System OS: Windows 11, Architecture: AMD64
Java Info: 21.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
.NET Core Info: 6.0.36


Version info:
FragPipe version 20.0
MSFragger version 3.8
IonQuant version 1.9.8
Philosopher version 5.0.0


LCMS files:
  Experiment/Group: 240411ko02SUDHL6_RAD21_IP_1_1_438
  - J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.d	DDA
  Experiment/Group: 240411ko03FL18_RAD21_IP_1_1_439
  - J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.d	DDA
  Experiment/Group: 240411ko04OCILy7_RAD21_IP_1_1_440
  - J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.d	DDA
  Experiment/Group: 240411ko05KIS1_RAD21_IP_1_1_441
  - J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.d	DDA


53 commands to execute:
CheckCentroid
java -Xmx72G -cp "D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.d 15
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\14ef7cbb-db8b-4f20-9f3a-eec0cb98c145
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\d79e64e9-8ff6-4f04-9ccc-ce7454f99fd4
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\ea40f307-31d1-4bfb-9c38-66349a4d4f1b
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\6b52a97d-50cd-429c-8a75-9d19bb722d72
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\d971f9c9-e0ed-467b-b338-2d196669ba16
MSFragger [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
java -jar -Dfile.encoding=UTF-8 -Xmx72G D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\fragger.params J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.d J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.d J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.d J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.d
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.pepXML J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438\240411ko02SUDHL6_RAD21_IP_1_1_438.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.pin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438\240411ko02SUDHL6_RAD21_IP_1_1_438.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.pepXML J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\240411ko03FL18_RAD21_IP_1_1_439.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.pin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\240411ko03FL18_RAD21_IP_1_1_439.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.pepXML J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440\240411ko04OCILy7_RAD21_IP_1_1_440.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.pin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440\240411ko04OCILy7_RAD21_IP_1_1_440.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.pepXML J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441\240411ko05KIS1_RAD21_IP_1_1_441.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.pin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441\240411ko05KIS1_RAD21_IP_1_1_441.pin
MSBooster [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
java -Xmx72G -cp "D:\Applications\FragPipe-20.0\fragpipe\tools\msbooster-1.1.11.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar" Features.MainClass --paramsList J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\msbooster_params.txt
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_target_psms.tsv --decoy-results-psms 240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240411ko02SUDHL6_RAD21_IP_1_1_438_edited.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240411ko04OCILy7_RAD21_IP_1_1_440_percolator_target_psms.tsv --decoy-results-psms 240411ko04OCILy7_RAD21_IP_1_1_440_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240411ko04OCILy7_RAD21_IP_1_1_440_edited.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240411ko05KIS1_RAD21_IP_1_1_441_percolator_target_psms.tsv --decoy-results-psms 240411ko05KIS1_RAD21_IP_1_1_441_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240411ko05KIS1_RAD21_IP_1_1_441_edited.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240411ko03FL18_RAD21_IP_1_1_439_percolator_target_psms.tsv --decoy-results-psms 240411ko03FL18_RAD21_IP_1_1_439_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240411ko03FL18_RAD21_IP_1_1_439_edited.pin
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240411ko02SUDHL6_RAD21_IP_1_1_438.pin 240411ko02SUDHL6_RAD21_IP_1_1_438 240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_target_psms.tsv 240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_decoy_psms.tsv interact-240411ko02SUDHL6_RAD21_IP_1_1_438 DDA 0.5 J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438\240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438\240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240411ko04OCILy7_RAD21_IP_1_1_440.pin 240411ko04OCILy7_RAD21_IP_1_1_440 240411ko04OCILy7_RAD21_IP_1_1_440_percolator_target_psms.tsv 240411ko04OCILy7_RAD21_IP_1_1_440_percolator_decoy_psms.tsv interact-240411ko04OCILy7_RAD21_IP_1_1_440 DDA 0.5 J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440\240411ko04OCILy7_RAD21_IP_1_1_440_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440\240411ko04OCILy7_RAD21_IP_1_1_440_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240411ko05KIS1_RAD21_IP_1_1_441.pin 240411ko05KIS1_RAD21_IP_1_1_441 240411ko05KIS1_RAD21_IP_1_1_441_percolator_target_psms.tsv 240411ko05KIS1_RAD21_IP_1_1_441_percolator_decoy_psms.tsv interact-240411ko05KIS1_RAD21_IP_1_1_441 DDA 0.5 J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441\240411ko05KIS1_RAD21_IP_1_1_441_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441\240411ko05KIS1_RAD21_IP_1_1_441_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240411ko03FL18_RAD21_IP_1_1_439.pin 240411ko03FL18_RAD21_IP_1_1_439 240411ko03FL18_RAD21_IP_1_1_439_percolator_target_psms.tsv 240411ko03FL18_RAD21_IP_1_1_439_percolator_decoy_psms.tsv interact-240411ko03FL18_RAD21_IP_1_1_439 DDA 0.5 J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\240411ko03FL18_RAD21_IP_1_1_439_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\240411ko03FL18_RAD21_IP_1_1_439_percolator_decoy_psms.tsv
ProteinProphet [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe database --annotate D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotHuman\2021-07-15-decoys-reviewed-contam-UP000005640.fas --prefix rev_
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438 --protxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\combined.prot.xml --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439 --protxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440 --protxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441 --protxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438 --razor
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
IonQuant [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
java -Xmx72G -Dlibs.bruker.dir="D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\bruker" -Dlibs.thermo.dir="D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\thermo" -cp "D:\Applications\FragPipe-20.0\fragpipe\tools\jfreechart-1.5.3.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\IonQuant-1.9.8.jar" ionquant.IonQuant --threads 15 --ionmobility 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 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\filelist_ionquant.txt --modlist J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\modmasses_ionquant.txt
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
    Cmd: [CheckCentroid], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
    Cmd: [MSFragger], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
    Cmd: [MSBooster], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
    Cmd: [Percolator], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
    Cmd: [ProteinProphet], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
    Cmd: [PhilosopherDbAnnotate], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
    Cmd: [PhilosopherFilter], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
    Cmd: [PhilosopherReport], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
    Cmd: [IonQuant], Work dir: [J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]

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

~~~~~~Sample of D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotHuman\2021-07-15-decoys-reviewed-contam-UP000005640.fas~~~~~~~
>rev_sp|A0A024RBG1|NUD4B_HUMAN Diphosphoinositol polyphosphate phosphohydrolase NUDT4B OS=Homo sapiens OX=9606 GN=NUDT4B PE=3 SV=1
>rev_sp|O60231|DHX16_HUMAN Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 OS=Homo sapiens OX=9606 GN=DHX16 PE=1 SV=2
>rev_sp|P0DSO1|F246C_HUMAN Protein FAM246C OS=Homo sapiens OX=9606 GN=FAM246C PE=3 SV=1
