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: 240120ko08Wapl_IP_1_1_1_40530
  - J:\MSFragger_process\Saitou-lab\240220ko\240120ko08Wapl_IP_1_1_1_40530.d	DDA
  Experiment/Group: 240120ko09Wapl_IP_2_1_1_40531
  - J:\MSFragger_process\Saitou-lab\240220ko\240120ko09Wapl_IP_2_1_1_40531.d	DDA
  Experiment/Group: 240220ko02whole_RAD21_1_1_1_170
  - J:\MSFragger_process\Saitou-lab\240220ko\240220ko02whole_RAD21_1_1_1_170.d	DDA
  Experiment/Group: 240220ko03whole_RAD21_2_1_1_171
  - J:\MSFragger_process\Saitou-lab\240220ko\240220ko03whole_RAD21_2_1_1_171.d	DDA
  Experiment/Group: 240220ko05chromatin_RAD21_3_1_1_173
  - J:\MSFragger_process\Saitou-lab\240220ko\240220ko05chromatin_RAD21_3_1_1_173.d	DDA
  Experiment/Group: 240220ko06chromatin_RAD21_4_1_1_174
  - J:\MSFragger_process\Saitou-lab\240220ko\240220ko06chromatin_RAD21_4_1_1_174.d	DDA
  Experiment/Group: 240220ko08chromatin_WAPL_5_1_1_176
  - J:\MSFragger_process\Saitou-lab\240220ko\240220ko08chromatin_WAPL_5_1_1_176.d	DDA
  Experiment/Group: 240220ko09chromatin_WAPL_6_1_1_177
  - J:\MSFragger_process\Saitou-lab\240220ko\240220ko09chromatin_WAPL_6_1_1_177.d	DDA


97 commands to execute:
CheckCentroid
java -Xmx81G -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\240220ko\240120ko08Wapl_IP_1_1_1_40530.d 15
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
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\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
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\fa488227-8733-4147-860b-3a542ff5a530
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
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\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
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\e25bd5a2-e142-40df-abc3-376f74f1b306
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
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\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
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\a315c1e4-9823-4e8a-b0b5-9e248d95db61
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
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\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
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\09081fac-1125-4f38-814e-317caca7f58f
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\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\240220ko\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\f6360d1f-c101-4fa2-ba25-ab4e2669cf1a
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
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\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
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\f203cfd1-2381-4058-89ed-e88d3b596e6f
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
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\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
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\9b6bb096-b8e3-4f46-9e66-795ea4516f9c
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
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\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
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\524bd1c9-cc5c-46f1-9e1f-193fca8bcf0f
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
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\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
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\90c321b4-ec88-48fc-92a6-42c5ea1db795
MSFragger [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
java -jar -Dfile.encoding=UTF-8 -Xmx81G D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\fragger.params J:\MSFragger_process\Saitou-lab\240220ko\240120ko08Wapl_IP_1_1_1_40530.d J:\MSFragger_process\Saitou-lab\240220ko\240120ko09Wapl_IP_2_1_1_40531.d J:\MSFragger_process\Saitou-lab\240220ko\240220ko02whole_RAD21_1_1_1_170.d J:\MSFragger_process\Saitou-lab\240220ko\240220ko03whole_RAD21_2_1_1_171.d J:\MSFragger_process\Saitou-lab\240220ko\240220ko05chromatin_RAD21_3_1_1_173.d J:\MSFragger_process\Saitou-lab\240220ko\240220ko06chromatin_RAD21_4_1_1_174.d J:\MSFragger_process\Saitou-lab\240220ko\240220ko08chromatin_WAPL_5_1_1_176.d J:\MSFragger_process\Saitou-lab\240220ko\240220ko09chromatin_WAPL_6_1_1_177.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\240220ko\240120ko08Wapl_IP_1_1_1_40530.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530\240120ko08Wapl_IP_1_1_1_40530.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\240220ko\240120ko08Wapl_IP_1_1_1_40530.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530\240120ko08Wapl_IP_1_1_1_40530.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\240220ko\240120ko09Wapl_IP_2_1_1_40531.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531\240120ko09Wapl_IP_2_1_1_40531.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\240220ko\240120ko09Wapl_IP_2_1_1_40531.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531\240120ko09Wapl_IP_2_1_1_40531.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\240220ko\240220ko02whole_RAD21_1_1_1_170.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170\240220ko02whole_RAD21_1_1_1_170.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\240220ko\240220ko02whole_RAD21_1_1_1_170.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170\240220ko02whole_RAD21_1_1_1_170.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\240220ko\240220ko03whole_RAD21_2_1_1_171.