, exit code: 0
[INFO:] Using statically set 15 PPM tolerance ... 
[INFO:] Writing file interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pep.xml.tmp.a20324 ...

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pep.xml ...
​
[INFO:] processed 17000/17212 spectrum_queries		 
[INFO:] done ... 
[INFO:] Computing EM Models ... 
[INFO:] Iterating PTM Model: ....5..done
[INFO:] done ... 
[INFO:] done ... 

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pep.xml ...
​
[INFO:] written 17000/17212 spectrum_queries		 
[INFO:] done ... 
[INFO:] Writing file interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.mod.pep.xml ...
'chmod' �́A�����R�}���h�܂��͊O���R�}���h�A
����\�ȃv���O�����܂��̓o�b�` �t�@�C���Ƃ��ĔF������Ă��܂���B
[INFO:] done ... 

command "chmod 664 interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.mod.pep.xml" failed: Operation not permitted
Process 'PTMProphet' finished, exit code: 0
[INFO:] Using statically set 15 PPM tolerance ... 
[INFO:] Writing file interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pep.xml.tmp.a07748 ...

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pep.xml ...
​
[INFO:] processed 22000/22468 spectrum_queries		 
[INFO:] done ... 
[INFO:] Computing EM Models ... 
[INFO:] Iterating PTM Model: ....5...done
[INFO:] done ... 
[INFO:] done ... 

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pep.xml ...
​
[INFO:] written 22000/22468 spectrum_queries		 
[INFO:] done ... 
[INFO:] Writing file interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.mod.pep.xml ...
'chmod' �́A�����R�}���h�܂��͊O���R�}���h�A
����\�ȃv���O�����܂��̓o�b�` �t�@�C���Ƃ��ĔF������Ă��܂���B
[INFO:] done ... 

command "chmod 664 interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.mod.pep.xml" failed: Operation not permitted
Process 'PTMProphet' finished, exit code: 0
[INFO:] Using statically set 15 PPM tolerance ... 
[INFO:] Writing file interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pep.xml.tmp.a07320 ...

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pep.xml ...
​
[INFO:] processed 22000/22077 spectrum_queries		 
[INFO:] done ... 
[INFO:] Computing EM Models ... 
[INFO:] Iterating PTM Model: ....5...done
[INFO:] done ... 
[INFO:] done ... 

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pep.xml ...
​
[INFO:] written 22000/22077 spectrum_queries		 
[INFO:] done ... 
[INFO:] Writing file interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.mod.pep.xml ...
'chmod' �́A�����R�}���h�܂��͊O���R�}���h�A
����\�ȃv���O�����܂��̓o�b�` �t�@�C���Ƃ��ĔF������Ă��܂���B
[INFO:] done ... 

command "chmod 664 interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.mod.pep.xml" failed: Operation not permitted
Process 'PTMProphet' finished, exit code: 0
[INFO:] Using statically set 15 PPM tolerance ... 
[INFO:] Writing file interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pep.xml.tmp.a02736 ...

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pep.xml ...
​
[INFO:] processed 21000/21017 spectrum_queries		 
[INFO:] done ... 
[INFO:] Computing EM Models ... 
[INFO:] Iterating PTM Model: ....5...done
[INFO:] done ... 
[INFO:] done ... 

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pep.xml ...
​
[INFO:] written 21000/21017 spectrum_queries		 
[INFO:] done ... 
[INFO:] Writing file interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.mod.pep.xml ...
'chmod' �́A�����R�}���h�܂��͊O���R�}���h�A
����\�ȃv���O�����܂��̓o�b�` �t�@�C���Ƃ��ĔF������Ă��܂���B
[INFO:] done ... 

command "chmod 664 interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.mod.pep.xml" failed: Operation not permitted
Process 'PTMProphet' finished, exit code: 0
ProteinProphet [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --output combined D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\filelist_proteinprophet.txt
time="18:51:40" level=info msg="Executing ProteinProphet  v5.1.1"
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:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pep.xml...
...read in 9 1+, 7616 2+, 9879 3+, 2873 4+, 640 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pep.xml...
...read in 5 1+, 7349 2+, 9985 3+, 3695 4+, 1043 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pep.xml...
...read in 2 1+, 5474 2+, 8197 3+, 2821 4+, 718 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pep.xml...
...read in 2 1+, 5122 2+, 6720 3+, 2065 4+, 441 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pep.xml...
...read in 3 1+, 5268 2+, 6868 3+, 2882 4+, 826 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pep.xml...