>rev_sp|P50897|PPT1_HUMAN Palmitoyl-protein thioesterase 1 OS=Homo sapiens OX=9606 GN=PPT1 PE=1 SV=1
>rev_sp|Q14562|DHX8_HUMAN ATP-dependent RNA helicase DHX8 OS=Homo sapiens OX=9606 GN=DHX8 PE=1 SV=1
>rev_sp|Q6GMV1|ALG1L_HUMAN Putative glycosyltransferase ALG1-like OS=Homo sapiens OX=9606 GN=ALG1L PE=2 SV=2
>rev_sp|Q8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 OS=Homo sapiens OX=9606 GN=SIRT2 PE=1 SV=2
>rev_sp|Q8WWM9|CYGB_HUMAN Cytoglobin OS=Homo sapiens OX=9606 GN=CYGB PE=1 SV=1
>rev_sp|Q9BS86|ZPBP1_HUMAN Zona pellucida-binding protein 1 OS=Homo sapiens OX=9606 GN=ZPBP PE=2 SV=1
>rev_sp|Q9NVI1|FANCI_HUMAN Fanconi anemia group I protein OS=Homo sapiens OX=9606 GN=FANCI PE=1 SV=4
>rev_sp|Q9Y6Z4|KIAS1_HUMAN Putative uncharacterized protein KIF25-AS1 OS=Homo sapiens OX=9606 GN=KIF25-AS1 PE=5 SV=2
>sp|O43929|ORC4_HUMAN Origin recognition complex subunit 4 OS=Homo sapiens OX=9606 GN=ORC4 PE=1 SV=2
>sp|P0DPK4|NT2NC_HUMAN Notch homolog 2 N-terminal-like protein C OS=Homo sapiens OX=9606 GN=NOTCH2NLC PE=1 SV=1
>sp|P50607|TUB_HUMAN Tubby protein homolog OS=Homo sapiens OX=9606 GN=TUB PE=1 SV=1
>sp|Q14526|HIC1_HUMAN Hypermethylated in cancer 1 protein OS=Homo sapiens OX=9606 GN=HIC1 PE=1 SV=5
>sp|Q6EKJ0|GTD2B_HUMAN General transcription factor II-I repeat domain-containing protein 2B OS=Homo sapiens OX=9606 GN=GTF2IRD2B PE=1 SV=1
>sp|Q8IXB1|DJC10_HUMAN DnaJ homolog subfamily C member 10 OS=Homo sapiens OX=9606 GN=DNAJC10 PE=1 SV=2
>sp|Q8WWG9|KCNE4_HUMAN Potassium voltage-gated channel subfamily E member 4 OS=Homo sapiens OX=9606 GN=KCNE4 PE=1 SV=4
>sp|Q9BRX8|PXL2A_HUMAN Peroxiredoxin-like 2A OS=Homo sapiens OX=9606 GN=PRXL2A PE=1 SV=3
>sp|Q9NVE4|CCD87_HUMAN Coiled-coil domain-containing protein 87 OS=Homo sapiens OX=9606 GN=CCDC87 PE=1 SV=2
>sp|Q9Y6X4|F169A_HUMAN Soluble lamin-associated protein of 75 kDa OS=Homo sapiens OX=9606 GN=FAM169A PE=1 SV=2
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v20.0ui state cache


# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\Users\\gt5oc\\Proteomics_Data\\Uniprot_data\\MSFragger\\UniprotHuman\\2021-07-15-decoys-reviewed-contam-UP000005640.fas

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
Table.editor=304.207146
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
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=D\:\\Applications\\FragPipe-21.1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=D\:\\Applications\\FragPipe-20.0\\fragpipe\\tools\\IonQuant-1.9.8.jar
fragpipe-config.bin-msfragger=D\:\\Applications\\FragPipe-20.0\\fragpipe\\tools\\MSFragger-3.8\\MSFragger-3.8.jar
fragpipe-config.bin-philosopher=D\:\\Applications\\FragPipe-20.0\\fragpipe\\tools\\philosopher_v5.0.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\gt5oc\\Anaconda3\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=true
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=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=0/1/2/3
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.output_report_topN_dia2=3
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=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=stricttrypsin
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; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.write_calibrated_mzml=false
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.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 --picked --prot 0.01
phi-report.pep-level-summary=true
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=00.2
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=00.1
ptmshepherd.diagmine_fragMinSpecDiff=00.1
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=00.2
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=2,0.5,0.1
ptmshepherd.prob_dhexY=2,0.5
ptmshepherd.prob_neuacOx=2,0.05,0.2
ptmshepherd.prob_neugcOx=2,0.05,0.2
ptmshepherd.prob_phosphoOx=2,0.05,0.2
ptmshepherd.prob_regY=5,0.5
ptmshepherd.prob_sulfoOx=2,0.05,0.2
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.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-diaumpire=false
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=J\:\\MSFragger_process\\Saitou-lab\\240411ko\\MSFragger_iBAQ
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.misc.save-sdrf=true
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=15

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx72G -cp "D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.d 15
Done in 0.0 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:29:05] Executing Workspace  v5.0.0                  
INFO[16:29:05] Removing workspace                           
WARN[16:29:05] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[16:29:05] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\14ef7cbb-db8b-4f20-9f3a-eec0cb98c145
INFO[16:29:05] Executing Workspace  v5.0.0                  
INFO[16:29:05] Creating workspace                           
INFO[16:29:05] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:29:05] Executing Workspace  v5.0.0                  
INFO[16:29:05] Removing workspace                           
WARN[16:29:05] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[16:29:05] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\d79e64e9-8ff6-4f04-9ccc-ce7454f99fd4
INFO[16:29:06] Executing Workspace  v5.0.0                  
INFO[16:29:06] Creating workspace                           
INFO[16:29:06] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:29:06] Executing Workspace  v5.0.0                  
INFO[16:29:06] Removing workspace                           
WARN[16:29:06] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[16:29:06] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\ea40f307-31d1-4bfb-9c38-66349a4d4f1b
INFO[16:29:07] Executing Workspace  v5.0.0                  
INFO[16:29:07] Creating workspace                           
INFO[16:29:07] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:29:07] Executing Workspace  v5.0.0                  
INFO[16:29:07] Removing workspace                           
WARN[16:29:07] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[16:29:07] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\6b52a97d-50cd-429c-8a75-9d19bb722d72
INFO[16:29:07] Executing Workspace  v5.0.0                  
INFO[16:29:07] Creating workspace                           
INFO[16:29:07] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:29:08] Executing Workspace  v5.0.0                  
INFO[16:29:08] Removing workspace                           
WARN[16:29:08] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[16:29:08] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\d971f9c9-e0ed-467b-b338-2d196669ba16
INFO[16:29:08] Executing Workspace  v5.0.0                  
INFO[16:29:08] Creating workspace                           
INFO[16:29:08] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
java -jar -Dfile.encoding=UTF-8 -Xmx72G D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\fragger.params J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.d J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.d J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.d J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.d
MSFragger version MSFragger-3.8
Batmass-IO version 1.28.12
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: 21.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 72 GB memory
Checking database...
Checking spectral files...
J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.d: Scans = 60881
J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.d: Scans = 60912
J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.d: Scans = 60870
J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.d: Scans = 60916
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.d converted with timsdata-2-21-0-4. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.d converted with timsdata-2-21-0-4. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.d converted with timsdata-2-21-0-4. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.d converted with timsdata-2-21-0-4. Will use this mzBIN file.
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 15
database_name = D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotHuman\2021-07-15-decoys-reviewed-contam-UP000005640.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 = 0
write_calibrated_mzml = 0
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 = 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
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
activation_types = all
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
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.10 Da.
