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: 230614ko02Stag3_IP_SUDHL6_1_1_22076
  - J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.d	DDA
  Experiment/Group: 230614ko04Stag3_IP_FL18_1_1_22078
  - J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.d	DDA
  Experiment/Group: 230614ko06Stag3_IP_OCILY7_1_1_22080
  - J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.d	DDA
  Experiment/Group: 230614ko08Stag3_IP_KIS1_1_1_22082
  - J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.d	DDA


52 commands to execute:
CheckCentroid
java -Xmx75G -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\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.d 15
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
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\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
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\d379b93f-e357-4543-8c96-095cdb4b556a
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\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\Revision\230613ko\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\d772fbe5-3594-4e01-bcb3-e6a70fefd4ad
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
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\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
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\01158a3c-97a9-40a2-99d6-57f73ffe75e7
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
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\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
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\5621e8a0-ffb5-4b56-bcdb-5ad597ed4ffc
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
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\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
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\7334489f-bd3c-4ee1-8f29-627435762529
MSFragger [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
java -jar -Dfile.encoding=UTF-8 -Xmx75G D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\fragger.params J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.d J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.d J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.d J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.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\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.pepXML J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076\230614ko02Stag3_IP_SUDHL6_1_1_22076.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\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.pin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076\230614ko02Stag3_IP_SUDHL6_1_1_22076.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\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.pepXML J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078\230614ko04Stag3_IP_FL18_1_1_22078.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\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.pin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078\230614ko04Stag3_IP_FL18_1_1_22078.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\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.pepXML J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080\230614ko06Stag3_IP_OCILY7_1_1_22080.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\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.pin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080\230614ko06Stag3_IP_OCILY7_1_1_22080.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\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.pepXML J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082\230614ko08Stag3_IP_KIS1_1_1_22082.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\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.pin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082\230614ko08Stag3_IP_KIS1_1_1_22082.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 230614ko02Stag3_IP_SUDHL6_1_1_22076_percolator_target_psms.tsv --decoy-results-psms 230614ko02Stag3_IP_SUDHL6_1_1_22076_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 230614ko02Stag3_IP_SUDHL6_1_1_22076.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 230614ko06Stag3_IP_OCILY7_1_1_22080_percolator_target_psms.tsv --decoy-results-psms 230614ko06Stag3_IP_OCILY7_1_1_22080_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 230614ko06Stag3_IP_OCILY7_1_1_22080.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 230614ko04Stag3_IP_FL18_1_1_22078_percolator_target_psms.tsv --decoy-results-psms 230614ko04Stag3_IP_FL18_1_1_22078_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 230614ko04Stag3_IP_FL18_1_1_22078.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 230614ko08Stag3_IP_KIS1_1_1_22082_percolator_target_psms.tsv --decoy-results-psms 230614ko08Stag3_IP_KIS1_1_1_22082_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 230614ko08Stag3_IP_KIS1_1_1_22082.pin
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230614ko02Stag3_IP_SUDHL6_1_1_22076.pin 230614ko02Stag3_IP_SUDHL6_1_1_22076 230614ko02Stag3_IP_SUDHL6_1_1_22076_percolator_target_psms.tsv 230614ko02Stag3_IP_SUDHL6_1_1_22076_percolator_decoy_psms.tsv interact-230614ko02Stag3_IP_SUDHL6_1_1_22076 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076_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\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076\230614ko02Stag3_IP_SUDHL6_1_1_22076_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\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076\230614ko02Stag3_IP_SUDHL6_1_1_22076_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230614ko06Stag3_IP_OCILY7_1_1_22080.pin 230614ko06Stag3_IP_OCILY7_1_1_22080 230614ko06Stag3_IP_OCILY7_1_1_22080_percolator_target_psms.tsv 230614ko06Stag3_IP_OCILY7_1_1_22080_percolator_decoy_psms.tsv interact-230614ko06Stag3_IP_OCILY7_1_1_22080 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080_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\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080\230614ko06Stag3_IP_OCILY7_1_1_22080_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\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080\230614ko06Stag3_IP_OCILY7_1_1_22080_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230614ko04Stag3_IP_FL18_1_1_22078.pin 230614ko04Stag3_IP_FL18_1_1_22078 230614ko04Stag3_IP_FL18_1_1_22078_percolator_target_psms.tsv 230614ko04Stag3_IP_FL18_1_1_22078_percolator_decoy_psms.tsv interact-230614ko04Stag3_IP_FL18_1_1_22078 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078_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\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078\230614ko04Stag3_IP_FL18_1_1_22078_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\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078\230614ko04Stag3_IP_FL18_1_1_22078_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230614ko08Stag3_IP_KIS1_1_1_22082.pin 230614ko08Stag3_IP_KIS1_1_1_22082 230614ko08Stag3_IP_KIS1_1_1_22082_percolator_target_psms.tsv 230614ko08Stag3_IP_KIS1_1_1_22082_percolator_decoy_psms.tsv interact-230614ko08Stag3_IP_KIS1_1_1_22082 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082_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\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082\230614ko08Stag3_IP_KIS1_1_1_22082_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\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082\230614ko08Stag3_IP_KIS1_1_1_22082_percolator_decoy_psms.tsv
ProteinProphet [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\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\Revision\230613ko\MSFragger_iBAQ\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
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\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076 --protxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\combined.prot.xml --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078 --protxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080 --protxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082 --protxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076 --razor
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
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\Revision\230613ko\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\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
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\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
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\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
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\Revision\230613ko\MSFragger_iBAQ]
java -Xmx75G -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 100 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 0 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\filelist_ionquant.txt --modlist J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\modmasses_ionquant.txt
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
    Cmd: [CheckCentroid], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
    Cmd: [MSFragger], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
    Cmd: [Percolator], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
    Cmd: [ProteinProphet], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
    Cmd: [PhilosopherDbAnnotate], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
    Cmd: [PhilosopherFilter], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
    Cmd: [PhilosopherReport], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
    Cmd: [IonQuant], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\230613ko\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=100
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=0
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=false
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
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=trypsin
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=-50
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=50
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.require_precursor=false
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=
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; 57.021465,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,KR,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 --prot 1.0 --ion 1.0 --pep 1.0
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\\Revision\\230613ko\\MSFragger_iBAQ
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.misc.save-sdrf=true
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=15

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx75G -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\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.d 15
Done in 0.0 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[14:03:06] Executing Workspace  v5.0.0                  
INFO[14:03:06] Removing workspace                           
WARN[14:03:06] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[14:03:06] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
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\d379b93f-e357-4543-8c96-095cdb4b556a
INFO[14:03:07] Executing Workspace  v5.0.0                  
INFO[14:03:07] Creating workspace                           
INFO[14:03:07] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[14:03:07] Executing Workspace  v5.0.0                  
INFO[14:03:07] Removing workspace                           
WARN[14:03:07] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[14:03:07] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\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\d772fbe5-3594-4e01-bcb3-e6a70fefd4ad
INFO[14:03:08] Executing Workspace  v5.0.0                  
INFO[14:03:08] Creating workspace                           
INFO[14:03:08] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[14:03:08] Executing Workspace  v5.0.0                  
INFO[14:03:08] Removing workspace                           
WARN[14:03:08] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[14:03:08] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
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\01158a3c-97a9-40a2-99d6-57f73ffe75e7
INFO[14:03:08] Executing Workspace  v5.0.0                  
INFO[14:03:08] Creating workspace                           
INFO[14:03:08] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[14:03:09] Executing Workspace  v5.0.0                  
INFO[14:03:09] Removing workspace                           
WARN[14:03:09] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[14:03:09] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
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\5621e8a0-ffb5-4b56-bcdb-5ad597ed4ffc
INFO[14:03:09] Executing Workspace  v5.0.0                  
INFO[14:03:09] Creating workspace                           
INFO[14:03:09] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[14:03:10] Executing Workspace  v5.0.0                  
INFO[14:03:10] Removing workspace                           
WARN[14:03:10] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[14:03:10] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
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\7334489f-bd3c-4ee1-8f29-627435762529
INFO[14:03:10] Executing Workspace  v5.0.0                  
INFO[14:03:10] Creating workspace                           
INFO[14:03:10] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
java -jar -Dfile.encoding=UTF-8 -Xmx75G D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\fragger.params J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.d J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.d J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.d J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.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 75 GB memory
Checking database...