...read in 1 1+, 9541 2+, 9468 3+, 2797 4+, 661 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 22677 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database D:\fasta_SpecLib\DAINN19\2024-09-14-decoys-Eglacilis.isoseq.cdhit95-transdecoder-longest.fasta.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........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
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........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
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........102000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........103000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........104000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........105000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........106000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........107000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........108000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........109000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........110000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........111000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........112000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........113000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........114000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........115000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........116000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........117000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........118000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........119000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........120000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........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
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........194000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........195000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........196000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........197000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........198000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........199000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........200000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........201000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........202000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........203000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........204000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........205000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........206000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........207000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........208000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........209000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........210000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........211000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........212000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........213000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........214000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........215000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........216000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........217000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........218000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........219000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........220000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........221000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........222000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........223000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........224000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........225000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........226000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........227000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........228000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........229000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........230000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........231000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........232000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........233000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........234000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........235000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........236000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........237000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........238000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........239000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........240000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........241000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........242000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........243000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........244000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........245000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........246000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........247000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........248000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........249000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........250000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........251000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........252000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........253000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........254000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........255000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........256000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........257000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........258000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........259000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........260000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........261000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........262000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........263000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........264000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........265000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........266000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........267000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........268000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........269000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........270000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........271000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........272000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........273000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........274000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........275000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........276000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........277000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........278000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........279000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........280000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........281000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........282000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........283000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........284000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........285000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........286000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........287000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........288000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........289000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........290000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........291000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........292000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........293000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........294000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........295000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........296000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........297000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........298000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........299000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........300000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........301000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........302000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........303000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........304000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........305000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........306000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........307000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........308000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........309000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........310000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........311000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........312000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........313000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........314000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........315000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