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171\240220ko03whole_RAD21_2_1_1_171.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\240220ko\240220ko03whole_RAD21_2_1_1_171.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171\240220ko03whole_RAD21_2_1_1_171.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\240220ko\240220ko05chromatin_RAD21_3_1_1_173.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173\240220ko05chromatin_RAD21_3_1_1_173.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\240220ko\240220ko05chromatin_RAD21_3_1_1_173.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173\240220ko05chromatin_RAD21_3_1_1_173.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\240220ko\240220ko06chromatin_RAD21_4_1_1_174.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174\240220ko06chromatin_RAD21_4_1_1_174.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\240220ko\240220ko06chromatin_RAD21_4_1_1_174.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174\240220ko06chromatin_RAD21_4_1_1_174.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\240220ko\240220ko08chromatin_WAPL_5_1_1_176.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\240220ko08chromatin_WAPL_5_1_1_176.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\240220ko\240220ko08chromatin_WAPL_5_1_1_176.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\240220ko08chromatin_WAPL_5_1_1_176.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\240220ko\240220ko09chromatin_WAPL_6_1_1_177.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177\240220ko09chromatin_WAPL_6_1_1_177.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\240220ko\240220ko09chromatin_WAPL_6_1_1_177.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177\240220ko09chromatin_WAPL_6_1_1_177.pin
MSBooster [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
java -Xmx81G -cp "D:\Applications\FragPipe-20.0\fragpipe\tools\msbooster-1.1.11.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar" Features.MainClass --paramsList J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\msbooster_params.txt
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko09chromatin_WAPL_6_1_1_177_percolator_target_psms.tsv --decoy-results-psms 240220ko09chromatin_WAPL_6_1_1_177_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko09chromatin_WAPL_6_1_1_177_edited.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240120ko09Wapl_IP_2_1_1_40531_percolator_target_psms.tsv --decoy-results-psms 240120ko09Wapl_IP_2_1_1_40531_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240120ko09Wapl_IP_2_1_1_40531_edited.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko08chromatin_WAPL_5_1_1_176_percolator_target_psms.tsv --decoy-results-psms 240220ko08chromatin_WAPL_5_1_1_176_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko08chromatin_WAPL_5_1_1_176_edited.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko02whole_RAD21_1_1_1_170_percolator_target_psms.tsv --decoy-results-psms 240220ko02whole_RAD21_1_1_1_170_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko02whole_RAD21_1_1_1_170_edited.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko06chromatin_RAD21_4_1_1_174_percolator_target_psms.tsv --decoy-results-psms 240220ko06chromatin_RAD21_4_1_1_174_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko06chromatin_RAD21_4_1_1_174_edited.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko03whole_RAD21_2_1_1_171_percolator_target_psms.tsv --decoy-results-psms 240220ko03whole_RAD21_2_1_1_171_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko03whole_RAD21_2_1_1_171_edited.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240120ko08Wapl_IP_1_1_1_40530_percolator_target_psms.tsv --decoy-results-psms 240120ko08Wapl_IP_1_1_1_40530_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240120ko08Wapl_IP_1_1_1_40530_edited.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko05chromatin_RAD21_3_1_1_173_percolator_target_psms.tsv --decoy-results-psms 240220ko05chromatin_RAD21_3_1_1_173_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko05chromatin_RAD21_3_1_1_173_edited.pin
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240220ko09chromatin_WAPL_6_1_1_177.pin 240220ko09chromatin_WAPL_6_1_1_177 240220ko09chromatin_WAPL_6_1_1_177_percolator_target_psms.tsv 240220ko09chromatin_WAPL_6_1_1_177_percolator_decoy_psms.tsv interact-240220ko09chromatin_WAPL_6_1_1_177 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240220ko09chromatin_WAPL_6_1_1_177_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\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177\240220ko09chromatin_WAPL_6_1_1_177_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\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177\240220ko09chromatin_WAPL_6_1_1_177_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240120ko09Wapl_IP_2_1_1_40531.pin 240120ko09Wapl_IP_2_1_1_40531 240120ko09Wapl_IP_2_1_1_40531_percolator_target_psms.tsv 240120ko09Wapl_IP_2_1_1_40531_percolator_decoy_psms.tsv interact-240120ko09Wapl_IP_2_1_1_40531 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240120ko09Wapl_IP_2_1_1_40531_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\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531\240120ko09Wapl_IP_2_1_1_40531_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\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531\240120ko09Wapl_IP_2_1_1_40531_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240220ko08chromatin_WAPL_5_1_1_176.pin 