Checking spectral files...
J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.d: Scans = 59773
J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.d: Scans = 58917
J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.d: Scans = 58718
J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.d: Scans = 59730
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.d converted with timsdata-2-7-0. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.d converted with timsdata-2-7-0. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.d converted with timsdata-2-7-0. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.d converted with timsdata-2-7-0. 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 = 0
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 0
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 = 57.021465
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Number of unique peptides
	of length 7: 287289
	of length 8: 278585
	of length 9: 277771
	of length 10: 262288
	of length 11: 248937
	of length 12: 238243
	of length 13: 231994
	of length 14: 217492
	of length 15: 206262
	of length 16: 192749
	of length 17: 180308
	of length 18: 173171
	of length 19: 170237
	of length 20: 152243
	of length 21: 145728
	of length 22: 136711
	of length 23: 127451
	of length 24: 120838
	of length 25: 113743
	of length 26: 105779
	of length 27: 100936
	of length 28: 96292
	of length 29: 87573
	of length 30: 83125
	of length 31: 77965
	of length 32: 73920
	of length 33: 69013
	of length 34: 64601
	of length 35: 58622
	of length 36: 56911
	of length 37: 51921
	of length 38: 48835
	of length 39: 43977
	of length 40: 41903
	of length 41: 39025
	of length 42: 35984
	of length 43: 30201
	of length 44: 24455
	of length 45: 18750
	of length 46: 12289
	of length 47: 7721
	of length 48: 4462
	of length 49: 2419
	of length 50: 1474
In total 5000193 peptides.
Generated 7800118 modified peptides.
Number of peptides with more than 5000 modification patterns: 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 2.99 s
	001. 230614ko02Stag3_IP_SUDHL6_1_1_22076.mzBIN 18.4 s | deisotoping 1.3 s
		[progress: 116529/116529 (100%) - 44992 spectra/s] 2.6s | postprocessing 0.3 s
	002. 230614ko04Stag3_IP_FL18_1_1_22078.mzBIN 10.0 s | deisotoping 0.4 s
		[progress: 91937/91937 (100%) - 67353 spectra/s] 1.4s | postprocessing 0.2 s
	003. 230614ko06Stag3_IP_OCILY7_1_1_22080.mzBIN 10.1 s | deisotoping 0.3 s
		[progress: 88116/88116 (100%) - 68096 spectra/s] 1.3s | postprocessing 0.1 s
	004. 230614ko08Stag3_IP_KIS1_1_1_22082.mzBIN 18.7 s | deisotoping 0.6 s
		[progress: 168793/168793 (100%) - 63744 spectra/s] 2.6s | postprocessing 0.2 s
***************************FIRST SEARCH DONE IN 1.386 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |  -13.66   3.96 |  -0.40   3.01 |  -11.75   7.29 |  -3.32   6.69  
 002 |  -15.60   3.36 |  -0.33   2.59 |  -12.69   6.86 |  -4.30   6.76  
 003 |  -15.76   3.30 |  -0.51   2.64 |  -12.78   6.84 |  -4.10   6.87  
 004 |  -15.63   3.14 |  -0.32   2.62 |  -12.96   6.61 |  -3.89   6.24  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count | skip  | skip  | skip  | skip  |  16655|  15834| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |  16387|  16476|  16572|  16655|  16717|  16670
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |  16912
-------|-------
-------|-------
 Rm P. |    1  
-------|-------
 Count |  17331
-------|-------
New fragment_mass_tolerance = 20 PPM
New use_topN_peaks = 125
New minimum_ratio = 0.010000
New intensity_transform = 1
New remove_precursor_peak = 1
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 1.139 MIN*********

************************************MAIN SEARCH************************************
output_format = pepXML_pin but report_alternative_proteins = 0. Change report_alternative_proteins to 1.
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 = -50.0
precursor_mass_upper = 50.0
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
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 = 125
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 1
activation_types = all
group_variable = 0
require_precursor = 0
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 = 57.021465
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Number of unique peptides
	of length 7: 287289
	of length 8: 278585
	of length 9: 277771
	of length 10: 262288
	of length 11: 248937
	of length 12: 238243
	of length 13: 231994
	of length 14: 217492
	of length 15: 206262
	of length 16: 192749
	of length 17: 180308
	of length 18: 173171
	of length 19: 170237
	of length 20: 152243
	of length 21: 145728
	of length 22: 136711
	of length 23: 127451
	of length 24: 120838
	of length 25: 113743
	of length 26: 105779
	of length 27: 100936
	of length 28: 96292
	of length 29: 87573
	of length 30: 83125
	of length 31: 77965
	of length 32: 73920
	of length 33: 69013
	of length 34: 64601
	of length 35: 58622
	of length 36: 56911
	of length 37: 51921
	of length 38: 48835
	of length 39: 43977
	of length 40: 41903
	of length 41: 39025
	of length 42: 35984
	of length 43: 30201
	of length 44: 24455
	of length 45: 18750
	of length 46: 12289
	of length 47: 7721
	of length 48: 4462
	of length 49: 2419
	of length 50: 1474
In total 5000193 peptides.
Generated 7800118 modified peptides.