........316000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........317000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........318000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........319000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........320000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........321000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........322000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........323000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........324000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........325000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........326000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........327000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........328000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........329000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........330000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........331000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........332000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........333000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........334000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........335000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........336000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........337000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........338000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........339000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........340000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........341000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........342000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........343000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........344000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........345000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........346000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........347000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........348000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........349000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........350000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........351000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........352000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........353000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........354000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........355000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........356000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........357000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........358000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........359000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........360000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........361000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........362000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........363000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........364000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........365000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........366000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........367000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........368000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........369000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........370000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........371000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........372000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........373000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........374000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........375000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........376000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........377000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........378000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........379000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........380000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........381000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........382000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........383000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........384000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........385000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........386000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........387000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........388000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........389000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........390000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........391000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........392000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........393000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........394000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........395000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........396000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........397000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........398000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........399000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........400000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........401000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........402000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........403000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........404000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........405000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........406000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........407000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........408000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........409000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........410000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........411000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........412000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........413000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........414000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........415000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........416000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........417000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........418000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........419000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........420000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........421000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........422000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........423000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........424000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........425000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........426000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........427000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........428000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........429000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........430000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........431000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........432000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........433000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........434000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........435000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........436000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........437000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........438000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........439000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........440000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........441000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........442000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........443000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........444000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........445000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........446000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........447000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........448000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........449000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........450000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........451000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........452000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........453000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........454000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........455000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........456000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........457000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........458000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........459000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........460000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........461000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........462000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........463000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........464000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........465000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........466000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........467000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........468000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........469000