240220ko08chromatin_WAPL_5_1_1_176 240220ko08chromatin_WAPL_5_1_1_176_percolator_target_psms.tsv 240220ko08chromatin_WAPL_5_1_1_176_percolator_decoy_psms.tsv interact-240220ko08chromatin_WAPL_5_1_1_176 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240220ko08chromatin_WAPL_5_1_1_176_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\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\240220ko08chromatin_WAPL_5_1_1_176_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\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\240220ko08chromatin_WAPL_5_1_1_176_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240220ko02whole_RAD21_1_1_1_170.pin 240220ko02whole_RAD21_1_1_1_170 240220ko02whole_RAD21_1_1_1_170_percolator_target_psms.tsv 240220ko02whole_RAD21_1_1_1_170_percolator_decoy_psms.tsv interact-240220ko02whole_RAD21_1_1_1_170 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240220ko02whole_RAD21_1_1_1_170_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\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170\240220ko02whole_RAD21_1_1_1_170_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\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170\240220ko02whole_RAD21_1_1_1_170_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240220ko06chromatin_RAD21_4_1_1_174.pin 240220ko06chromatin_RAD21_4_1_1_174 240220ko06chromatin_RAD21_4_1_1_174_percolator_target_psms.tsv 240220ko06chromatin_RAD21_4_1_1_174_percolator_decoy_psms.tsv interact-240220ko06chromatin_RAD21_4_1_1_174 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240220ko06chromatin_RAD21_4_1_1_174_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\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174\240220ko06chromatin_RAD21_4_1_1_174_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\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174\240220ko06chromatin_RAD21_4_1_1_174_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240220ko03whole_RAD21_2_1_1_171.pin 240220ko03whole_RAD21_2_1_1_171 240220ko03whole_RAD21_2_1_1_171_percolator_target_psms.tsv 240220ko03whole_RAD21_2_1_1_171_percolator_decoy_psms.tsv interact-240220ko03whole_RAD21_2_1_1_171 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240220ko03whole_RAD21_2_1_1_171_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\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171\240220ko03whole_RAD21_2_1_1_171_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\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171\240220ko03whole_RAD21_2_1_1_171_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240120ko08Wapl_IP_1_1_1_40530.pin 240120ko08Wapl_IP_1_1_1_40530 240120ko08Wapl_IP_1_1_1_40530_percolator_target_psms.tsv 240120ko08Wapl_IP_1_1_1_40530_percolator_decoy_psms.tsv interact-240120ko08Wapl_IP_1_1_1_40530 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240120ko08Wapl_IP_1_1_1_40530_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\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530\240120ko08Wapl_IP_1_1_1_40530_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\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530\240120ko08Wapl_IP_1_1_1_40530_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240220ko05chromatin_RAD21_3_1_1_173.pin 240220ko05chromatin_RAD21_3_1_1_173 240220ko05chromatin_RAD21_3_1_1_173_percolator_target_psms.tsv 240220ko05chromatin_RAD21_3_1_1_173_percolator_decoy_psms.tsv interact-240220ko05chromatin_RAD21_3_1_1_173 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240220ko05chromatin_RAD21_3_1_1_173_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\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173\240220ko05chromatin_RAD21_3_1_1_173_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\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173\240220ko05chromatin_RAD21_3_1_1_173_percolator_decoy_psms.tsv
ProteinProphet [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\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\240220ko\MSFragger_iBAQ\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
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\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas --prefix rev_
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
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\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
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\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
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\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
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\240220ko\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\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
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\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
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\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
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\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
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\240220ko\MSFragger_iBAQ]