Number of peptides with more than 5000 modification patterns: 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 2.03 s
	001. 230614ko02Stag3_IP_SUDHL6_1_1_22076.mzBIN_calibrated 1.1 s
		[progress: 113532/113532 (100%) - 53377 spectra/s] 2.1s | remapping alternative proteins and postprocessing 3.3 s
	002. 230614ko04Stag3_IP_FL18_1_1_22078.mzBIN_calibrated 0.9 s
		[progress: 89111/89111 (100%) - 47858 spectra/s] 1.9s | remapping alternative proteins and postprocessing 1.8 s
	003. 230614ko06Stag3_IP_OCILY7_1_1_22080.mzBIN_calibrated 0.9 s
		[progress: 85475/85475 (100%) - 48074 spectra/s] 1.8s | remapping alternative proteins and postprocessing 1.7 s
	004. 230614ko08Stag3_IP_KIS1_1_1_22082.mzBIN_calibrated 2.1 s
		[progress: 164823/164823 (100%) - 46312 spectra/s] 3.6s | remapping alternative proteins and postprocessing 3.2 s
***************************MAIN SEARCH DONE IN 0.554 MIN***************************

*******************************TOTAL TIME 3.079 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\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.pepXML J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076\230614ko02Stag3_IP_SUDHL6_1_1_22076.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\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.pin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076\230614ko02Stag3_IP_SUDHL6_1_1_22076.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\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.pepXML J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078\230614ko04Stag3_IP_FL18_1_1_22078.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\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.pin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078\230614ko04Stag3_IP_FL18_1_1_22078.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\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.pepXML J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080\230614ko06Stag3_IP_OCILY7_1_1_22080.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\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.pin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080\230614ko06Stag3_IP_OCILY7_1_1_22080.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\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.pepXML J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082\230614ko08Stag3_IP_KIS1_1_1_22082.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\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.pin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082\230614ko08Stag3_IP_KIS1_1_1_22082.pin
Process 'MSFragger move pin' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 230614ko02Stag3_IP_SUDHL6_1_1_22076_percolator_target_psms.tsv --decoy-results-psms 230614ko02Stag3_IP_SUDHL6_1_1_22076_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 230614ko02Stag3_IP_SUDHL6_1_1_22076.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 230614ko02Stag3_IP_SUDHL6_1_1_22076_percolator_target_psms.tsv --decoy-results-psms 230614ko02Stag3_IP_SUDHL6_1_1_22076_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 230614ko02Stag3_IP_SUDHL6_1_1_22076.pin
Started Thu Jan 16 14:06:17 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230614ko02Stag3_IP_SUDHL6_1_1_22076.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 
Found 31388 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 26242 positives and 5146 negatives, size ratio=5.09949 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 11367 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 11239 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 11481 training set positives with q<0.01 in that direction.
Found 17068 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3630 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 19143 PSMs with q<0.01
Iteration 2:	Estimated 19572 PSMs with q<0.01
Iteration 3:	Estimated 19686 PSMs with q<0.01
Iteration 4:	Estimated 19672 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 19673 PSMs with q<0.01
Iteration 9:	Estimated 19677 PSMs with q<0.01
Iteration 10:	Estimated 19672 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
-0.9541	-0.7325	-0.8484	abs_ppm
-0.3221	-0.1970	-0.3182	isotope_errors
-1.5918	-1.0623	-1.7384	log10_evalue
-0.7774	-0.1935	-0.8907	hyperscore
 1.0409	 0.8671	 1.0065	delta_hyperscore
 2.7938	 2.1820	 2.9797	matched_ion_num
-0.9601	-0.7986	-1.0686	complementary_ions
 0.3600	 0.2576	 0.4127	ion_series
-0.2839	-0.2396	-0.3154	weighted_average_abs_fragment_ppm
 0.0105	 0.0141	 0.0113	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.3184	-0.2046	-0.2682	nmc
-0.0944	-0.0430	-0.0387	charge_1
 0.0304	 0.0287	 0.0298	charge_2
 0.0225	 0.0363	 0.0569	charge_3
-0.0671	-0.0742	-0.1020	charge_4
-0.0287	-0.0862	-0.1163	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
-0.2173	-0.0699	-0.1735	15.9949M
 1.8233	 0.9027	 1.9720	m0
Found 19607 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 26242 target PSMs and 5146 decoy PSMs.
Calculating q values.
Final list yields 19615 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 4.3260 cpu seconds or 4 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 230614ko06Stag3_IP_OCILY7_1_1_22080_percolator_target_psms.tsv --decoy-results-psms 230614ko06Stag3_IP_OCILY7_1_1_22080_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 230614ko06Stag3_IP_OCILY7_1_1_22080.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 230614ko06Stag3_IP_OCILY7_1_1_22080_percolator_target_psms.tsv --decoy-results-psms 230614ko06Stag3_IP_OCILY7_1_1_22080_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 230614ko06Stag3_IP_OCILY7_1_1_22080.pin
Started Thu Jan 16 14:06:22 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230614ko06Stag3_IP_OCILY7_1_1_22080.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 
Found 22187 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 17667 positives and 4520 negatives, size ratio=3.90863 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 6660 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 6833 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 6720 training set positives with q<0.01 in that direction.
Found 10038 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.2470 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 11353 PSMs with q<0.01
Iteration 2:	Estimated 11555 PSMs with q<0.01
Iteration 3:	Estimated 11652 PSMs with q<0.01
Iteration 4:	Estimated 11676 PSMs with q<0.01
Iteration 5:	Estimated 11668 PSMs with q<0.01
Iteration 6:	Estimated 11672 PSMs with q<0.01
Iteration 7:	Estimated 11658 PSMs with q<0.01
Iteration 8:	Estimated 11629 PSMs with q<0.01
Iteration 9:	Estimated 11637 PSMs with q<0.01
Iteration 10:	Estimated 11633 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
-0.7725	-0.6271	-0.7470	abs_ppm
-0.5291	-0.4698	-0.4457	isotope_errors
-1.0899	-1.0015	-0.5430	log10_evalue
-0.8674	-0.5483	-1.0493	hyperscore
 1.0316	 0.8792	 0.9007	delta_hyperscore
 3.7032	 2.5862	 3.3692	matched_ion_num
-1.2498	-0.7213	-0.6581	complementary_ions
 0.4531	 0.6182	 0.5736	ion_series
-0.1633	-0.1317	-0.1679	weighted_average_abs_fragment_ppm
-0.2647	-0.1901	-0.2421	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.3720	-0.3236	-0.3911	nmc
-0.0521	-0.0591	-0.0758	charge_1
-0.0458	-0.0862	-0.1423	charge_2
 0.0564	 0.1575	 0.1273	charge_3
-0.0228	-0.1280	 0.0090	charge_4
 0.0459	 0.0437	 0.1082	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
-0.0555	-0.0459	-0.1339	15.9949M
 1.1188	 0.7275	 0.5632	m0
Found 11488 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 17667 target PSMs and 4520 decoy PSMs.
Calculating q values.
Final list yields 11493 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 3.1990 cpu seconds or 3 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 230614ko04Stag3_IP_FL18_1_1_22078_percolator_target_psms.tsv --decoy-results-psms 230614ko04Stag3_IP_FL18_1_1_22078_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 230614ko04Stag3_IP_FL18_1_1_22078.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 230614ko04Stag3_IP_FL18_1_1_22078_percolator_target_psms.tsv --decoy-results-psms 230614ko04Stag3_IP_FL18_1_1_22078_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 230614ko04Stag3_IP_FL18_1_1_22078.pin
Started Thu Jan 16 14:06:26 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230614ko04Stag3_IP_FL18_1_1_22078.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 
Found 21565 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 16838 positives and 4727 negatives, size ratio=3.56209 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 6062 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 5932 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 5915 training set positives with q<0.01 in that direction.