.........:.........:.........:.........:.........:.........:.........:........  Total: 469788
Computing degenerate peptides for 21072 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 24623 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 24623 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 24623 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 24623 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 24623 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 24623 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=1.21286e-05, db_size=203798756
Computing MU for 24623 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
time="18:51:55" level=info msg=Done
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe database --annotate D:\fasta_SpecLib\DAINN19\2024-09-14-decoys-Eglacilis.isoseq.cdhit95-transdecoder-longest.fasta.fas --prefix rev_
time="18:51:56" level=info msg="Executing Database  v5.1.1"
time="18:51:56" level=info msg="Annotating the database"
time="18:51:56" level=info msg=Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --protxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\combined.prot.xml --razor
time="18:51:56" level=info msg="Executing Filter  v5.1.1"
time="18:51:56" level=info msg="Processing peptide identification files"
time="18:51:56" level=info msg="Parsing D:\\timsTOF_HT\\PJ1314_Tamaki_Kgg_DDA\\result\\Aerabic_1\\interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.mod.pep.xml"
time="18:51:58" level=info msg="1+ Charge profile" decoy=4 target=5
time="18:51:58" level=info msg="2+ Charge profile" decoy=275 target=7341
time="18:51:58" level=info msg="3+ Charge profile" decoy=313 target=9566
time="18:51:58" level=info msg="4+ Charge profile" decoy=94 target=2779
time="18:51:58" level=info msg="5+ Charge profile" decoy=16 target=624
time="18:51:58" level=info msg="6+ Charge profile" decoy=0 target=0
time="18:51:58" level=info msg="Database search results" ions=10352 peptides=7996 psms=21017
time="18:51:58" level=info msg="Converged to 1.00 % FDR with 18847 PSMs" decoy=188 threshold=0.811147 total=19035
time="18:51:58" level=info msg="Converged to 1.00 % FDR with 6311 Peptides" decoy=63 threshold=0.921359 total=6374
time="18:51:58" level=info msg="Converged to 0.99 % FDR with 8569 Ions" decoy=85 threshold=0.897624 total=8654
time="18:51:58" level=info msg="Protein inference results" decoy=2786 target=8843
time="18:51:58" level=info msg="Converged to 0.99 % FDR with 3230 Proteins" decoy=32 threshold=0.9907 total=3262
time="18:51:58" level=info msg="Applying sequential FDR estimation" ions=8643 peptides=6405 psms=18604
time="18:51:58" level=info msg="Converged to 0.16 % FDR with 18574 PSMs" decoy=30 threshold=0.811539 total=18604
time="18:51:58" level=info msg="Converged to 0.25 % FDR with 6389 Peptides" decoy=16 threshold=0.811936 total=6405
time="18:51:58" level=info msg="Converged to 0.22 % FDR with 8624 Ions" decoy=19 threshold=0.811936 total=8643
time="18:51:58" level=info msg="Post processing identifications"
time="18:51:58" level=info msg="Assigning protein identifications to layers"
time="18:51:59" level=info msg="Processing protein inference"
time="18:51:59" level=info msg="Synchronizing PSMs and proteins"
time="18:51:59" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=8622 peptides=6387 proteins=2403 psms=18569
time="18:51:59" level=info msg=Saving
time="18:51:59" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2 --dbbin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --protxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\combined.prot.xml --probin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --razor
time="18:52:00" level=info msg="Executing Filter  v5.1.1"
time="18:52:00" level=info msg="Fetching protein inference from D:\\timsTOF_HT\\PJ1314_Tamaki_Kgg_DDA\\result\\Aerabic_1"
time="18:52:00" level=info msg="Processing peptide identification files"
time="18:52:00" level=info msg="Parsing D:\\timsTOF_HT\\PJ1314_Tamaki_Kgg_DDA\\result\\Aerabic_2\\interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.mod.pep.xml"
time="18:52:01" level=info msg="1+ Charge profile" decoy=1 target=4
time="18:52:01" level=info msg="2+ Charge profile" decoy=246 target=7103
time="18:52:01" level=info msg="3+ Charge profile" decoy=316 target=9669
time="18:52:01" level=info msg="4+ Charge profile" decoy=136 target=3559
time="18:52:01" level=info msg="5+ Charge profile" decoy=47 target=996
time="18:52:01" level=info msg="6+ Charge profile" decoy=0 target=0
time="18:52:01" level=info msg="Database search results" ions=10638 peptides=8139 psms=22077
time="18:52:01" level=info msg="Converged to 1.00 % FDR with 19648 PSMs" decoy=197 threshold=0.809089 total=19845
time="18:52:01" level=info msg="Converged to 0.99 % FDR with 6237 Peptides" decoy=62 threshold=0.922377 total=6299
time="18:52:01" level=info msg="Converged to 0.99 % FDR with 8578 Ions" decoy=85 threshold=0.900853 total=8663
time="18:52:01" level=info msg="Protein inference results" decoy=2786 target=8843
time="18:52:01" level=info msg="Converged to 0.99 % FDR with 3230 Proteins" decoy=32 threshold=0.9907 total=3262
time="18:52:01" level=info msg="Applying sequential FDR estimation" ions=8734 peptides=6383 psms=19415
time="18:52:01" level=info msg="Converged to 0.13 % FDR with 19389 PSMs" decoy=26 threshold=0.809169 total=19415
time="18:52:01" level=info msg="Converged to 0.20 % FDR with 6370 Peptides" decoy=13 threshold=0.809515 total=6383
time="18:52:01" level=info msg="Converged to 0.20 % FDR with 8717 Ions" decoy=17 threshold=0.809515 total=8734
time="18:52:01" level=info msg="Post processing identifications"
time="18:52:02" level=info msg="Assigning protein identifications to layers"
time="18:52:03" level=info msg="Processing protein inference"
time="18:52:03" level=info msg="Synchronizing PSMs and proteins"
time="18:52:03" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=8715 peptides=6368 proteins=2579 psms=19382
time="18:52:03" level=info msg=Saving
time="18:52:03" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3 --dbbin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --protxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\combined.prot.xml --probin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --razor
time="18:52:04" level=info msg="Executing Filter  v5.1.1"
time="18:52:04" level=info msg="Fetching protein inference from D:\\timsTOF_HT\\PJ1314_Tamaki_Kgg_DDA\\result\\Aerabic_1"
time="18:52:04" level=info msg="Processing peptide identification files"
time="18:52:04" level=info msg="Parsing D:\\timsTOF_HT\\PJ1314_Tamaki_Kgg_DDA\\result\\Aerabic_3\\interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.mod.pep.xml"
time="18:52:05" level=info msg="1+ Charge profile" decoy=1 target=1
time="18:52:05" level=info msg="2+ Charge profile" decoy=179 target=5295
time="18:52:05" level=info msg="3+ Charge profile" decoy=241 target=7956
time="18:52:05" level=info msg="4+ Charge profile" decoy=87 target=2734
time="18:52:05" level=info msg="5+ Charge profile" decoy=37 target=681
time="18:52:05" level=info msg="6+ Charge profile" decoy=0 target=0
time="18:52:05" level=info msg="Database search results" ions=8030 peptides=6210 psms=17212
time="18:52:05" level=info msg="Converged to 0.99 % FDR with 15496 PSMs" decoy=154 threshold=0.808115 total=15650
time="18:52:05" level=info msg="Converged to 0.98 % FDR with 4878 Peptides" decoy=48 threshold=0.923803 total=4926
time="18:52:05" level=info msg="Converged to 0.99 % FDR with 6645 Ions" decoy=66 threshold=0.899819 total=6711
time="18:52:05" level=info msg="Protein inference results" decoy=2786 target=8843
time="18:52:05" level=info msg="Converged to 0.99 % FDR with 3230 Proteins" decoy=32 threshold=0.9907 total=3262
time="18:52:05" level=info msg="Applying sequential FDR estimation" ions=6719 peptides=4987 psms=15318
time="18:52:05" level=info msg="Converged to 0.16 % FDR with 15293 PSMs" decoy=25 threshold=0.808115 total=15318
time="18:52:05" level=info msg="Converged to 0.20 % FDR with 4977 Peptides" decoy=10 threshold=0.808603 total=4987
time="18:52:05" level=info msg="Converged to 0.18 % FDR with 6707 Ions" decoy=12 threshold=0.808603 total=6719
time="18:52:05" level=info msg="Post processing identifications"
time="18:52:05" level=info msg="Assigning protein identifications to layers"
time="18:52:06" level=info msg="Processing protein inference"
time="18:52:06" level=info msg="Synchronizing PSMs and proteins"
time="18:52:06" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=6705 peptides=4975 proteins=2141 psms=15289
time="18:52:06" level=info msg=Saving
time="18:52:07" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1 --dbbin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --protxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\combined.prot.xml --probin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --razor
time="18:52:07" level=info msg="Executing Filter  v5.1.1"
time="18:52:07" level=info msg="Fetching protein inference from D:\\timsTOF_HT\\PJ1314_Tamaki_Kgg_DDA\\result\\Aerabic_1"
time="18:52:07" level=info msg="Processing peptide identification files"
time="18:52:07" level=info msg="Parsing D:\\timsTOF_HT\\PJ1314_Tamaki_Kgg_DDA\\result\\Anaerabic_1\\interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.mod.pep.xml"
time="18:52:08" level=info msg="1+ Charge profile" decoy=1 target=1
time="18:52:08" level=info msg="2+ Charge profile" decoy=198 target=4924
time="18:52:08" level=info msg="3+ Charge profile" decoy=232 target=6488
time="18:52:08" level=info msg="4+ Charge profile" decoy=67 target=1998
time="18:52:08" level=info msg="5+ Charge profile" decoy=12 target=429
time="18:52:08" level=info msg="6+ Charge profile" decoy=0 target=0
time="18:52:08" level=info msg="Database search results" ions=6816 peptides=5478 psms=14350