318306494 fragments to be searched in 1 slices (4.74 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 3.12 s
	001. 240411ko02SUDHL6_RAD21_IP_1_1_438.mzBIN 29.9 s | deisotoping 1.4 s
		[progress: 174622/174622 (100%) - 38548 spectra/s] 4.5s | postprocessing 0.5 s
	002. 240411ko03FL18_RAD21_IP_1_1_439.mzBIN 27.2 s | deisotoping 1.2 s
		[progress: 190264/190264 (100%) - 53626 spectra/s] 3.5s | postprocessing 0.3 s
	003. 240411ko04OCILy7_RAD21_IP_1_1_440.mzBIN 27.2 s | deisotoping 1.8 s
		[progress: 199638/199638 (100%) - 47096 spectra/s] 4.2s | postprocessing 0.3 s
	004. 240411ko05KIS1_RAD21_IP_1_1_441.mzBIN 29.5 s | deisotoping 2.3 s
		[progress: 201532/201532 (100%) - 53514 spectra/s] 3.8s | postprocessing 0.3 s
***************************FIRST SEARCH DONE IN 2.447 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |   0.07   4.44 |  -0.07   4.07 |  -0.92   7.59 |  -0.10   7.56  
 002 |   0.18   4.19 |   0.06   3.83 |  -0.90   7.58 |  -0.17   7.54  
 003 |   0.15   4.18 |  -0.13   3.97 |  -0.79   7.49 |  -0.27   7.48  
 004 |   0.56   4.37 |  -0.05   4.06 |  -0.58   7.61 |  -0.11   7.56  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count | skip  | skip  | skip  | skip  |  19711|  19089| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |  18952|  19441|  19480|  19711|  19860|  19941
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |  19292
-------|-------
-------|-------
 Rm P. |    0  
-------|-------
 Count |  18318
-------|-------
New fragment_mass_tolerance = 20 PPM
New use_topN_peaks = 100
New minimum_ratio = 0.010000
New intensity_transform = 0
New remove_precursor_peak = 1
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 2.029 MIN*********

************************************MAIN SEARCH************************************
Checking database...
Parameters:
num_threads = 15
database_name = D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotHuman\2021-07-15-decoys-reviewed-contam-UP000005640.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 = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1/2/3
mass_offsets = 0.0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 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
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 100
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
activation_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
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.10 Da.
318306494 fragments to be searched in 1 slices (4.74 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 2.25 s
	001. 240411ko02SUDHL6_RAD21_IP_1_1_438.mzBIN_calibrated 3.2 s
		[progress: 172591/172591 (100%) - 47717 spectra/s] 3.6s | remapping alternative proteins and postprocessing 4.2 s
	002. 240411ko03FL18_RAD21_IP_1_1_439.mzBIN_calibrated 3.2 s
		[progress: 187539/187539 (100%) - 51864 spectra/s] 3.6s | remapping alternative proteins and postprocessing 3.3 s
	003. 240411ko04OCILy7_RAD21_IP_1_1_440.mzBIN_calibrated 3.3 s
		[progress: 196410/196410 (100%) - 52742 spectra/s] 3.7s | remapping alternative proteins and postprocessing 2.3 s
	004. 240411ko05KIS1_RAD21_IP_1_1_441.mzBIN_calibrated 3.4 s
		[progress: 198524/198524 (100%) - 52133 spectra/s] 3.8s | remapping alternative proteins and postprocessing 2.8 s
***************************MAIN SEARCH DONE IN 0.759 MIN***************************

*******************************TOTAL TIME 5.236 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.pepXML J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438\240411ko02SUDHL6_RAD21_IP_1_1_438.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.pin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438\240411ko02SUDHL6_RAD21_IP_1_1_438.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.pepXML J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\240411ko03FL18_RAD21_IP_1_1_439.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.pin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\240411ko03FL18_RAD21_IP_1_1_439.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.pepXML J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440\240411ko04OCILy7_RAD21_IP_1_1_440.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.pin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440\240411ko04OCILy7_RAD21_IP_1_1_440.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.pepXML J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441\240411ko05KIS1_RAD21_IP_1_1_441.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.pin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441\240411ko05KIS1_RAD21_IP_1_1_441.pin
Process 'MSFragger move pin' finished, exit code: 0
MSBooster [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
java -Xmx72G -cp "D:\Applications\FragPipe-20.0\fragpipe\tools\msbooster-1.1.11.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar" Features.MainClass --paramsList J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\msbooster_params.txt
MSBooster v1.1.11
Using 15 threads
Generating input file for DIA-NN
61647 unique peptides from 148576 PSMs
Writing DIA-NN input file
Diann input file generation took 967 milliseconds
Input file at  J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\spectraRT.tsv
61647 unique peptides from 148576 PSMs
createFull input file generation took 407 milliseconds
Input file at  J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\spectraRT_full.tsv
Generating DIA-NN predictions
D:\Applications\FragPipe-20.0\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\spectraRT.tsv --predict --threads 15 --strip-unknown-mods --mod TMT,229.1629 --predict-n-frag 100
DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks)
Compiled on Sep 15 2022 18:28:57
Current date and time: Wed Jan 22 16:34:31 2025
CPU: GenuineIntel Intel(R) Core(TM) i7-7820X CPU @ 3.60GHz
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 16
Predicted spectra will be saved in a binary format
Thread number set to 15
DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option
Modification TMT with mass delta 229.163 added to the list of recognised modifications for spectral library-based search
Deep learning predictor will predict 100 fragments
Cannot find a UniMod modification match for TMT: 73.0618 minimal mass discrepancy; using the original modificaiton name

0 files will be processed
[0:00] Loading spectral library J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\spectraRT.tsv
[0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 61647 precursors in 58553 elution groups.
[0:00] Encoding peptides for spectra and RTs prediction
[0:00] Predicting spectra and IMs
[0:12] Predicting RTs
[0:17] Decoding predicted spectra and IMs
[0:18] Decoding RTs
[0:18] Saving the list of predictions to J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\spectraRT.predicted.bin
Finished
Done generating DIA-NN predictions
Model running took 22203 milliseconds
Generating edited pin with following features: [unweightedSpectralEntropy, deltaRTLOESS]
Loading predicted spectra
Processing 240411ko02SUDHL6_RAD21_IP_1_1_438_uncalibrated.mzML
RT regression using 1249 PSMs
Edited pin file at J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438\240411ko02SUDHL6_RAD21_IP_1_1_438_edited.pin
Processing 240411ko03FL18_RAD21_IP_1_1_439_uncalibrated.mzML
RT regression using 1621 PSMs
Edited pin file at J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\240411ko03FL18_RAD21_IP_1_1_439_edited.pin
Processing 240411ko04OCILy7_RAD21_IP_1_1_440_uncalibrated.mzML
RT regression using 1220 PSMs
Edited pin file at J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440\240411ko04OCILy7_RAD21_IP_1_1_440_edited.pin
Processing 240411ko05KIS1_RAD21_IP_1_1_441_uncalibrated.mzML
RT regression using 1400 PSMs
Edited pin file at J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441\240411ko05KIS1_RAD21_IP_1_1_441_edited.pin
Done in 32772 ms
Process 'MSBooster' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_target_psms.tsv --decoy-results-psms 240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240411ko02SUDHL6_RAD21_IP_1_1_438_edited.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_target_psms.tsv --decoy-results-psms 240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240411ko02SUDHL6_RAD21_IP_1_1_438_edited.pin
Started Wed Jan 22 16:35:26 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 240411ko02SUDHL6_RAD21_IP_1_1_438_edited.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 34329 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 28090 positives and 6239 negatives, size ratio=4.50232 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 26 as initial direction. Could separate 11562 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 26 as initial direction. Could separate 11547 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 26 as initial direction. Could separate 11682 training set positives with q<0.01 in that direction.