Found 8912 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.2460 cpu seconds or 0 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 10391 PSMs with q<0.01
Iteration 2:	Estimated 10731 PSMs with q<0.01
Iteration 3:	Estimated 10869 PSMs with q<0.01
Iteration 4:	Estimated 10898 PSMs with q<0.01
Iteration 5:	Estimated 10887 PSMs with q<0.01
Iteration 6:	Estimated 10907 PSMs with q<0.01
Iteration 7:	Estimated 10891 PSMs with q<0.01
Iteration 8:	Estimated 10903 PSMs with q<0.01
Iteration 9:	Estimated 10887 PSMs with q<0.01
Iteration 10:	Estimated 10886 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
-0.7416	-0.9371	-0.8369	abs_ppm
-0.4183	-0.4706	-0.2633	isotope_errors
-0.7957	-0.9911	-1.0627	log10_evalue
-0.2558	-0.3092	-0.6748	hyperscore
 0.6976	 0.8082	 0.7990	delta_hyperscore
 2.2690	 1.9614	 2.2953	matched_ion_num
-0.6762	-0.6423	-0.4132	complementary_ions
 0.5164	 0.5840	 0.6392	ion_series
-0.1834	-0.2486	-0.2063	weighted_average_abs_fragment_ppm
-0.2002	-0.1825	-0.2398	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.3963	-0.3125	-0.3931	nmc
-0.0968	-0.1082	-0.1059	charge_1
-0.0432	-0.1244	-0.1094	charge_2
 0.0401	 0.0942	 0.0568	charge_3
-0.0190	 0.0212	 0.0618	charge_4
 0.1067	 0.1374	 0.1294	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
-0.0666	-0.1814	-0.1610	15.9949M
 0.4125	 0.2906	 0.5397	m0
Found 10799 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 16838 target PSMs and 4727 decoy PSMs.
Calculating q values.
Final list yields 10803 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.8590 cpu seconds or 3 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 230614ko08Stag3_IP_KIS1_1_1_22082_percolator_target_psms.tsv --decoy-results-psms 230614ko08Stag3_IP_KIS1_1_1_22082_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 230614ko08Stag3_IP_KIS1_1_1_22082.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 230614ko08Stag3_IP_KIS1_1_1_22082_percolator_target_psms.tsv --decoy-results-psms 230614ko08Stag3_IP_KIS1_1_1_22082_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 230614ko08Stag3_IP_KIS1_1_1_22082.pin
Started Thu Jan 16 14:06:30 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230614ko08Stag3_IP_KIS1_1_1_22082.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 
Found 54390 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 43202 positives and 11188 negatives, size ratio=3.86146 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 16657 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 16646 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 16559 training set positives with q<0.01 in that direction.
Found 24927 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.6690 cpu seconds or 0 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 27560 PSMs with q<0.01
Iteration 2:	Estimated 28066 PSMs with q<0.01
Iteration 3:	Estimated 28288 PSMs with q<0.01
Iteration 4:	Estimated 28362 PSMs with q<0.01
Iteration 5:	Estimated 28372 PSMs with q<0.01
Iteration 6:	Estimated 28364 PSMs with q<0.01
Iteration 7:	Estimated 28370 PSMs with q<0.01
Iteration 8:	Estimated 28364 PSMs with q<0.01
Iteration 9:	Estimated 28362 PSMs with q<0.01
Iteration 10:	Estimated 28344 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
-0.7610	-0.8826	-0.7267	abs_ppm
-0.3710	-0.3499	-0.3625	isotope_errors
-1.5197	-1.3290	-1.4309	log10_evalue
-0.5328	-0.5006	-0.0640	hyperscore
 0.7229	 0.7935	 0.7563	delta_hyperscore
 2.5861	 2.6458	 2.1836	matched_ion_num
-0.8682	-0.7387	-0.9360	complementary_ions
 0.4104	 0.4415	 0.4377	ion_series
-0.2253	-0.1972	-0.2215	weighted_average_abs_fragment_ppm
-0.0846	-0.0359	 0.0457	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.2407	-0.3436	-0.3583	nmc
-0.0500	-0.0417	-0.0648	charge_1
-0.0034	 0.0044	 0.0737	charge_2
 0.0190	 0.0076	-0.0412	charge_3
-0.0328	-0.0395	-0.0400	charge_4
 0.0386	 0.0611	-0.0230	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
-0.0827	-0.1346	-0.1409	15.9949M
 1.1380	 1.1177	 1.1152	m0
Found 28199 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 43202 target PSMs and 11188 decoy PSMs.
Calculating q values.
Final list yields 28215 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 6.2070 cpu seconds or 7 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230614ko02Stag3_IP_SUDHL6_1_1_22076.pin 230614ko02Stag3_IP_SUDHL6_1_1_22076 230614ko02Stag3_IP_SUDHL6_1_1_22076_percolator_target_psms.tsv 230614ko02Stag3_IP_SUDHL6_1_1_22076_percolator_decoy_psms.tsv interact-230614ko02Stag3_IP_SUDHL6_1_1_22076 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076_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\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076\230614ko02Stag3_IP_SUDHL6_1_1_22076_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\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076\230614ko02Stag3_IP_SUDHL6_1_1_22076_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230614ko06Stag3_IP_OCILY7_1_1_22080.pin 230614ko06Stag3_IP_OCILY7_1_1_22080 230614ko06Stag3_IP_OCILY7_1_1_22080_percolator_target_psms.tsv 230614ko06Stag3_IP_OCILY7_1_1_22080_percolator_decoy_psms.tsv interact-230614ko06Stag3_IP_OCILY7_1_1_22080 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080_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\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080\230614ko06Stag3_IP_OCILY7_1_1_22080_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\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080\230614ko06Stag3_IP_OCILY7_1_1_22080_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230614ko04Stag3_IP_FL18_1_1_22078.pin 230614ko04Stag3_IP_FL18_1_1_22078 230614ko04Stag3_IP_FL18_1_1_22078_percolator_target_psms.tsv 230614ko04Stag3_IP_FL18_1_1_22078_percolator_decoy_psms.tsv interact-230614ko04Stag3_IP_FL18_1_1_22078 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078_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\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078\230614ko04Stag3_IP_FL18_1_1_22078_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\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078\230614ko04Stag3_IP_FL18_1_1_22078_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230614ko08Stag3_IP_KIS1_1_1_22082.pin 230614ko08Stag3_IP_KIS1_1_1_22082 230614ko08Stag3_IP_KIS1_1_1_22082_percolator_target_psms.tsv 230614ko08Stag3_IP_KIS1_1_1_22082_percolator_decoy_psms.tsv interact-230614ko08Stag3_IP_KIS1_1_1_22082 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082_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\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082\230614ko08Stag3_IP_KIS1_1_1_22082_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\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082\230614ko08Stag3_IP_KIS1_1_1_22082_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
ProteinProphet [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\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\Revision\230613ko\MSFragger_iBAQ\filelist_proteinprophet.txt
INFO[14:06:46] 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\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076\interact-230614ko02Stag3_IP_SUDHL6_1_1_22076.pep.xml...
...read in 43 1+, 14009 2+, 6740 3+, 836 4+, 133 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078\interact-230614ko04Stag3_IP_FL18_1_1_22078.pep.xml...
...read in 14 1+, 7932 2+, 3996 3+, 462 4+, 145 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080\interact-230614ko06Stag3_IP_OCILY7_1_1_22080.pep.xml...
...read in 37 1+, 8846 2+, 4246 3+, 379 4+, 113 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082\interact-230614ko08Stag3_IP_KIS1_1_1_22082.pep.xml...