time="18:52:08" level=info msg="Converged to 1.00 % FDR with 12732 PSMs" decoy=127 threshold=0.815205 total=12859
time="18:52:08" level=info msg="Converged to 1.00 % FDR with 4218 Peptides" decoy=42 threshold=0.928493 total=4260
time="18:52:08" level=info msg="Converged to 0.99 % FDR with 5458 Ions" decoy=54 threshold=0.916806 total=5512
time="18:52:08" level=info msg="Protein inference results" decoy=2786 target=8843
time="18:52:08" level=info msg="Converged to 0.99 % FDR with 3230 Proteins" decoy=32 threshold=0.9907 total=3262
time="18:52:08" level=info msg="Applying sequential FDR estimation" ions=5647 peptides=4380 psms=12601
time="18:52:08" level=info msg="Converged to 0.17 % FDR with 12580 PSMs" decoy=21 threshold=0.815205 total=12601
time="18:52:08" level=info msg="Converged to 0.23 % FDR with 4370 Peptides" decoy=10 threshold=0.81574 total=4380
time="18:52:08" level=info msg="Converged to 0.27 % FDR with 5632 Ions" decoy=15 threshold=0.81574 total=5647
time="18:52:08" level=info msg="Post processing identifications"
time="18:52:08" level=info msg="Assigning protein identifications to layers"
time="18:52:09" level=info msg="Processing protein inference"
time="18:52:09" level=info msg="Synchronizing PSMs and proteins"
time="18:52:10" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=5630 peptides=4368 proteins=1791 psms=12574
time="18:52:10" level=info msg=Saving
time="18:52:10" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2 --dbbin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --protxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\combined.prot.xml --probin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --razor
time="18:52:10" level=info msg="Executing Filter  v5.1.1"
time="18:52:10" level=info msg="Fetching protein inference from D:\\timsTOF_HT\\PJ1314_Tamaki_Kgg_DDA\\result\\Aerabic_1"
time="18:52:10" level=info msg="Processing peptide identification files"
time="18:52:10" level=info msg="Parsing D:\\timsTOF_HT\\PJ1314_Tamaki_Kgg_DDA\\result\\Anaerabic_2\\interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.mod.pep.xml"
time="18:52:11" level=info msg="1+ Charge profile" decoy=1 target=2
time="18:52:11" level=info msg="2+ Charge profile" decoy=223 target=5045
time="18:52:11" level=info msg="3+ Charge profile" decoy=244 target=6624
time="18:52:11" level=info msg="4+ Charge profile" decoy=104 target=2778
time="18:52:11" level=info msg="5+ Charge profile" decoy=29 target=797
time="18:52:11" level=info msg="6+ Charge profile" decoy=0 target=0
time="18:52:11" level=info msg="Database search results" ions=6971 peptides=5353 psms=15847
time="18:52:11" level=info msg="Converged to 0.99 % FDR with 13893 PSMs" decoy=138 threshold=0.81972 total=14031
time="18:52:11" level=info msg="Converged to 0.98 % FDR with 3968 Peptides" decoy=39 threshold=0.927977 total=4007
time="18:52:11" level=info msg="Converged to 0.99 % FDR with 5529 Ions" decoy=55 threshold=0.89967 total=5584
time="18:52:11" level=info msg="Protein inference results" decoy=2786 target=8843
time="18:52:11" level=info msg="Converged to 0.99 % FDR with 3230 Proteins" decoy=32 threshold=0.9907 total=3262
time="18:52:11" level=info msg="Applying sequential FDR estimation" ions=5591 peptides=4074 psms=13744
time="18:52:11" level=info msg="Converged to 0.17 % FDR with 13721 PSMs" decoy=23 threshold=0.81972 total=13744
time="18:52:11" level=info msg="Converged to 0.32 % FDR with 4061 Peptides" decoy=13 threshold=0.819799 total=4074
time="18:52:11" level=info msg="Converged to 0.25 % FDR with 5577 Ions" decoy=14 threshold=0.819799 total=5591
time="18:52:11" level=info msg="Post processing identifications"
time="18:52:11" level=info msg="Assigning protein identifications to layers"
time="18:52:12" level=info msg="Processing protein inference"
time="18:52:13" level=info msg="Synchronizing PSMs and proteins"
time="18:52:13" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=5574 peptides=4058 proteins=1819 psms=13715
time="18:52:13" level=info msg=Saving
time="18:52:13" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3 --dbbin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --protxml D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\combined.prot.xml --probin D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1 --razor
time="18:52:13" level=info msg="Executing Filter  v5.1.1"
time="18:52:13" level=info msg="Fetching protein inference from D:\\timsTOF_HT\\PJ1314_Tamaki_Kgg_DDA\\result\\Aerabic_1"
time="18:52:13" level=info msg="Processing peptide identification files"
time="18:52:13" level=info msg="Parsing D:\\timsTOF_HT\\PJ1314_Tamaki_Kgg_DDA\\result\\Anaerabic_3\\interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.mod.pep.xml"
time="18:52:14" level=info msg="1+ Charge profile" decoy=1 target=0
time="18:52:14" level=info msg="2+ Charge profile" decoy=307 target=9234
time="18:52:14" level=info msg="3+ Charge profile" decoy=345 target=9123
time="18:52:14" level=info msg="4+ Charge profile" decoy=96 target=2701
time="18:52:14" level=info msg="5+ Charge profile" decoy=22 target=639
time="18:52:14" level=info msg="6+ Charge profile" decoy=0 target=0
time="18:52:14" level=info msg="Database search results" ions=10819 peptides=8679 psms=22468
time="18:52:14" level=info msg="Converged to 1.00 % FDR with 20047 PSMs" decoy=200 threshold=0.812905 total=20247
time="18:52:15" level=info msg="Converged to 0.99 % FDR with 6745 Peptides" decoy=67 threshold=0.930314 total=6812
time="18:52:15" level=info msg="Converged to 1.00 % FDR with 8841 Ions" decoy=88 threshold=0.907204 total=8929
time="18:52:15" level=info msg="Protein inference results" decoy=2786 target=8843
time="18:52:15" level=info msg="Converged to 0.99 % FDR with 3230 Proteins" decoy=32 threshold=0.9907 total=3262
time="18:52:15" level=info msg="Applying sequential FDR estimation" ions=9009 peptides=6988 psms=19833
time="18:52:15" level=info msg="Converged to 0.13 % FDR with 19807 PSMs" decoy=26 threshold=0.812905 total=19833
time="18:52:15" level=info msg="Converged to 0.23 % FDR with 6972 Peptides" decoy=16 threshold=0.815743 total=6988
time="18:52:15" level=info msg="Converged to 0.20 % FDR with 8991 Ions" decoy=18 threshold=0.813512 total=9009
time="18:52:15" level=info msg="Post processing identifications"
time="18:52:15" level=info msg="Assigning protein identifications to layers"
time="18:52:16" level=info msg="Processing protein inference"
time="18:52:16" level=info msg="Synchronizing PSMs and proteins"
time="18:52:16" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=8989 peptides=6970 proteins=2135 psms=19799
time="18:52:16" level=info msg=Saving
time="18:52:17" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
time="18:52:17" level=info msg="Executing Report  v5.1.1"
time="18:52:17" level=info msg="Creating reports"
time="18:52:17" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
time="18:52:17" level=info msg="Executing Report  v5.1.1"
time="18:52:17" level=info msg="Creating reports"
time="18:52:18" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
time="18:52:18" level=info msg="Executing Report  v5.1.1"
time="18:52:18" level=info msg="Creating reports"
time="18:52:18" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
time="18:52:19" level=info msg="Executing Report  v5.1.1"
time="18:52:19" level=info msg="Creating reports"
time="18:52:19" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
time="18:52:19" level=info msg="Executing Report  v5.1.1"
time="18:52:19" level=info msg="Creating reports"
time="18:52:20" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
time="18:52:20" level=info msg="Executing Report  v5.1.1"
time="18:52:20" level=info msg="Creating reports"
time="18:52:20" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:52:21" level=info msg="Executing Workspace  v5.1.1"
time="18:52:21" level=info msg="Removing workspace"
time="18:52:21" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:52:22" level=info msg="Executing Workspace  v5.1.1"
time="18:52:22" level=info msg="Removing workspace"
time="18:52:22" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:52:22" level=info msg="Executing Workspace  v5.1.1"
time="18:52:22" level=info msg="Removing workspace"
time="18:52:22" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:52:23" level=info msg="Executing Workspace  v5.1.1"
time="18:52:23" level=info msg="Removing workspace"
time="18:52:23" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:52:24" level=info msg="Executing Workspace  v5.1.1"
time="18:52:24" level=info msg="Removing workspace"
time="18:52:24" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:52:25" level=info msg="Executing Workspace  v5.1.1"
time="18:52:25" level=info msg="Removing workspace"
time="18:52:25" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="18:52:25" level=info msg="Executing Workspace  v5.1.1"
time="18:52:25" level=info msg="Removing workspace"
time="18:52:25" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
IonQuant [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -Xmx54G -Dlibs.bruker.dir=C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\..\tools\MSFragger-4.1\ext\bruker -Dlibs.thermo.dir=C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\jfreechart-1.5.3.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\IonQuant-1.10.27.jar ionquant.IonQuant --threads 20 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 1 --site-reports 1 --msstats 1 --minexps 1 --mbr 1 --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 1 --locprob 0.75 --uniqueness 0 --multidir . --filelist D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\filelist_ionquant.txt --modlist D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\modmasses_ionquant.txt
IonQuant version IonQuant-1.10.27
Batmass-IO version 1.33.4
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
System OS: Windows 11, Architecture: AMD64
Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium
JVM started with 54 GB memory
2024-09-14 18:52:26 [INFO] - Collecting variable modifications from all psm.tsv files...
2024-09-14 18:52:26 [INFO] - Loading and indexing all psm.tsv files...