Found 17410 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4870 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 21002 PSMs with q<0.01
Iteration 2:	Estimated 21324 PSMs with q<0.01
Iteration 3:	Estimated 21367 PSMs with q<0.01
Iteration 4:	Estimated 21385 PSMs with q<0.01
Iteration 5:	Estimated 21390 PSMs with q<0.01
Iteration 6:	Estimated 21394 PSMs with q<0.01
Iteration 7:	Estimated 21392 PSMs with q<0.01
Iteration 8:	Estimated 21394 PSMs with q<0.01
Iteration 9:	Estimated 21393 PSMs with q<0.01
Iteration 10:	Estimated 21391 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
-0.2917	-0.2777	-0.3548	abs_ppm
-0.2381	-0.3692	-0.3355	isotope_errors
-0.4336	-0.3791	-0.5077	log10_evalue
 1.1325	 1.2877	 1.2638	hyperscore
 0.6910	 0.7633	 0.8593	delta_hyperscore
 0.6467	 0.8452	 0.9814	matched_ion_num
-0.6998	-0.8142	-0.8004	complementary_ions
-0.3245	-0.2494	-0.3789	ion_series
-0.1690	-0.1236	-0.2551	weighted_average_abs_fragment_ppm
 0.2805	 0.3598	 0.3016	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1335	-0.1213	-0.2087	nmc
 0.0234	 0.0655	 0.0229	charge_1
 0.1084	 0.0754	 0.1011	charge_2
-0.0156	 0.0081	-0.0256	charge_3
-0.1457	-0.1235	-0.1284	charge_4
-0.0947	-0.1166	-0.0571	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
-0.0131	-0.0093	 0.0263	15.9949M
 1.2257	 1.3723	 1.3175	unweighted_spectral_entropy
-0.5281	-0.4878	-0.6115	delta_RT_loess
 0.7063	 0.8258	 1.3375	m0
Found 21372 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 28090 target PSMs and 6239 decoy PSMs.
Calculating q values.
Final list yields 21377 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 4.9230 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240411ko04OCILy7_RAD21_IP_1_1_440_percolator_target_psms.tsv --decoy-results-psms 240411ko04OCILy7_RAD21_IP_1_1_440_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240411ko04OCILy7_RAD21_IP_1_1_440_edited.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240411ko04OCILy7_RAD21_IP_1_1_440_percolator_target_psms.tsv --decoy-results-psms 240411ko04OCILy7_RAD21_IP_1_1_440_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240411ko04OCILy7_RAD21_IP_1_1_440_edited.pin
Started Wed Jan 22 16:35:32 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 240411ko04OCILy7_RAD21_IP_1_1_440_edited.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 35825 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 27980 positives and 7845 negatives, size ratio=3.5666 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 10438 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 26 as initial direction. Could separate 10303 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 10456 training set positives with q<0.01 in that direction.
Found 15244 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.5260 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 19236 PSMs with q<0.01
Iteration 2:	Estimated 19574 PSMs with q<0.01
Iteration 3:	Estimated 19639 PSMs with q<0.01
Iteration 4:	Estimated 19667 PSMs with q<0.01
Iteration 5:	Estimated 19680 PSMs with q<0.01
Iteration 6:	Estimated 19680 PSMs with q<0.01
Iteration 7:	Estimated 19680 PSMs with q<0.01
Iteration 8:	Estimated 19683 PSMs with q<0.01
Iteration 9:	Estimated 19684 PSMs with q<0.01
Iteration 10:	Estimated 19684 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
-0.3125	-0.2841	-0.3395	abs_ppm
-0.3363	-0.2924	-0.3202	isotope_errors
-1.1398	-0.6710	-0.8112	log10_evalue
 0.6432	 0.8582	 0.7676	hyperscore
 0.6298	 0.6520	 0.7201	delta_hyperscore
 0.7364	 0.7338	 0.7565	matched_ion_num
-0.8027	-0.7177	-0.7166	complementary_ions
-0.2514	-0.1650	-0.1933	ion_series
-0.2202	-0.1981	-0.1752	weighted_average_abs_fragment_ppm
 0.3450	 0.3936	 0.3348	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1282	-0.1647	-0.1131	nmc
-0.0104	-0.0121	 0.0216	charge_1
 0.1282	 0.1313	 0.1291	charge_2
 0.0203	-0.0341	-0.0159	charge_3
-0.2043	-0.1302	-0.1503	charge_4
-0.1366	-0.1065	-0.1340	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
-0.0167	-0.0243	-0.0211	15.9949M
 1.4452	 1.3545	 1.3264	unweighted_spectral_entropy
-0.5404	-0.5143	-0.4821	delta_RT_loess
 0.5653	 0.3210	 0.2793	m0
Found 19588 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 27980 target PSMs and 7845 decoy PSMs.
Calculating q values.
Final list yields 19588 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.1530 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240411ko05KIS1_RAD21_IP_1_1_441_percolator_target_psms.tsv --decoy-results-psms 240411ko05KIS1_RAD21_IP_1_1_441_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240411ko05KIS1_RAD21_IP_1_1_441_edited.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240411ko05KIS1_RAD21_IP_1_1_441_percolator_target_psms.tsv --decoy-results-psms 240411ko05KIS1_RAD21_IP_1_1_441_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240411ko05KIS1_RAD21_IP_1_1_441_edited.pin
Started Wed Jan 22 16:35:38 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 240411ko05KIS1_RAD21_IP_1_1_441_edited.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 37529 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 29496 positives and 8033 negatives, size ratio=3.67185 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 10931 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 10952 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 11152 training set positives with q<0.01 in that direction.
Found 16397 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.5150 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 20632 PSMs with q<0.01
Iteration 2:	Estimated 20984 PSMs with q<0.01
Iteration 3:	Estimated 21020 PSMs with q<0.01
Iteration 4:	Estimated 21053 PSMs with q<0.01
Iteration 5:	Estimated 21058 PSMs with q<0.01
Iteration 6:	Estimated 21062 PSMs with q<0.01
Iteration 7:	Estimated 21067 PSMs with q<0.01
Iteration 8:	Estimated 21070 PSMs with q<0.01
Iteration 9:	Estimated 21070 PSMs with q<0.01
Iteration 10:	Estimated 21070 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
-0.2825	-0.2477	-0.2984	abs_ppm
-0.2887	-0.2835	-0.2419	isotope_errors
-0.5448	-0.5187	-0.5908	log10_evalue
 1.0176	 0.8142	 0.8852	hyperscore
 0.6251	 0.7456	 0.6545	delta_hyperscore
 0.8434	 1.1621	 0.8222	matched_ion_num
-0.7630	-0.7243	-0.6583	complementary_ions
-0.1294	-0.1309	-0.1740	ion_series
-0.2057	-0.2260	-0.2339	weighted_average_abs_fragment_ppm
 0.3705	 0.3747	 0.3076	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.2173	-0.2821	-0.2688	nmc
-0.0086	-0.0073	-0.0107	charge_1
 0.1179	 0.1307	 0.1039	charge_2
 0.0171	 0.0231	 0.0295	charge_3
-0.1940	-0.2096	-0.2220	charge_4
-0.1098	-0.1522	-0.0345	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
 0.0106	-0.0354	-0.0338	15.9949M
 1.2988	 1.3085	 1.2634	unweighted_spectral_entropy
-0.6990	-0.7212	-0.5505	delta_RT_loess
 0.6948	 0.8024	 0.7299	m0
Found 20992 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 29496 target PSMs and 8033 decoy PSMs.
Calculating q values.