...read in 120 1+, 20902 2+, 10174 3+, 1255 4+, 212 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 23237 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
.........:.........:.........:.........:.........:.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry rev_sp|P22352|GPX3_HUMAN : U
KRKVGLAAQRRMYSLIDMKVNSVTTRHHWRMIPIGDPGVLFKEFNWRIDHVKMPEWFLRDSTGLLESTPPCSNKLFTYFKQEKEGNVDGKEFLQFNPVFGGGPRVYKLTPLIESNEGPEQKGFQNCPFGLIVLGFPALEEQLANLEIYQGTLGUYSAVNVFLVYKGAYQKFPIYEEGDITLAGYEYITGSIGGHCDMKSKEQGRSQSVFGALLLSLLCSAQLLRAM
.....:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry rev_sp|Q92813|IOD2_HUMAN : UU
GALRTKKURKSFNKELWHRVEQLNYSFPGKGGLYAIKQRQVICVREFAVGYAINANNDMRDAVVRCQPPLSFRELLQQAAACRDEQNQHKKVEFSLSSDGPIAWGDSPHAEDIYVLLFDAVSSFEEVLKRFAPLQSTFPPUTASGFNVVLPREPSAFDLLHCTAGEAIKEQTGNGSNDGGETSSVHVVSSNPADEGLKVQKYADLLFSKWVCRLGESTLMRRWEGRTSKSRSLLLVVHKLLIVSDYLALFLCNSFFVPLIQLTILLDVSLIGM
..:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9BVL4|SELO_HUMAN : U
SSUTVCLEAAWLPPKSSYSRQRGDAGDAETAEADTAAGAECHYPTELLKLVRRVESFDGREAAEIANQAIYNRLVYKPNNAHMVRVHEAQWAAADGAGELDKDLRARYAQLWDAWHGQNRSQLEAASLQELRSQQEVRELERAIGARTGMLAFLQPNSQALMLMMSLQRPDMQPRFALRLEELSACQEMLRALFEALGPSELEVPFSSLLYFTNTFDAGTLHMTELLKSVLAGDEELEVQVLGLKRRMKQLYHRQFEADFEEALIAEGLELPLEPQLAEALKRLNWRCVEPQKSYAYRGTNDSANCVHDPDYRDLFGFPGYDITLGLISMNDTNLVGHCFGVCQWEAVMRATRRTVERFFAANRQVSDSAHAAQIEPYFSSIVYDLLQVRIDNRGVSPGARGTHEDASKFIEFSGFRIFTSAVRLVVTCQEYKPNGDYFVDRVVTSESTVCAGARTTPVGLHFMAESCLFERISSRLVKRGDAQRSFPTPGAGKLQLEWREGTATCVEGLYMAAGDGLQGAFQGFQHGCYCHAAPEAGPLLANGSFFLAAEAEAERAPPAGLGLLALAPESLAVLRPQRLPTPQVRTFCAGPVPRPASPAGEPGPPPAEVPLARLARNDFRLGALWRPAPEMAAGSLTSRPAPSPSCRGLPLLRAAALSAGLAARYVAM
.......:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9NZV5|SELN_HUMAN : UU
PQLLPLGRRLGEKLFQMYTATSPDEFTSSFSFLNSEIEEPKVSTIDLFYNANIHHVVTGNPLCIMMEVPFSYKELHLGALKQHSSNEQNNQLEELEKVLSWTSIFSENLLTLIPSSELVTERLTRGSGUCSQDDLAGWLLISHVLKNEAKARDFAETFPLYSVKKFPYMAVELRRAAEEWSLEQQWKIEEFVFQLPEGSPLHSDIMSGDEDLIVSPVSPGTAELEMQPIYGIDVEMNSSESAGYLWEMDVNLSRHNPVFLRFDRVHTADKSLIIHGTFQAPSFWFPFDPPESLQFEAHIRFMVTYYFDSIATLCAVAGQPAFRTKVFPRPHFMSLLRHIIVEKGKPPPPYFRNNSLYGTFMSLESPIIWWPEGLEQGPPPLFPQFHRTAFVASPSAAATWNRLGSLALRSVGLFGDKSKTMTEPLLPQFRAEITLTEESPDPPLEEEECSAAPTSRLLSLCSSUNLWPLQPQLSSHSCWQVGTQTVSCSGTLKEAIPKFEEPSIYMDGDTDLSSFLFLGDTGLTKLALEQRAAAQAEAHRACVRVAAAAAAALLAGLLALSRARRRPPAPPQAAPGPSPPGRQGPRARGM
.......:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000
.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q9NZV5|SELN_HUMAN : UU
MGRARPGQRGPPSPGPAAQPPAPPRRRARSLALLGALLAAAAAAAVRVCARHAEAQAAARQELALKTLGTDGLFLFSSLDTDGDMYISPEEFKPIAEKLTGSCSVTQTGVQWCSHSSLQPQLPWLNUSSCLSLLRSTPAASCEEEELPPDPSEETLTIEARFQPLLPETMTKSKDGFLGVSRLALSGLRNWTAAASPSAVFATRHFQPFLPPPGQELGEPWWIIPSELSMFTGYLSNNRFYPPPPKGKEVIIHRLLSMFHPRPFVKTRFAPQGAVACLTAISDFYYTVMFRIHAEFQLSEPPDFPFWFSPAQFTGHIILSKDATHVRDFRLFVPNHRSLNVDMEWLYGASESSNMEVDIGYIPQMELEATGPSVPSVILDEDGSMIDSHLPSGEPLQFVFEEIKWQQELSWEEAARRLEVAMYPFKKVSYLPFTEAFDRAKAENKLVHSILLWGALDDQSCUGSGRTLRETVLESSPILTLLNESFISTWSLVKELEELQNNQENSSHQKLAGLHLEKYSFPVEMMICLPNGTVVHHINANYFLDITSVKPEEIESNLFSFSSTFEDPSTATYMQFLKEGLRRGLPLLQP
.....:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:....  Total: 40840
Computing degenerate peptides for 7056 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 7278 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 7278 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 7278 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 7278 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 7278 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 7278 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=4.13391e-05, db_size=45492565
Computing MU for 7278 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO[14:06:53] Done                                         
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
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[14:06:53] Executing Database  v5.0.0                   
INFO[14:06:53] Annotating the database                      
INFO[14:06:53] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076 --protxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\combined.prot.xml --razor
INFO[14:06:53] Executing Filter  v5.0.0                     
INFO[14:06:53] Processing peptide identification files      
INFO[14:06:53] Parsing J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076\interact-230614ko02Stag3_IP_SUDHL6_1_1_22076.pep.xml 
INFO[14:06:54] 1+ Charge profile                             decoy=4 target=39
INFO[14:06:54] 2+ Charge profile                             decoy=437 target=13572
INFO[14:06:54] 3+ Charge profile                             decoy=194 target=6546
INFO[14:06:54] 4+ Charge profile                             decoy=34 target=802
INFO[14:06:54] 5+ Charge profile                             decoy=6 target=127
INFO[14:06:54] 6+ Charge profile                             decoy=0 target=0
INFO[14:06:54] Database search results                       ions=10070 peptides=8511 psms=21761
INFO[14:06:54] Converged to 1.00 % FDR with 19616 PSMs       decoy=196 threshold=0.830432 total=19812
INFO[14:06:54] Converged to 8.09 % FDR with 7874 Peptides    decoy=637 threshold=0.500113 total=8511
INFO[14:06:54] Converged to 6.80 % FDR with 9429 Ions        decoy=641 threshold=0.500113 total=10070
INFO[14:06:54] Protein inference results                     decoy=2297 target=4210
INFO[14:06:54] Converged to 58.33 % FDR with 3876 Proteins   decoy=2261 threshold=0.4995 total=6137
INFO[14:06:55] Applying sequential FDR estimation            ions=8859 peptides=7392 psms=19812
INFO[14:06:55] Converged to 1.00 % FDR with 19616 PSMs       decoy=196 threshold=0.830432 total=19812
INFO[14:06:55] Converged to 2.57 % FDR with 7207 Peptides    decoy=185 threshold=0.830503 total=7392
INFO[14:06:55] Converged to 2.13 % FDR with 8674 Ions        decoy=185 threshold=0.830432 total=8859
INFO[14:06:55] Post processing identifications              
INFO[14:06:55] Assigning protein identifications to layers  
INFO[14:06:57] Processing protein inference                 
INFO[14:06:57] Synchronizing PSMs and proteins              
INFO[14:06:57] Final report numbers after FDR filtering, and post-processing  ions=8673 peptides=7206 proteins=1193 psms=19615
INFO[14:06:57] Saving                                       
INFO[14:06:57] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078 --protxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076 --razor
INFO[14:06:58] Executing Filter  v5.0.0                     
INFO[14:06:58] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076 
INFO[14:06:58] Processing peptide identification files      