2024-09-14 18:52:29 [INFO] - Parameters:
2024-09-14 18:52:29 [INFO] - perform-ms1quant = 1
2024-09-14 18:52:29 [INFO] - perform-isoquant = 0
2024-09-14 18:52:29 [INFO] - isotol = 20.0
2024-09-14 18:52:29 [INFO] - isolevel = 2
2024-09-14 18:52:29 [INFO] - isotype = tmt10
2024-09-14 18:52:29 [INFO] - site-reports = 1
2024-09-14 18:52:29 [INFO] - msstats = 1
2024-09-14 18:52:29 [INFO] - threads = 20
2024-09-14 18:52:29 [INFO] - mztol = 10.0
2024-09-14 18:52:29 [INFO] - rttol = 0.4
2024-09-14 18:52:29 [INFO] - imtol = 0.05
2024-09-14 18:52:29 [INFO] - minisotopes = 2
2024-09-14 18:52:29 [INFO] - minscans = 3
2024-09-14 18:52:29 [INFO] - psm = D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\psm.tsv
2024-09-14 18:52:29 [INFO] - psm = D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\psm.tsv
2024-09-14 18:52:29 [INFO] - psm = D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\psm.tsv
2024-09-14 18:52:29 [INFO] - psm = D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\psm.tsv
2024-09-14 18:52:29 [INFO] - psm = D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\psm.tsv
2024-09-14 18:52:29 [INFO] - psm = D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\psm.tsv
2024-09-14 18:52:29 [INFO] - multidir = D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\.\
2024-09-14 18:52:29 [INFO] - excludemods = 
2024-09-14 18:52:29 [INFO] - minions = 1
2024-09-14 18:52:29 [INFO] - maxlfq = 1
2024-09-14 18:52:29 [INFO] - ibaq = 0
2024-09-14 18:52:29 [INFO] - normalization = 1
2024-09-14 18:52:29 [INFO] - minexps = 1
2024-09-14 18:52:29 [INFO] - minfreq = 0.0
2024-09-14 18:52:29 [INFO] - tp = 0
2024-09-14 18:52:29 [INFO] - mbr = 1
2024-09-14 18:52:29 [INFO] - mbrrttol = 1.0
2024-09-14 18:52:29 [INFO] - mbrimtol = 0.05
2024-09-14 18:52:29 [INFO] - mbrtoprun = 10
2024-09-14 18:52:29 [INFO] - mbrmincorr = 0.0
2024-09-14 18:52:29 [INFO] - ionmobility = 1
2024-09-14 18:52:29 [INFO] - ionfdr = 0.01
2024-09-14 18:52:29 [INFO] - peptidefdr = 1.0
2024-09-14 18:52:29 [INFO] - proteinfdr = 1.0
2024-09-14 18:52:29 [INFO] - light = 
2024-09-14 18:52:29 [INFO] - medium = 
2024-09-14 18:52:29 [INFO] - heavy = 
2024-09-14 18:52:29 [INFO] - requantify = 0
2024-09-14 18:52:29 [INFO] - writeindex = 0
2024-09-14 18:52:29 [INFO] - locprob = 0.75
2024-09-14 18:52:29 [INFO] - uniqueness = 0
2024-09-14 18:52:29 [INFO] - filelist = D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\filelist_ionquant.txt
2024-09-14 18:52:29 [INFO] - specdir = D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA
2024-09-14 18:52:29 [INFO] - modlist = D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\modmasses_ionquant.txt
2024-09-14 18:52:29 [INFO] - mod masses:
2024-09-14 18:52:29 [INFO] - 15.9949
2024-09-14 18:52:29 [INFO] - 42.0106
2024-09-14 18:52:29 [INFO] - 57.02146
2024-09-14 18:52:29 [INFO] - 114.04293
2024-09-14 18:52:29 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2024-09-14 18:52:29 [INFO] - Loading D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.d...
2024-09-14 18:52:29 [INFO] - ...40%...60%...80%...100%
2024-09-14 18:52:31 [INFO] - Building index...
2024-09-14 18:52:56 [INFO] - Writing index to D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.quantindex
2024-09-14 18:52:57 [INFO] - Quantifying...
2024-09-14 18:52:58 [INFO] - Loading D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.d...
2024-09-14 18:52:58 [INFO] - ...40%...80%...100%
2024-09-14 18:52:59 [INFO] - Building index...
2024-09-14 18:53:23 [INFO] - Writing index to D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.quantindex
2024-09-14 18:53:24 [INFO] - Quantifying...
2024-09-14 18:53:25 [INFO] - Loading D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.d...
2024-09-14 18:53:25 [INFO] - ...40%...60%...80%...100%
2024-09-14 18:53:27 [INFO] - Building index...
2024-09-14 18:53:52 [INFO] - Writing index to D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.quantindex
2024-09-14 18:53:53 [INFO] - Quantifying...
2024-09-14 18:53:54 [INFO] - Loading D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.d...
2024-09-14 18:53:54 [INFO] - ...40%...80%...100%
2024-09-14 18:53:55 [INFO] - Building index...
2024-09-14 18:54:20 [INFO] - Writing index to D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.quantindex
2024-09-14 18:54:21 [INFO] - Quantifying...
2024-09-14 18:54:21 [INFO] - Loading D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.d...
2024-09-14 18:54:21 [INFO] - ...40%...60%...80%...100%
2024-09-14 18:54:24 [INFO] - Building index...
2024-09-14 18:54:48 [INFO] - Writing index to D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.quantindex
2024-09-14 18:54:49 [INFO] - Quantifying...
2024-09-14 18:54:49 [INFO] - Loading D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.d...
2024-09-14 18:54:49 [INFO] - ...40%...60%...80%...100%
2024-09-14 18:54:52 [INFO] - Building index...