java -Xmx81G -Dlibs.bruker.dir="D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\bruker" -Dlibs.thermo.dir="D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\thermo" -cp "D:\Applications\FragPipe-20.0\fragpipe\tools\jfreechart-1.5.3.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\IonQuant-1.9.8.jar" ionquant.IonQuant --threads 15 --ionmobility 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\filelist_ionquant.txt --modlist J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\modmasses_ionquant.txt
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
    Cmd: [CheckCentroid], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
    Cmd: [MSFragger], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
    Cmd: [MSBooster], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
    Cmd: [Percolator], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
    Cmd: [ProteinProphet], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
    Cmd: [PhilosopherDbAnnotate], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
    Cmd: [PhilosopherFilter], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
    Cmd: [PhilosopherReport], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
    Cmd: [IonQuant], Work dir: [J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]

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

~~~~~~Sample of D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas~~~~~~~
>rev_sp|A0A087WPF7|AUTS2_MOUSE Autism susceptibility gene 2 protein homolog OS=Mus musculus OX=10090 GN=Auts2 PE=1 SV=2
>rev_sp|O88998|NOE1_MOUSE Noelin OS=Mus musculus OX=10090 GN=Olfm1 PE=1 SV=1
>rev_sp|P43267|SOX15_MOUSE Protein SOX-15 OS=Mus musculus OX=10090 GN=Sox15 PE=1 SV=3
>rev_sp|Q08ED0|B2L15_MOUSE Bcl-2-like protein 15 OS=Mus musculus OX=10090 GN=Bcl2l15 PE=2 SV=2
>rev_sp|Q60898|SLAP1_MOUSE Src-like-adapter OS=Mus musculus OX=10090 GN=Sla PE=1 SV=3
>rev_sp|Q7TNS2|MIC10_MOUSE MICOS complex subunit Mic10 OS=Mus musculus OX=10090 GN=Micos10 PE=1 SV=1
>rev_sp|Q8BY79|S35G1_MOUSE Solute carrier family 35 member G1 OS=Mus musculus OX=10090 GN=Slc35g1 PE=2 SV=1
>rev_sp|Q8R4U1|MYPOP_MOUSE Myb-related transcription factor, partner of profilin OS=Mus musculus OX=10090 GN=Mypop PE=1 SV=1
>rev_sp|Q9CQ60|6PGL_MOUSE 6-phosphogluconolactonase OS=Mus musculus OX=10090 GN=Pgls PE=1 SV=1
>rev_sp|Q9EQ20|MMSA_MOUSE Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial OS=Mus musculus OX=10090 GN=Aldh6a1 PE=1 SV=1
>rev_sp|T1NXB5|VSTM4_MOUSE V-set and transmembrane domain-containing protein 4 OS=Mus musculus OX=10090 GN=Vstm4 PE=1 SV=1
>sp|O88990|ACTN3_MOUSE Alpha-actinin-3 OS=Mus musculus OX=10090 GN=Actn3 PE=2 SV=1
>sp|P43241|CDX2_MOUSE Homeobox protein CDX-2 OS=Mus musculus OX=10090 GN=Cdx2 PE=1 SV=1
>sp|Q08AU9|CQ058_MOUSE UPF0450 protein C17orf58 homolog OS=Mus musculus OX=10090 PE=3 SV=1
>sp|Q60893|OL151_MOUSE Olfactory receptor 151 OS=Mus musculus OX=10090 GN=Olfr151 PE=2 SV=2
>sp|Q7TNP2|2AAB_MOUSE Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform OS=Mus musculus OX=10090 GN=Ppp2r1b PE=1 SV=2
>sp|Q8BY35|FGD2_MOUSE FYVE, RhoGEF and PH domain-containing protein 2 OS=Mus musculus OX=10090 GN=Fgd2 PE=1 SV=1
>sp|Q8R4T1|CYS1_MOUSE Cystin-1 OS=Mus musculus OX=10090 GN=Cys1 PE=1 SV=1
>sp|Q9CQ54|NDUC2_MOUSE NADH dehydrogenase [ubiquinone] 1 subunit C2 OS=Mus musculus OX=10090 GN=Ndufc2 PE=1 SV=1
>sp|Q9EQ14|IL23A_MOUSE Interleukin-23 subunit alpha OS=Mus musculus OX=10090 GN=Il23a PE=1 SV=1
>sp|Q9Z351|KCNQ2_MOUSE Potassium voltage-gated channel subfamily KQT member 2 OS=Mus musculus OX=10090 GN=Kcnq2 PE=1 SV=1
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ 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\\UniprotMouse\\2021-07-15-decoys-reviewed-contam-UP000000589.fas

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
Table.editor=304.207146
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
diann.quantification-strategy-2=QuantUMS (high accuracy)
diann.run-dia-nn=false
diann.run-dia-plex=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=true
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fpop.fpop-tmt=false
fpop.label_control=
fpop.label_fpop=
fpop.region_size=1
fpop.run-fpop=false
fpop.subtract-control=false
fragpipe-config.bin-diann=D\:\\Applications\\FragPipe-21.1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=D\:\\Applications\\FragPipe-20.0\\fragpipe\\tools\\IonQuant-1.9.8.jar
fragpipe-config.bin-msfragger=D\:\\Applications\\FragPipe-20.0\\fragpipe\\tools\\MSFragger-3.8\\MSFragger-3.8.jar
fragpipe-config.bin-philosopher=D\:\\Applications\\FragPipe-20.0\\fragpipe\\tools\\philosopher_v5.0.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\gt5oc\\Anaconda3\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=true
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2/3
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
msfragger.output_report_topN_dia2=3
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=true
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name=stricttrypsin
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.write_calibrated_mzml=false
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=4
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --picked --prot 0.01
phi-report.pep-level-summary=true
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=00.2
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=00.1
ptmshepherd.diagmine_fragMinSpecDiff=00.1
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=00.2
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=2,0.5,0.1
ptmshepherd.prob_dhexY=2,0.5