INFO[14:06:58] Parsing J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078\interact-230614ko04Stag3_IP_FL18_1_1_22078.pep.xml 
INFO[14:06:58] 1+ Charge profile                             decoy=3 target=11
INFO[14:06:58] 2+ Charge profile                             decoy=318 target=7614
INFO[14:06:58] 3+ Charge profile                             decoy=131 target=3865
INFO[14:06:58] 4+ Charge profile                             decoy=37 target=425
INFO[14:06:58] 5+ Charge profile                             decoy=10 target=135
INFO[14:06:58] 6+ Charge profile                             decoy=0 target=0
INFO[14:06:58] Database search results                       ions=5270 peptides=4619 psms=12549
INFO[14:06:58] Converged to 1.00 % FDR with 10811 PSMs       decoy=108 threshold=0.859268 total=10919
INFO[14:06:58] Converged to 11.03 % FDR with 4160 Peptides   decoy=459 threshold=0.500042 total=4619
INFO[14:06:58] Converged to 9.59 % FDR with 4809 Ions        decoy=461 threshold=0.500042 total=5270
INFO[14:06:58] Protein inference results                     decoy=2297 target=4210
INFO[14:06:58] Converged to 58.33 % FDR with 3876 Proteins   decoy=2261 threshold=0.4995 total=6137
INFO[14:06:59] Applying sequential FDR estimation            ions=4297 peptides=3705 psms=10919
INFO[14:06:59] Converged to 1.00 % FDR with 10811 PSMs       decoy=108 threshold=0.859268 total=10919
INFO[14:06:59] Converged to 2.69 % FDR with 3608 Peptides    decoy=97 threshold=0.859297 total=3705
INFO[14:06:59] Converged to 2.31 % FDR with 4200 Ions        decoy=97 threshold=0.859297 total=4297
INFO[14:06:59] Post processing identifications              
INFO[14:06:59] Assigning protein identifications to layers  
INFO[14:07:00] Processing protein inference                 
INFO[14:07:00] Synchronizing PSMs and proteins              
INFO[14:07:00] Final report numbers after FDR filtering, and post-processing  ions=4199 peptides=3607 proteins=737 psms=10810
INFO[14:07:00] Saving                                       
INFO[14:07:00] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080 --protxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076 --razor
INFO[14:07:00] Executing Filter  v5.0.0                     
INFO[14:07:00] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076 
INFO[14:07:00] Processing peptide identification files      
INFO[14:07:00] Parsing J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080\interact-230614ko06Stag3_IP_OCILY7_1_1_22080.pep.xml 
INFO[14:07:01] 1+ Charge profile                             decoy=4 target=33
INFO[14:07:01] 2+ Charge profile                             decoy=357 target=8489
INFO[14:07:01] 3+ Charge profile                             decoy=189 target=4057
INFO[14:07:01] 4+ Charge profile                             decoy=17 target=362
INFO[14:07:01] 5+ Charge profile                             decoy=6 target=107
INFO[14:07:01] 6+ Charge profile                             decoy=0 target=0
INFO[14:07:01] Database search results                       ions=5601 peptides=4830 psms=13621
INFO[14:07:01] Converged to 1.00 % FDR with 11506 PSMs       decoy=115 threshold=0.873495 total=11621
INFO[14:07:01] Converged to 11.99 % FDR with 4313 Peptides   decoy=517 threshold=0.500022 total=4830
INFO[14:07:01] Converged to 10.19 % FDR with 5083 Ions       decoy=518 threshold=0.500022 total=5601
INFO[14:07:01] Protein inference results                     decoy=2297 target=4210
INFO[14:07:01] Converged to 58.33 % FDR with 3876 Proteins   decoy=2261 threshold=0.4995 total=6137
INFO[14:07:01] Applying sequential FDR estimation            ions=4475 peptides=3788 psms=11621
INFO[14:07:01] Converged to 1.00 % FDR with 11506 PSMs       decoy=115 threshold=0.873495 total=11621
INFO[14:07:01] Converged to 2.71 % FDR with 3688 Peptides    decoy=100 threshold=0.873495 total=3788
INFO[14:07:01] Converged to 2.29 % FDR with 4375 Ions        decoy=100 threshold=0.873495 total=4475
INFO[14:07:01] Post processing identifications              
INFO[14:07:01] Assigning protein identifications to layers  
INFO[14:07:02] Processing protein inference                 
INFO[14:07:02] Synchronizing PSMs and proteins              
INFO[14:07:02] Final report numbers after FDR filtering, and post-processing  ions=4375 peptides=3688 proteins=732 psms=11506
INFO[14:07:02] Saving                                       
INFO[14:07:03] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082 --protxml J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076 --razor
INFO[14:07:03] Executing Filter  v5.0.0                     
INFO[14:07:03] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076 
INFO[14:07:03] Processing peptide identification files      
INFO[14:07:03] Parsing J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082\interact-230614ko08Stag3_IP_KIS1_1_1_22082.pep.xml 
INFO[14:07:05] 1+ Charge profile                             decoy=11 target=109
INFO[14:07:05] 2+ Charge profile                             decoy=862 target=20040
INFO[14:07:05] 3+ Charge profile                             decoy=316 target=9858
INFO[14:07:05] 4+ Charge profile                             decoy=53 target=1202
INFO[14:07:05] 5+ Charge profile                             decoy=17 target=195
INFO[14:07:05] 6+ Charge profile                             decoy=0 target=0
INFO[14:07:05] Database search results                       ions=14986 peptides=12611 psms=32663
INFO[14:07:05] Converged to 1.00 % FDR with 28221 PSMs       decoy=282 threshold=0.858992 total=28503
INFO[14:07:05] Converged to 10.20 % FDR with 11444 Peptides  decoy=1167 threshold=0.500231 total=12611
INFO[14:07:05] Converged to 8.51 % FDR with 13811 Ions       decoy=1175 threshold=0.500231 total=14986
INFO[14:07:05] Protein inference results                     decoy=2297 target=4210
INFO[14:07:05] Converged to 58.33 % FDR with 3876 Proteins   decoy=2261 threshold=0.4995 total=6137
INFO[14:07:05] Applying sequential FDR estimation            ions=12437 peptides=10318 psms=28503
INFO[14:07:05] Converged to 1.00 % FDR with 28221 PSMs       decoy=282 threshold=0.858992 total=28503
INFO[14:07:05] Converged to 2.61 % FDR with 10056 Peptides   decoy=262 threshold=0.858992 total=10318
INFO[14:07:05] Converged to 2.16 % FDR with 12174 Ions       decoy=263 threshold=0.858992 total=12437
INFO[14:07:05] Post processing identifications              
INFO[14:07:05] Assigning protein identifications to layers  
INFO[14:07:09] Processing protein inference                 
INFO[14:07:09] Synchronizing PSMs and proteins              