Final list yields 20992 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 4.9370 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240411ko03FL18_RAD21_IP_1_1_439_percolator_target_psms.tsv --decoy-results-psms 240411ko03FL18_RAD21_IP_1_1_439_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240411ko03FL18_RAD21_IP_1_1_439_edited.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240411ko03FL18_RAD21_IP_1_1_439_percolator_target_psms.tsv --decoy-results-psms 240411ko03FL18_RAD21_IP_1_1_439_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240411ko03FL18_RAD21_IP_1_1_439_edited.pin
Started Wed Jan 22 16:35:44 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 240411ko03FL18_RAD21_IP_1_1_439_edited.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 40893 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 33116 positives and 7777 negatives, size ratio=4.2582 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 26 as initial direction. Could separate 13758 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 26 as initial direction. Could separate 13438 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 26 as initial direction. Could separate 13860 training set positives with q<0.01 in that direction.
Found 20316 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.5680 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 24470 PSMs with q<0.01
Iteration 2:	Estimated 24931 PSMs with q<0.01
Iteration 3:	Estimated 24986 PSMs with q<0.01
Iteration 4:	Estimated 25022 PSMs with q<0.01
Iteration 5:	Estimated 25037 PSMs with q<0.01
Iteration 6:	Estimated 25048 PSMs with q<0.01
Iteration 7:	Estimated 25042 PSMs with q<0.01
Iteration 8:	Estimated 25045 PSMs with q<0.01
Iteration 9:	Estimated 25044 PSMs with q<0.01
Iteration 10:	Estimated 25046 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
-0.1973	-0.2799	-0.2368	abs_ppm
-0.3129	-0.3132	-0.3029	isotope_errors
-0.5904	-0.4814	-0.5778	log10_evalue
 0.7520	 0.5961	 0.6179	hyperscore
 0.5797	 0.7144	 0.6863	delta_hyperscore
 0.7738	 0.8093	 0.6765	matched_ion_num
-0.5893	-0.6483	-0.5804	complementary_ions
-0.1172	-0.0719	-0.0998	ion_series
-0.1607	-0.1083	-0.1318	weighted_average_abs_fragment_ppm
 0.3439	 0.3991	 0.4096	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1200	-0.1268	-0.0852	nmc
 0.0260	 0.0277	 0.0213	charge_1
 0.0942	 0.1245	 0.1224	charge_2
 0.0132	-0.0440	 0.0016	charge_3
-0.1638	-0.1136	-0.1880	charge_4
-0.1136	-0.1256	-0.1339	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
-0.0123	-0.0043	 0.0133	15.9949M
 1.2775	 1.3455	 1.4248	unweighted_spectral_entropy
-0.5796	-0.5532	-0.4990	delta_RT_loess
 0.9890	 0.9208	 0.9012	m0
Found 25015 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 33116 target PSMs and 7777 decoy PSMs.
Calculating q values.
Final list yields 25028 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 6.3380 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240411ko02SUDHL6_RAD21_IP_1_1_438.pin 240411ko02SUDHL6_RAD21_IP_1_1_438 240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_target_psms.tsv 240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_decoy_psms.tsv interact-240411ko02SUDHL6_RAD21_IP_1_1_438 DDA 0.5 J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438\240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438\240411ko02SUDHL6_RAD21_IP_1_1_438_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240411ko04OCILy7_RAD21_IP_1_1_440.pin 240411ko04OCILy7_RAD21_IP_1_1_440 240411ko04OCILy7_RAD21_IP_1_1_440_percolator_target_psms.tsv 240411ko04OCILy7_RAD21_IP_1_1_440_percolator_decoy_psms.tsv interact-240411ko04OCILy7_RAD21_IP_1_1_440 DDA 0.5 J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440\240411ko04OCILy7_RAD21_IP_1_1_440_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440\240411ko04OCILy7_RAD21_IP_1_1_440_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240411ko05KIS1_RAD21_IP_1_1_441.pin 240411ko05KIS1_RAD21_IP_1_1_441 240411ko05KIS1_RAD21_IP_1_1_441_percolator_target_psms.tsv 240411ko05KIS1_RAD21_IP_1_1_441_percolator_decoy_psms.tsv interact-240411ko05KIS1_RAD21_IP_1_1_441 DDA 0.5 J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441\240411ko05KIS1_RAD21_IP_1_1_441_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441\240411ko05KIS1_RAD21_IP_1_1_441_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240411ko03FL18_RAD21_IP_1_1_439.pin 240411ko03FL18_RAD21_IP_1_1_439 240411ko03FL18_RAD21_IP_1_1_439_percolator_target_psms.tsv 240411ko03FL18_RAD21_IP_1_1_439_percolator_decoy_psms.tsv interact-240411ko03FL18_RAD21_IP_1_1_439 DDA 0.5 J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\240411ko03FL18_RAD21_IP_1_1_439_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\240411ko03FL18_RAD21_IP_1_1_439_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
ProteinProphet [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\filelist_proteinprophet.txt
INFO[16:36:02] Executing ProteinProphet  v5.0.0             
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 J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438\interact-240411ko02SUDHL6_RAD21_IP_1_1_438.pep.xml...
...read in 14 1+, 14121 2+, 7241 3+, 785 4+, 100 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\interact-240411ko03FL18_RAD21_IP_1_1_439.pep.xml...
...read in 7 1+, 17045 2+, 8021 3+, 964 4+, 81 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440\interact-240411ko04OCILy7_RAD21_IP_1_1_440.pep.xml...
...read in 5 1+, 13650 2+, 6347 3+, 743 4+, 72 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441\interact-240411ko05KIS1_RAD21_IP_1_1_441.pep.xml...
...read in 4 1+, 14298 2+, 6923 3+, 837 4+, 125 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 18228 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotHuman\2021-07-15-decoys-reviewed-contam-UP000005640.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:........WARNING: Found the following zero-mass residues in protein entry sp|O60613|SEP15_HUMAN : U
MVAMAAGPSGCLVPAFGLRLLLATVLQAVSAFGAEFSSEACRELGFSSNLLCSSCDLLGQFNLLQLDPDCRGCCQEEAQFETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEELSILKWNTDSVEEFLSEKLERI
.:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:..WARNING: Found the following zero-mass residues in protein entry sp|Q86VQ6|TRXR3_HUMAN : U
 
.......:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:....  Total: 40840
Computing degenerate peptides for 5056 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 5218 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 5218 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 5218 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 5218 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 5218 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 5218 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 5218 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=2.05247e-05, db_size=45492565
Computing MU for 5218 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO[16:36:08] Done                                         
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe database --annotate D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotHuman\2021-07-15-decoys-reviewed-contam-UP000005640.fas --prefix rev_
INFO[16:36:09] Executing Database  v5.0.0                   
INFO[16:36:09] Annotating the database                      
INFO[16:36:09] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438 --protxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\combined.prot.xml --razor
INFO[16:36:09] Executing Filter  v5.0.0                     
INFO[16:36:09] Processing peptide identification files      
INFO[16:36:09] Parsing J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438\interact-240411ko02SUDHL6_RAD21_IP_1_1_438.pep.xml 