2024-09-14 18:55:17 [INFO] - Writing index to D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.quantindex
2024-09-14 18:55:18 [INFO] - Quantifying...
2024-09-14 18:55:18 [INFO] - Updating Philosopher's tables...
2024-09-14 18:55:20 [INFO] - Matching-between-runs: PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352...
2024-09-14 18:55:20 [INFO] - Calculating correlations between all other runs...
2024-09-14 18:55:20 [INFO] - Reading index from D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.quantindex
2024-09-14 18:55:22 [INFO] - Transferring PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354...
2024-09-14 18:55:22 [INFO] - Transferring PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356...
2024-09-14 18:55:23 [INFO] - Transferring PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346...
2024-09-14 18:55:23 [INFO] - Transferring PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348...
2024-09-14 18:55:23 [INFO] - Transferring PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350...
2024-09-14 18:55:24 [INFO] - Training LDA models for all matched features.
2024-09-14 18:55:24 [INFO] - #{+1} = 3231, #{-1} = 196, #{+2} = 3827, #{-2} = 254
2024-09-14 18:55:24 [INFO] - Standardized coefficients:
2024-09-14 18:55:24 [INFO] - log10(intensity): 0.9113148626933874
2024-09-14 18:55:24 [INFO] - log10(KL): -0.15870610298328403
2024-09-14 18:55:24 [INFO] - abs(ppm): -0.1932071219753899
2024-09-14 18:55:24 [INFO] - IM diff: -0.3004054700576685
2024-09-14 18:55:24 [INFO] - RT diff: -0.12940307371701004
2024-09-14 18:55:24 [INFO] - Fitting a mixture model...
2024-09-14 18:55:25 [INFO] - Matching-between-runs: PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354...
2024-09-14 18:55:25 [INFO] - Calculating correlations between all other runs...
2024-09-14 18:55:25 [INFO] - Reading index from D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.quantindex
2024-09-14 18:55:26 [INFO] - Transferring PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352...
2024-09-14 18:55:26 [INFO] - Transferring PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356...
2024-09-14 18:55:27 [INFO] - Transferring PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346...
2024-09-14 18:55:27 [INFO] - Transferring PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348...
2024-09-14 18:55:27 [INFO] - Transferring PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350...
2024-09-14 18:55:28 [INFO] - Training LDA models for all matched features.
2024-09-14 18:55:28 [INFO] - #{+1} = 3952, #{-1} = 171, #{+2} = 4626, #{-2} = 200
2024-09-14 18:55:28 [INFO] - Standardized coefficients:
2024-09-14 18:55:28 [INFO] - log10(intensity): 0.8702912663315616
2024-09-14 18:55:28 [INFO] - log10(KL): -0.15512229002233688
2024-09-14 18:55:28 [INFO] - abs(ppm): -0.25852608115024134
2024-09-14 18:55:28 [INFO] - IM diff: -0.3198333819492525
2024-09-14 18:55:28 [INFO] - RT diff: -0.22226349237163442
2024-09-14 18:55:28 [INFO] - Fitting a mixture model...
2024-09-14 18:55:28 [INFO] - Matching-between-runs: PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356...
2024-09-14 18:55:28 [INFO] - Calculating correlations between all other runs...
2024-09-14 18:55:28 [INFO] - Reading index from D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.quantindex
2024-09-14 18:55:30 [INFO] - Transferring PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352...
2024-09-14 18:55:30 [INFO] - Transferring PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354...
2024-09-14 18:55:30 [INFO] - Transferring PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346...
2024-09-14 18:55:31 [INFO] - Transferring PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348...
2024-09-14 18:55:31 [INFO] - Transferring PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350...
2024-09-14 18:55:31 [INFO] - Training LDA models for all matched features.
2024-09-14 18:55:32 [INFO] - #{+1} = 3568, #{-1} = 211, #{+2} = 4985, #{-2} = 425
2024-09-14 18:55:32 [INFO] - Standardized coefficients:
2024-09-14 18:55:32 [INFO] - log10(intensity): 0.8878577238473526
2024-09-14 18:55:32 [INFO] - log10(KL): -0.15327565151545108
2024-09-14 18:55:32 [INFO] - abs(ppm): -0.2124779738425781
2024-09-14 18:55:32 [INFO] - IM diff: -0.31387082999912197
2024-09-14 18:55:32 [INFO] - RT diff: -0.21107688069641142
2024-09-14 18:55:32 [INFO] - Fitting a mixture model...
2024-09-14 18:55:32 [INFO] - Matching-between-runs: PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346...
2024-09-14 18:55:32 [INFO] - Calculating correlations between all other runs...
2024-09-14 18:55:32 [INFO] - Reading index from D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.quantindex
2024-09-14 18:55:33 [INFO] - Transferring PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352...
2024-09-14 18:55:33 [INFO] - Transferring PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354...
2024-09-14 18:55:34 [INFO] - Transferring PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356...
2024-09-14 18:55:34 [INFO] - Transferring PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348...
2024-09-14 18:55:34 [INFO] - Transferring PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350...
2024-09-14 18:55:35 [INFO] - Training LDA models for all matched features.
2024-09-14 18:55:35 [INFO] - #{+1} = 3512, #{-1} = 186, #{+2} = 5780, #{-2} = 282
2024-09-14 18:55:35 [INFO] - Standardized coefficients:
2024-09-14 18:55:35 [INFO] - log10(intensity): 0.846036092670715
2024-09-14 18:55:35 [INFO] - log10(KL): -0.13027667376512123
2024-09-14 18:55:35 [INFO] - abs(ppm): -0.3473245164206834
2024-09-14 18:55:35 [INFO] - IM diff: -0.3379490362385077
2024-09-14 18:55:35 [INFO] - RT diff: -0.18001957496274587
2024-09-14 18:55:35 [INFO] - Fitting a mixture model...