INFO[14:07:09] Final report numbers after FDR filtering, and post-processing  ions=12173 peptides=10055 proteins=1701 psms=28220
INFO[14:07:09] Saving                                       
INFO[14:07:09] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[14:07:09] Executing Report  v5.0.0                     
INFO[14:07:09] Creating reports                             
INFO[14:07:10] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[14:07:10] Executing Report  v5.0.0                     
INFO[14:07:10] Creating reports                             
INFO[14:07:10] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[14:07:10] Executing Report  v5.0.0                     
INFO[14:07:10] Creating reports                             
INFO[14:07:11] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[14:07:11] Executing Report  v5.0.0                     
INFO[14:07:11] Creating reports                             
INFO[14:07:11] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[14:07:11] Executing Workspace  v5.0.0                  
INFO[14:07:11] Removing workspace                           
INFO[14:07:11] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[14:07:12] Executing Workspace  v5.0.0                  
INFO[14:07:12] Removing workspace                           
INFO[14:07:12] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[14:07:12] Executing Workspace  v5.0.0                  
INFO[14:07:12] Removing workspace                           
INFO[14:07:12] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[14:07:13] Executing Workspace  v5.0.0                  
INFO[14:07:13] Removing workspace                           
INFO[14:07:13] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[14:07:13] Executing Workspace  v5.0.0                  
INFO[14:07:13] Removing workspace                           
INFO[14:07:13] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
IonQuant [Work dir: J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ]
java -Xmx75G -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 100 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 0 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\filelist_ionquant.txt --modlist J:\MSFragger_process\Saitou-lab\Revision\230613ko\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 75 GB memory
2025-01-16 14:07:14 [INFO] - Collecting variable modifications from all psm.tsv files...
2025-01-16 14:07:14 [INFO] - Loading and indexing all psm.tsv files...
2025-01-16 14:07:16 [INFO] - Parameters:
2025-01-16 14:07:16 [INFO] - threads = 15
2025-01-16 14:07:16 [INFO] - mztol = 10.0
2025-01-16 14:07:16 [INFO] - rttol = 0.4
2025-01-16 14:07:16 [INFO] - imtol = 0.05
2025-01-16 14:07:16 [INFO] - minisotopes = 2
2025-01-16 14:07:16 [INFO] - minscans = 3
2025-01-16 14:07:16 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko02Stag3_IP_SUDHL6_1_1_22076\psm.tsv
2025-01-16 14:07:16 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko04Stag3_IP_FL18_1_1_22078\psm.tsv
2025-01-16 14:07:16 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko06Stag3_IP_OCILY7_1_1_22080\psm.tsv
2025-01-16 14:07:16 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\230614ko08Stag3_IP_KIS1_1_1_22082\psm.tsv
2025-01-16 14:07:16 [INFO] - multidir = J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\.\
2025-01-16 14:07:16 [INFO] - excludemods = 
2025-01-16 14:07:16 [INFO] - minions = 2
2025-01-16 14:07:16 [INFO] - maxlfq = 1
2025-01-16 14:07:16 [INFO] - ibaq = 0
2025-01-16 14:07:16 [INFO] - normalization = 0
2025-01-16 14:07:16 [INFO] - minexps = 1
2025-01-16 14:07:16 [INFO] - minfreq = 0.0
2025-01-16 14:07:16 [INFO] - tp = 0
2025-01-16 14:07:16 [INFO] - mbr = 1
2025-01-16 14:07:16 [INFO] - mbrrttol = 1.0
2025-01-16 14:07:16 [INFO] - mbrimtol = 0.05
2025-01-16 14:07:16 [INFO] - mbrtoprun = 100
2025-01-16 14:07:16 [INFO] - mbrmincorr = 0.0
2025-01-16 14:07:16 [INFO] - ionmobility = 1
2025-01-16 14:07:16 [INFO] - ionfdr = 0.01
2025-01-16 14:07:16 [INFO] - peptidefdr = 1.0
2025-01-16 14:07:16 [INFO] - proteinfdr = 1.0
2025-01-16 14:07:16 [INFO] - light = 
2025-01-16 14:07:16 [INFO] - medium = 
2025-01-16 14:07:16 [INFO] - heavy = 
2025-01-16 14:07:16 [INFO] - requantify = 0
2025-01-16 14:07:16 [INFO] - writeindex = 0
2025-01-16 14:07:16 [INFO] - locprob = 0.75
2025-01-16 14:07:16 [INFO] - uniqueness = 0
2025-01-16 14:07:16 [INFO] - filelist = J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\filelist_ionquant.txt
2025-01-16 14:07:16 [INFO] - specdir = J:\MSFragger_process\Saitou-lab\Revision\230613ko
2025-01-16 14:07:16 [INFO] - modlist = J:\MSFragger_process\Saitou-lab\Revision\230613ko\MSFragger_iBAQ\modmasses_ionquant.txt
2025-01-16 14:07:16 [INFO] - mod masses:
2025-01-16 14:07:16 [INFO] - 15.9949
2025-01-16 14:07:16 [INFO] - 42.0106
2025-01-16 14:07:16 [INFO] - 57.021465
2025-01-16 14:07:16 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.d...
2025-01-16 14:07:17 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.d...
2025-01-16 14:07:17 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.d...
2025-01-16 14:07:17 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.d...
2025-01-16 14:07:17 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.d...
2025-01-16 14:07:17 [INFO] - ...20%...40%...60%...80%...100%
2025-01-16 14:07:40 [INFO] - Building index...
2025-01-16 14:08:12 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.quantindex
2025-01-16 14:08:14 [INFO] - Loading 230614ko02Stag3_IP_SUDHL6_1_1_22076....
2025-01-16 14:08:14 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 14:08:14 [INFO] - Quantifying...
2025-01-16 14:08:16 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.d...
2025-01-16 14:08:16 [INFO] - ...20%...40%...60%...80%...100%
2025-01-16 14:08:39 [INFO] - Building index...
2025-01-16 14:09:16 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.quantindex
2025-01-16 14:09:17 [INFO] - Loading 230614ko04Stag3_IP_FL18_1_1_22078....
2025-01-16 14:09:17 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 14:09:17 [INFO] - Quantifying...
2025-01-16 14:09:18 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.d...
2025-01-16 14:09:18 [INFO] - ...20%...40%...60%...80%...100%
2025-01-16 14:09:39 [INFO] - Building index...
2025-01-16 14:10:06 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.quantindex
2025-01-16 14:10:08 [INFO] - Loading 230614ko06Stag3_IP_OCILY7_1_1_22080....
2025-01-16 14:10:08 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 14:10:08 [INFO] - Quantifying...
2025-01-16 14:10:08 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.d...