INFO[16:36:10] 1+ Charge profile                             decoy=4 target=10
INFO[16:36:10] 2+ Charge profile                             decoy=255 target=13866
INFO[16:36:10] 3+ Charge profile                             decoy=138 target=7103
INFO[16:36:10] 4+ Charge profile                             decoy=25 target=760
INFO[16:36:10] 5+ Charge profile                             decoy=3 target=97
INFO[16:36:10] 6+ Charge profile                             decoy=0 target=0
INFO[16:36:10] Database search results                       ions=9797 peptides=8098 psms=22261
INFO[16:36:10] Converged to 1.00 % FDR with 21381 PSMs       decoy=213 threshold=0.725436 total=21594
INFO[16:36:10] Converged to 0.99 % FDR with 7282 Peptides    decoy=72 threshold=0.90715 total=7354
INFO[16:36:10] Converged to 0.99 % FDR with 8992 Ions        decoy=89 threshold=0.876871 total=9081
INFO[16:36:10] Protein inference results                     decoy=1346 target=3227
INFO[16:36:10] Converged to 0.96 % FDR with 1668 Proteins    decoy=16 threshold=0.9922 total=1684
INFO[16:36:10] Applying sequential FDR estimation            ions=8998 peptides=7325 psms=21181
INFO[16:36:10] Converged to 0.07 % FDR with 21167 PSMs       decoy=14 threshold=0.725436 total=21181
INFO[16:36:10] Converged to 0.15 % FDR with 7314 Peptides    decoy=11 threshold=0.729314 total=7325
INFO[16:36:10] Converged to 0.12 % FDR with 8987 Ions        decoy=11 threshold=0.729314 total=8998
INFO[16:36:10] Post processing identifications              
INFO[16:36:11] Assigning protein identifications to layers  
INFO[16:36:13] Processing protein inference                 
INFO[16:36:13] Synchronizing PSMs and proteins              
INFO[16:36:13] Final report numbers after FDR filtering, and post-processing  ions=8987 peptides=7314 proteins=1244 psms=21167
INFO[16:36:13] Saving                                       
INFO[16:36:13] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439 --protxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438 --razor
INFO[16:36:13] Executing Filter  v5.0.0                     
INFO[16:36:13] Fetching protein inference from J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438 
INFO[16:36:13] Processing peptide identification files      
INFO[16:36:13] Parsing J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\interact-240411ko03FL18_RAD21_IP_1_1_439.pep.xml 
INFO[16:36:15] 1+ Charge profile                             decoy=3 target=4
INFO[16:36:15] 2+ Charge profile                             decoy=305 target=16740
INFO[16:36:15] 3+ Charge profile                             decoy=143 target=7878
INFO[16:36:15] 4+ Charge profile                             decoy=31 target=933
INFO[16:36:15] 5+ Charge profile                             decoy=6 target=75
INFO[16:36:15] 6+ Charge profile                             decoy=0 target=0
INFO[16:36:15] Database search results                       ions=11951 peptides=9933 psms=26118
INFO[16:36:15] Converged to 1.00 % FDR with 25034 PSMs       decoy=250 threshold=0.731449 total=25284
INFO[16:36:15] Converged to 0.99 % FDR with 8852 Peptides    decoy=88 threshold=0.920576 total=8940
INFO[16:36:15] Converged to 0.99 % FDR with 10857 Ions       decoy=108 threshold=0.891016 total=10965
INFO[16:36:15] Protein inference results                     decoy=1346 target=3227
INFO[16:36:15] Converged to 0.96 % FDR with 1668 Proteins    decoy=16 threshold=0.9922 total=1684
INFO[16:36:15] Applying sequential FDR estimation            ions=10926 peptides=8940 psms=24757
INFO[16:36:15] Converged to 0.09 % FDR with 24735 PSMs       decoy=22 threshold=0.731449 total=24757
INFO[16:36:15] Converged to 0.10 % FDR with 8931 Peptides    decoy=9 threshold=0.731449 total=8940
INFO[16:36:15] Converged to 0.08 % FDR with 10917 Ions       decoy=9 threshold=0.731449 total=10926
INFO[16:36:15] Post processing identifications              
INFO[16:36:15] Assigning protein identifications to layers  
INFO[16:36:17] Processing protein inference                 
INFO[16:36:18] Synchronizing PSMs and proteins              
INFO[16:36:18] Final report numbers after FDR filtering, and post-processing  ions=10917 peptides=8931 proteins=1425 psms=24735
INFO[16:36:18] Saving                                       
INFO[16:36:18] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440 --protxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438 --razor
INFO[16:36:18] Executing Filter  v5.0.0                     
INFO[16:36:18] Fetching protein inference from J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438 
INFO[16:36:18] Processing peptide identification files      
INFO[16:36:18] Parsing J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440\interact-240411ko04OCILy7_RAD21_IP_1_1_440.pep.xml 
INFO[16:36:19] 1+ Charge profile                             decoy=1 target=4
INFO[16:36:19] 2+ Charge profile                             decoy=291 target=13359
INFO[16:36:19] 3+ Charge profile                             decoy=173 target=6174
INFO[16:36:19] 4+ Charge profile                             decoy=32 target=711
INFO[16:36:19] 5+ Charge profile                             decoy=2 target=70
INFO[16:36:19] 6+ Charge profile                             decoy=0 target=0
INFO[16:36:19] Database search results                       ions=9178 peptides=7538 psms=20817
INFO[16:36:19] Converged to 1.00 % FDR with 19588 PSMs       decoy=195 threshold=0.780762 total=19783
INFO[16:36:19] Converged to 1.00 % FDR with 6525 Peptides    decoy=65 threshold=0.924002 total=6590
INFO[16:36:19] Converged to 1.00 % FDR with 8125 Ions        decoy=81 threshold=0.899915 total=8206
INFO[16:36:19] Protein inference results                     decoy=1346 target=3227
INFO[16:36:19] Converged to 0.96 % FDR with 1668 Proteins    decoy=16 threshold=0.9922 total=1684
INFO[16:36:19] Applying sequential FDR estimation            ions=8209 peptides=6621 psms=19423
INFO[16:36:19] Converged to 0.05 % FDR with 19414 PSMs       decoy=9 threshold=0.782114 total=19423
INFO[16:36:19] Converged to 0.09 % FDR with 6615 Peptides    decoy=6 threshold=0.784088 total=6621
INFO[16:36:19] Converged to 0.07 % FDR with 8203 Ions        decoy=6 threshold=0.78362 total=8209
INFO[16:36:19] Post processing identifications              
INFO[16:36:20] Assigning protein identifications to layers  
INFO[16:36:21] Processing protein inference                 
INFO[16:36:21] Synchronizing PSMs and proteins              
INFO[16:36:22] Final report numbers after FDR filtering, and post-processing  ions=8203 peptides=6615 proteins=1137 psms=19414
INFO[16:36:22] Saving                                       
INFO[16:36:22] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441 --protxml J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438 --razor
INFO[16:36:22] Executing Filter  v5.0.0                     
INFO[16:36:22] Fetching protein inference from J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438 
INFO[16:36:22] Processing peptide identification files      
INFO[16:36:22] Parsing J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441\interact-240411ko05KIS1_RAD21_IP_1_1_441.pep.xml 
INFO[16:36:23] 1+ Charge profile                             decoy=1 target=3
INFO[16:36:23] 2+ Charge profile                             decoy=287 target=14011
INFO[16:36:23] 3+ Charge profile                             decoy=169 target=6754
INFO[16:36:23] 4+ Charge profile                             decoy=25 target=812
INFO[16:36:23] 5+ Charge profile                             decoy=5 target=120
INFO[16:36:23] 6+ Charge profile                             decoy=0 target=0
INFO[16:36:23] Database search results                       ions=9891 peptides=8072 psms=22187
INFO[16:36:23] Converged to 1.00 % FDR with 21003 PSMs       decoy=210 threshold=0.771085 total=21213