2024-09-14 18:55:35 [INFO] - Matching-between-runs: PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348...
2024-09-14 18:55:35 [INFO] - Calculating correlations between all other runs...
2024-09-14 18:55:35 [INFO] - Reading index from D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.quantindex
2024-09-14 18:55:36 [INFO] - Transferring PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352...
2024-09-14 18:55:36 [INFO] - Transferring PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354...
2024-09-14 18:55:37 [INFO] - Transferring PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356...
2024-09-14 18:55:37 [INFO] - Transferring PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346...
2024-09-14 18:55:37 [INFO] - Transferring PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350...
2024-09-14 18:55:38 [INFO] - Training LDA models for all matched features.
2024-09-14 18:55:38 [INFO] - #{+1} = 3705, #{-1} = 114, #{+2} = 4045, #{-2} = 119
2024-09-14 18:55:38 [INFO] - Standardized coefficients:
2024-09-14 18:55:38 [INFO] - log10(intensity): 0.7960561131630828
2024-09-14 18:55:38 [INFO] - log10(KL): -0.34737392585506116
2024-09-14 18:55:38 [INFO] - abs(ppm): -0.31307011516538813
2024-09-14 18:55:38 [INFO] - IM diff: -0.361181178249476
2024-09-14 18:55:38 [INFO] - RT diff: -0.1310010679360232
2024-09-14 18:55:38 [INFO] - Fitting a mixture model...
2024-09-14 18:55:38 [INFO] - Matching-between-runs: PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350...
2024-09-14 18:55:38 [INFO] - Calculating correlations between all other runs...
2024-09-14 18:55:38 [INFO] - Reading index from D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.quantindex
2024-09-14 18:55:39 [INFO] - Transferring PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352...
2024-09-14 18:55:40 [INFO] - Transferring PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354...
2024-09-14 18:55:40 [INFO] - Transferring PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356...
2024-09-14 18:55:41 [INFO] - Transferring PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346...
2024-09-14 18:55:41 [INFO] - Transferring PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348...
2024-09-14 18:55:41 [INFO] - Training LDA models for all matched features.
2024-09-14 18:55:41 [INFO] - #{+1} = 3931, #{-1} = 377, #{+2} = 5945, #{-2} = 500
2024-09-14 18:55:41 [INFO] - Standardized coefficients:
2024-09-14 18:55:41 [INFO] - log10(intensity): 0.9336957763738918
2024-09-14 18:55:41 [INFO] - log10(KL): -0.17497702247096486
2024-09-14 18:55:41 [INFO] - abs(ppm): -0.17450368280581444
2024-09-14 18:55:41 [INFO] - IM diff: -0.20739558410681722
2024-09-14 18:55:41 [INFO] - RT diff: -0.15534083548426908
2024-09-14 18:55:41 [INFO] - Fitting a mixture model...
2024-09-14 18:55:42 [INFO] - Estimating match-between-runs FDR...
2024-09-14 18:55:42 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.975200
2024-09-14 18:55:42 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100
2024-09-14 18:55:42 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100
2024-09-14 18:55:42 [INFO] - Updating Philosopher's tables...
2024-09-14 18:55:43 [INFO] - Combining experiments and estimating protein intensity...
2024-09-14 18:55:45 [INFO] - Generating modification reports...
2024-09-14 18:55:45 [INFO] - Done!
Process 'IonQuant' finished, exit code: 0
Skyline [Work dir: D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result]
C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -Xmx54G -cp C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\commons-lang3-3.14.0.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\maven-artifact-3.9.6.jar;C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.skyline.Skyline C:\Users\tokus\OneDrive\デスクトップ\FragPipe-jre-22.0\fragpipe\tools\SkylineDailyRunner.exe D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result 24.0.9.184 0 0
No speclib files found in D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result but Skyline was set to use the speclib as input. Let Skyline build its own speclib.
Running command: C:\Users\tokus\OneDrive\�f�X�N�g�b�v\FragPipe-jre-22.0\fragpipe\tools\SkylineDailyRunner.exe --timestamp --dir=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result --batch-commands=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\filelist_skyline.txt
Process java.lang.ProcessBuilder@6ab7a896 returned non zero value. Message:

[2024/09/14 18:55:51]	�G���[�F�l�uion 3�v�͈���--tran-product-start-ion�ɑ΂��ėL���ł͂���܂���B�C�I��1, �C�I��2, �C�I��3, �C�I��4, m/z >�v���J�[�T�[, �im/z >�v���J�[�T�[�j - 1, �im/z >�v���J�[�T�[�j - 2, �im/z >�v���J�[�T�[�j + 1, �im/z >�v���J�[�T�[�j + 2��1���g�p���܂��B
[2024/09/14 18:55:51]	�I����...
Process 'Skyline' 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)
(timsTOF ddaPASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19:1575 (2020)
(Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020)
(Glyco search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125 (2020)
(Labile search) MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics. Mol Cell Proteomics 22:100538 (2023)
(PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923 (2007)
(PTM localization with PTMProphet)PTMProphet: fast and accurate mass modification localization for the trans-proteomic pipeline
. J. Proteome Res. 18:4262 (2019)
(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 FragPipe-PDV) PDV: an integrative proteomics data viewer. Bioinformatics. 35(7):1249 (2019)
(Visualization with Skyline) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics. 26(7):966 (2010)

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