2025-01-16 14:10:08 [INFO] - ...20%...40%...60%...80%...100%
2025-01-16 14:10:37 [INFO] - Building index...
2025-01-16 14:11:13 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.quantindex
2025-01-16 14:11:16 [INFO] - Loading 230614ko08Stag3_IP_KIS1_1_1_22082....
2025-01-16 14:11:16 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 14:11:16 [INFO] - Quantifying...
2025-01-16 14:11:17 [INFO] - Updating Philosopher's tables...
2025-01-16 14:11:19 [INFO] - Matching-between-runs: 230614ko02Stag3_IP_SUDHL6_1_1_22076...
2025-01-16 14:11:19 [INFO] - Calculating correlations between all other runs...
2025-01-16 14:11:19 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko02Stag3_IP_SUDHL6_1_1_22076.quantindex
2025-01-16 14:11:22 [INFO] - Transferring 230614ko04Stag3_IP_FL18_1_1_22078...
2025-01-16 14:11:22 [INFO] - Transferring 230614ko06Stag3_IP_OCILY7_1_1_22080...
2025-01-16 14:11:23 [INFO] - Transferring 230614ko08Stag3_IP_KIS1_1_1_22082...
2025-01-16 14:11:23 [INFO] - Training LDA models for all matched features.
2025-01-16 14:11:23 [INFO] - #{+1} = 495, #{-1} = 12, #{+2} = 2467, #{-2} = 30
2025-01-16 14:11:23 [INFO] - Standardized coefficients:
2025-01-16 14:11:23 [INFO] - log10(intensity): 0.5419376113699244
2025-01-16 14:11:23 [INFO] - log10(KL): -0.2542502238650157
2025-01-16 14:11:23 [INFO] - abs(ppm): -0.330796333680045
2025-01-16 14:11:23 [INFO] - IM diff: -0.6986826654831654
2025-01-16 14:11:23 [INFO] - RT diff: -0.20994467753298535
2025-01-16 14:11:23 [INFO] - Fitting a mixture model...
2025-01-16 14:11:24 [INFO] - Matching-between-runs: 230614ko04Stag3_IP_FL18_1_1_22078...
2025-01-16 14:11:24 [INFO] - Calculating correlations between all other runs...
2025-01-16 14:11:24 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko04Stag3_IP_FL18_1_1_22078.quantindex
2025-01-16 14:11:27 [INFO] - Transferring 230614ko02Stag3_IP_SUDHL6_1_1_22076...
2025-01-16 14:11:27 [INFO] - Transferring 230614ko06Stag3_IP_OCILY7_1_1_22080...
2025-01-16 14:11:27 [INFO] - Transferring 230614ko08Stag3_IP_KIS1_1_1_22082...
2025-01-16 14:11:28 [INFO] - Training LDA models for all matched features.
2025-01-16 14:11:28 [INFO] - #{+1} = 497, #{-1} = 8, #{+2} = 1420, #{-2} = 10
2025-01-16 14:11:28 [INFO] - Standardized coefficients:
2025-01-16 14:11:28 [INFO] - log10(intensity): 0.8640674948043463
2025-01-16 14:11:28 [INFO] - log10(KL): -0.15958128815028796
2025-01-16 14:11:28 [INFO] - abs(ppm): -0.448690241928923
2025-01-16 14:11:28 [INFO] - IM diff: -0.1326483636233784
2025-01-16 14:11:28 [INFO] - RT diff: -0.09488232354153381
2025-01-16 14:11:28 [INFO] - Fitting a mixture model...
2025-01-16 14:11:28 [WARNING] - There are not enough data points to fix a mixture model (decoy = 8, target = 497, id = 1420). Will estimate the probability using a simplified approach.
2025-01-16 14:11:28 [INFO] - Matching-between-runs: 230614ko06Stag3_IP_OCILY7_1_1_22080...
2025-01-16 14:11:28 [INFO] - Calculating correlations between all other runs...
2025-01-16 14:11:28 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko06Stag3_IP_OCILY7_1_1_22080.quantindex
2025-01-16 14:11:30 [INFO] - Transferring 230614ko02Stag3_IP_SUDHL6_1_1_22076...
2025-01-16 14:11:30 [INFO] - Transferring 230614ko04Stag3_IP_FL18_1_1_22078...
2025-01-16 14:11:31 [INFO] - Transferring 230614ko08Stag3_IP_KIS1_1_1_22082...
2025-01-16 14:11:31 [INFO] - Training LDA models for all matched features.
2025-01-16 14:11:31 [INFO] - #{+1} = 559, #{-1} = 7, #{+2} = 1575, #{-2} = 18
2025-01-16 14:11:31 [INFO] - Standardized coefficients:
2025-01-16 14:11:31 [INFO] - log10(intensity): 0.6605674304908282
2025-01-16 14:11:31 [INFO] - log10(KL): 0.02110277004109588
2025-01-16 14:11:31 [INFO] - abs(ppm): -0.20019677953409168
2025-01-16 14:11:31 [INFO] - IM diff: -0.44834320099697156
2025-01-16 14:11:31 [INFO] - RT diff: -0.5687752335500136
2025-01-16 14:11:31 [INFO] - Fitting a mixture model...
2025-01-16 14:11:31 [WARNING] - There are not enough data points to fix a mixture model (decoy = 7, target = 559, id = 1575). Will estimate the probability using a simplified approach.
2025-01-16 14:11:31 [INFO] - Matching-between-runs: 230614ko08Stag3_IP_KIS1_1_1_22082...
2025-01-16 14:11:31 [INFO] - Calculating correlations between all other runs...
2025-01-16 14:11:31 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\230613ko\230614ko08Stag3_IP_KIS1_1_1_22082.quantindex
2025-01-16 14:11:35 [INFO] - Transferring 230614ko02Stag3_IP_SUDHL6_1_1_22076...
2025-01-16 14:11:35 [INFO] - Transferring 230614ko04Stag3_IP_FL18_1_1_22078...
2025-01-16 14:11:35 [INFO] - Transferring 230614ko06Stag3_IP_OCILY7_1_1_22080...
2025-01-16 14:11:35 [INFO] - Training LDA models for all matched features.
2025-01-16 14:11:36 [INFO] - #{+1} = 687, #{-1} = 33, #{+2} = 2654, #{-2} = 84
2025-01-16 14:11:36 [INFO] - Standardized coefficients:
2025-01-16 14:11:36 [INFO] - log10(intensity): 0.6253055460735372
2025-01-16 14:11:36 [INFO] - log10(KL): -0.36795002302503327
2025-01-16 14:11:36 [INFO] - abs(ppm): -0.31510493327717026
2025-01-16 14:11:36 [INFO] - IM diff: -0.5512315553078294
2025-01-16 14:11:36 [INFO] - RT diff: -0.26927044057578753
2025-01-16 14:11:36 [INFO] - Fitting a mixture model...
2025-01-16 14:11:36 [INFO] - Estimating match-between-runs FDR...
2025-01-16 14:11:36 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.918300
2025-01-16 14:11:36 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100
2025-01-16 14:11:36 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100
2025-01-16 14:11:36 [INFO] - Updating Philosopher's tables...
2025-01-16 14:11:37 [INFO] - Combining experiments and estimating protein intensity...
2025-01-16 14:11:39 [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 8.6 MINUTES=============================================================