INFO[16:36:23] Converged to 0.99 % FDR with 7087 Peptides    decoy=70 threshold=0.915282 total=7157
INFO[16:36:23] Converged to 0.99 % FDR with 8872 Ions        decoy=88 threshold=0.899234 total=8960
INFO[16:36:23] Protein inference results                     decoy=1346 target=3227
INFO[16:36:23] Converged to 0.96 % FDR with 1668 Proteins    decoy=16 threshold=0.9922 total=1684
INFO[16:36:23] Applying sequential FDR estimation            ions=8972 peptides=7191 psms=20834
INFO[16:36:23] Converged to 0.06 % FDR with 20821 PSMs       decoy=13 threshold=0.771085 total=20834
INFO[16:36:23] Converged to 0.13 % FDR with 7182 Peptides    decoy=9 threshold=0.771085 total=7191
INFO[16:36:23] Converged to 0.10 % FDR with 8963 Ions        decoy=9 threshold=0.771085 total=8972
INFO[16:36:23] Post processing identifications              
INFO[16:36:24] Assigning protein identifications to layers  
INFO[16:36:26] Processing protein inference                 
INFO[16:36:26] Synchronizing PSMs and proteins              
INFO[16:36:26] Final report numbers after FDR filtering, and post-processing  ions=8963 peptides=7182 proteins=1155 psms=20821
INFO[16:36:26] Saving                                       
INFO[16:36:26] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:36:26] Executing Report  v5.0.0                     
INFO[16:36:26] Creating reports                             
INFO[16:36:27] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:36:27] Executing Report  v5.0.0                     
INFO[16:36:27] Creating reports                             
INFO[16:36:27] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:36:27] Executing Report  v5.0.0                     
INFO[16:36:27] Creating reports                             
INFO[16:36:27] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:36:28] Executing Report  v5.0.0                     
INFO[16:36:28] Creating reports                             
INFO[16:36:28] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:36:28] Executing Workspace  v5.0.0                  
INFO[16:36:28] Removing workspace                           
INFO[16:36:28] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:36:29] Executing Workspace  v5.0.0                  
INFO[16:36:29] Removing workspace                           
INFO[16:36:29] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:36:29] Executing Workspace  v5.0.0                  
INFO[16:36:29] Removing workspace                           
INFO[16:36:29] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:36:30] Executing Workspace  v5.0.0                  
INFO[16:36:30] Removing workspace                           
INFO[16:36:30] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:36:30] Executing Workspace  v5.0.0                  
INFO[16:36:30] Removing workspace                           
INFO[16:36:30] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
IonQuant [Work dir: J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ]
java -Xmx72G -Dlibs.bruker.dir="D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\bruker" -Dlibs.thermo.dir="D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\thermo" -cp "D:\Applications\FragPipe-20.0\fragpipe\tools\jfreechart-1.5.3.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\IonQuant-1.9.8.jar" ionquant.IonQuant --threads 15 --ionmobility 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 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\filelist_ionquant.txt --modlist J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\modmasses_ionquant.txt
IonQuant version IonQuant-1.9.8
Batmass-IO version 1.28.12
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
System OS: Windows 11, Architecture: AMD64
Java Info: 21.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 72 GB memory
2025-01-22 16:36:31 [INFO] - Collecting variable modifications from all psm.tsv files...
2025-01-22 16:36:31 [INFO] - Loading and indexing all psm.tsv files...
2025-01-22 16:36:33 [INFO] - Parameters:
2025-01-22 16:36:33 [INFO] - threads = 15
2025-01-22 16:36:33 [INFO] - mztol = 10.0
2025-01-22 16:36:33 [INFO] - rttol = 0.4
2025-01-22 16:36:33 [INFO] - imtol = 0.05
2025-01-22 16:36:33 [INFO] - minisotopes = 2
2025-01-22 16:36:33 [INFO] - minscans = 3
2025-01-22 16:36:33 [INFO] - psm = J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko02SUDHL6_RAD21_IP_1_1_438\psm.tsv
2025-01-22 16:36:33 [INFO] - psm = J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko03FL18_RAD21_IP_1_1_439\psm.tsv
2025-01-22 16:36:33 [INFO] - psm = J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko04OCILy7_RAD21_IP_1_1_440\psm.tsv
2025-01-22 16:36:33 [INFO] - psm = J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\240411ko05KIS1_RAD21_IP_1_1_441\psm.tsv
2025-01-22 16:36:33 [INFO] - multidir = J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\.\
2025-01-22 16:36:33 [INFO] - excludemods = 
2025-01-22 16:36:33 [INFO] - minions = 2
2025-01-22 16:36:33 [INFO] - maxlfq = 1
2025-01-22 16:36:33 [INFO] - ibaq = 0
2025-01-22 16:36:33 [INFO] - normalization = 1
2025-01-22 16:36:33 [INFO] - minexps = 1
2025-01-22 16:36:33 [INFO] - minfreq = 0.0
2025-01-22 16:36:33 [INFO] - tp = 0
2025-01-22 16:36:33 [INFO] - mbr = 1
2025-01-22 16:36:33 [INFO] - mbrrttol = 1.0
2025-01-22 16:36:33 [INFO] - mbrimtol = 0.05
2025-01-22 16:36:33 [INFO] - mbrtoprun = 10
2025-01-22 16:36:33 [INFO] - mbrmincorr = 0.0
2025-01-22 16:36:33 [INFO] - ionmobility = 1
2025-01-22 16:36:33 [INFO] - ionfdr = 0.01
2025-01-22 16:36:33 [INFO] - peptidefdr = 1.0
2025-01-22 16:36:33 [INFO] - proteinfdr = 1.0
2025-01-22 16:36:33 [INFO] - light = 
2025-01-22 16:36:33 [INFO] - medium = 
2025-01-22 16:36:33 [INFO] - heavy = 
2025-01-22 16:36:33 [INFO] - requantify = 0
2025-01-22 16:36:33 [INFO] - writeindex = 0
2025-01-22 16:36:33 [INFO] - locprob = 0.75
2025-01-22 16:36:33 [INFO] - uniqueness = 0
2025-01-22 16:36:33 [INFO] - filelist = J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\filelist_ionquant.txt
2025-01-22 16:36:33 [INFO] - specdir = J:\MSFragger_process\Saitou-lab\240411ko
2025-01-22 16:36:33 [INFO] - modlist = J:\MSFragger_process\Saitou-lab\240411ko\MSFragger_iBAQ\modmasses_ionquant.txt
2025-01-22 16:36:33 [INFO] - mod masses:
2025-01-22 16:36:33 [INFO] - 15.9949
2025-01-22 16:36:33 [INFO] - 42.0106
2025-01-22 16:36:33 [INFO] - 57.02146
2025-01-22 16:36:33 [INFO] - Checking J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.d...
2025-01-22 16:36:34 [INFO] - Checking J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.d...
2025-01-22 16:36:34 [INFO] - Checking J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.d...
2025-01-22 16:36:34 [INFO] - Checking J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.d...
2025-01-22 16:36:34 [INFO] - Loading J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.d...
2025-01-22 16:36:34 [INFO] - ...20%...40%...60%...80%...100%
2025-01-22 16:37:38 [INFO] - Building index...
2025-01-22 16:38:13 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.quantindex
2025-01-22 16:38:16 [INFO] - Loading 240411ko02SUDHL6_RAD21_IP_1_1_438....
2025-01-22 16:38:16 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-22 16:38:16 [INFO] - Quantifying...
2025-01-22 16:38:18 [INFO] - Loading J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.d...
2025-01-22 16:38:18 [INFO] - ...20%...40%...60%...80%...100%
2025-01-22 16:39:13 [INFO] - Building index...
2025-01-22 16:39:51 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.quantindex
2025-01-22 16:39:55 [INFO] - Loading 240411ko03FL18_RAD21_IP_1_1_439....
2025-01-22 16:39:55 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-22 16:39:55 [INFO] - Quantifying...
2025-01-22 16:39:56 [INFO] - Loading J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.d...
2025-01-22 16:39:56 [INFO] - ...20%...40%...60%...80%...100%
2025-01-22 16:40:58 [INFO] - Building index...
2025-01-22 16:41:26 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.quantindex
2025-01-22 16:41:30 [INFO] - Loading 240411ko04OCILy7_RAD21_IP_1_1_440....
2025-01-22 16:41:30 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-22 16:41:30 [INFO] - Quantifying...
2025-01-22 16:41:31 [INFO] - Loading J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.d...
2025-01-22 16:41:31 [INFO] - ...20%...40%...60%...80%...100%
2025-01-22 16:42:31 [INFO] - Building index...
2025-01-22 16:43:00 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.quantindex
2025-01-22 16:43:03 [INFO] - Loading 240411ko05KIS1_RAD21_IP_1_1_441....
2025-01-22 16:43:03 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-22 16:43:03 [INFO] - Quantifying...
2025-01-22 16:43:04 [INFO] - Updating Philosopher's tables...
2025-01-22 16:43:06 [INFO] - Matching-between-runs: 240411ko02SUDHL6_RAD21_IP_1_1_438...
2025-01-22 16:43:07 [INFO] - Calculating correlations between all other runs...
2025-01-22 16:43:07 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\240411ko\240411ko02SUDHL6_RAD21_IP_1_1_438.quantindex
2025-01-22 16:43:11 [INFO] - Transferring 240411ko03FL18_RAD21_IP_1_1_439...
2025-01-22 16:43:12 [INFO] - Transferring 240411ko04OCILy7_RAD21_IP_1_1_440...
2025-01-22 16:43:13 [INFO] - Transferring 240411ko05KIS1_RAD21_IP_1_1_441...
2025-01-22 16:43:13 [INFO] - Training LDA models for all matched features.
2025-01-22 16:43:14 [INFO] - #{+1} = 1544, #{-1} = 47, #{+2} = 4386, #{-2} = 112
2025-01-22 16:43:14 [INFO] - Standardized coefficients:
2025-01-22 16:43:14 [INFO] - log10(intensity): 0.5130810367447822
2025-01-22 16:43:14 [INFO] - log10(KL): -0.11303023636601077
2025-01-22 16:43:14 [INFO] - abs(ppm): -0.5503111779064253
2025-01-22 16:43:14 [INFO] - IM diff: -0.5417517138557245
2025-01-22 16:43:14 [INFO] - RT diff: -0.36192497589568695
2025-01-22 16:43:14 [INFO] - Fitting a mixture model...
2025-01-22 16:43:15 [INFO] - Matching-between-runs: 240411ko03FL18_RAD21_IP_1_1_439...
2025-01-22 16:43:16 [INFO] - Calculating correlations between all other runs...
2025-01-22 16:43:16 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\240411ko\240411ko03FL18_RAD21_IP_1_1_439.quantindex
2025-01-22 16:43:20 [INFO] - Transferring 240411ko02SUDHL6_RAD21_IP_1_1_438...
2025-01-22 16:43:21 [INFO] - Transferring 240411ko04OCILy7_RAD21_IP_1_1_440...
2025-01-22 16:43:22 [INFO] - Transferring 240411ko05KIS1_RAD21_IP_1_1_441...
2025-01-22 16:43:22 [INFO] - Training LDA models for all matched features.
2025-01-22 16:43:22 [INFO] - #{+1} = 1427, #{-1} = 55, #{+2} = 4981, #{-2} = 168
2025-01-22 16:43:22 [INFO] - Standardized coefficients:
2025-01-22 16:43:22 [INFO] - log10(intensity): 0.5600660386584029
2025-01-22 16:43:22 [INFO] - log10(KL): -0.11834765274589287
2025-01-22 16:43:22 [INFO] - abs(ppm): -0.5969796281727016
2025-01-22 16:43:22 [INFO] - IM diff: -0.4715859445772511
2025-01-22 16:43:22 [INFO] - RT diff: -0.305846180056228
2025-01-22 16:43:22 [INFO] - Fitting a mixture model...
2025-01-22 16:43:22 [INFO] - Matching-between-runs: 240411ko04OCILy7_RAD21_IP_1_1_440...
2025-01-22 16:43:23 [INFO] - Calculating correlations between all other runs...
2025-01-22 16:43:23 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\240411ko\240411ko04OCILy7_RAD21_IP_1_1_440.quantindex
2025-01-22 16:43:27 [INFO] - Transferring 240411ko02SUDHL6_RAD21_IP_1_1_438...
2025-01-22 16:43:28 [INFO] - Transferring 240411ko03FL18_RAD21_IP_1_1_439...
2025-01-22 16:43:29 [INFO] - Transferring 240411ko05KIS1_RAD21_IP_1_1_441...
2025-01-22 16:43:29 [INFO] - Training LDA models for all matched features.
2025-01-22 16:43:29 [INFO] - #{+1} = 1899, #{-1} = 88, #{+2} = 4335, #{-2} = 125
2025-01-22 16:43:29 [INFO] - Standardized coefficients:
2025-01-22 16:43:29 [INFO] - log10(intensity): 0.5438862995770823
2025-01-22 16:43:29 [INFO] - log10(KL): -0.3369274137311372
2025-01-22 16:43:29 [INFO] - abs(ppm): -0.5115400762133205
2025-01-22 16:43:29 [INFO] - IM diff: -0.43271172669486174
2025-01-22 16:43:29 [INFO] - RT diff: -0.37650354980692635
2025-01-22 16:43:29 [INFO] - Fitting a mixture model...
2025-01-22 16:43:30 [INFO] - Matching-between-runs: 240411ko05KIS1_RAD21_IP_1_1_441...
2025-01-22 16:43:30 [INFO] - Calculating correlations between all other runs...
2025-01-22 16:43:30 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\240411ko\240411ko05KIS1_RAD21_IP_1_1_441.quantindex
2025-01-22 16:43:35 [INFO] - Transferring 240411ko02SUDHL6_RAD21_IP_1_1_438...
2025-01-22 16:43:35 [INFO] - Transferring 240411ko03FL18_RAD21_IP_1_1_439...
2025-01-22 16:43:36 [INFO] - Transferring 240411ko04OCILy7_RAD21_IP_1_1_440...
2025-01-22 16:43:37 [INFO] - Training LDA models for all matched features.
2025-01-22 16:43:37 [INFO] - #{+1} = 1834, #{-1} = 69, #{+2} = 4362, #{-2} = 141
2025-01-22 16:43:37 [INFO] - Standardized coefficients:
2025-01-22 16:43:37 [INFO] - log10(intensity): 0.579264328725982
2025-01-22 16:43:37 [INFO] - log10(KL): -0.22057618713335858
2025-01-22 16:43:37 [INFO] - abs(ppm): -0.5372640388659503
2025-01-22 16:43:37 [INFO] - IM diff: -0.45907809409326616
2025-01-22 16:43:37 [INFO] - RT diff: -0.3411651201405095
2025-01-22 16:43:37 [INFO] - Fitting a mixture model...
2025-01-22 16:43:37 [INFO] - Estimating match-between-runs FDR...
2025-01-22 16:43:38 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.978600
2025-01-22 16:43:38 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100
2025-01-22 16:43:38 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100
2025-01-22 16:43:38 [INFO] - Updating Philosopher's tables...
2025-01-22 16:43:39 [INFO] - Combining experiments and estimating protein intensity...
2025-01-22 16:43:41 [INFO] - Done!
Process 'IonQuant' finished, exit code: 0

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

=============================================================ALL JOBS DONE IN 14.7 MINUTES=============================================================