ptmshepherd.prob_neuacOx=2,0.05,0.2
ptmshepherd.prob_neugcOx=2,0.05,0.2
ptmshepherd.prob_phosphoOx=2,0.05,0.2
ptmshepherd.prob_regY=5,0.5
ptmshepherd.prob_sulfoOx=2,0.05,0.2
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
run-diaumpire=false
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=J\:\\MSFragger_process\\Saitou-lab\\240220ko\\MSFragger_iBAQ
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.misc.save-sdrf=true
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=15

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx81G -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\240220ko\240120ko08Wapl_IP_1_1_1_40530.d 15
Done in 0.0 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:22:31] Executing Workspace  v5.0.0                  
INFO[18:22:31] Removing workspace                           
WARN[18:22:31] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[18:22:31] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
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\fa488227-8733-4147-860b-3a542ff5a530
INFO[18:22:32] Executing Workspace  v5.0.0                  
INFO[18:22:32] Creating workspace                           
INFO[18:22:32] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:22:32] Executing Workspace  v5.0.0                  
INFO[18:22:32] Removing workspace                           
WARN[18:22:32] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[18:22:32] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
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\e25bd5a2-e142-40df-abc3-376f74f1b306
INFO[18:22:32] Executing Workspace  v5.0.0                  
INFO[18:22:32] Creating workspace                           
INFO[18:22:32] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:22:33] Executing Workspace  v5.0.0                  
INFO[18:22:33] Removing workspace                           
WARN[18:22:33] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[18:22:33] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
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\a315c1e4-9823-4e8a-b0b5-9e248d95db61
INFO[18:22:33] Executing Workspace  v5.0.0                  
INFO[18:22:33] Creating workspace                           
INFO[18:22:33] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:22:34] Executing Workspace  v5.0.0                  
INFO[18:22:34] Removing workspace                           
WARN[18:22:34] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[18:22:34] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
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\09081fac-1125-4f38-814e-317caca7f58f
INFO[18:22:34] Executing Workspace  v5.0.0                  
INFO[18:22:34] Creating workspace                           
INFO[18:22:34] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:22:34] Executing Workspace  v5.0.0                  
INFO[18:22:34] Removing workspace                           
WARN[18:22:34] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[18:22:34] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\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\f6360d1f-c101-4fa2-ba25-ab4e2669cf1a
INFO[18:22:35] Executing Workspace  v5.0.0                  
INFO[18:22:35] Creating workspace                           
INFO[18:22:35] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:22:35] Executing Workspace  v5.0.0                  
INFO[18:22:35] Removing workspace                           
WARN[18:22:35] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[18:22:35] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
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\f203cfd1-2381-4058-89ed-e88d3b596e6f
INFO[18:22:36] Executing Workspace  v5.0.0                  
INFO[18:22:36] Creating workspace                           
INFO[18:22:36] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:22:36] Executing Workspace  v5.0.0                  
INFO[18:22:36] Removing workspace                           
WARN[18:22:36] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[18:22:36] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
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\9b6bb096-b8e3-4f46-9e66-795ea4516f9c
INFO[18:22:37] Executing Workspace  v5.0.0                  
INFO[18:22:37] Creating workspace                           
INFO[18:22:37] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:22:37] Executing Workspace  v5.0.0                  
INFO[18:22:37] Removing workspace                           
WARN[18:22:37] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[18:22:37] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
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\524bd1c9-cc5c-46f1-9e1f-193fca8bcf0f
INFO[18:22:37] Executing Workspace  v5.0.0                  
INFO[18:22:37] Creating workspace                           
INFO[18:22:37] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:22:38] Executing Workspace  v5.0.0                  
INFO[18:22:38] Removing workspace                           
WARN[18:22:38] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[18:22:38] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
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\90c321b4-ec88-48fc-92a6-42c5ea1db795
INFO[18:22:38] Executing Workspace  v5.0.0                  
INFO[18:22:38] Creating workspace                           
INFO[18:22:38] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
java -jar -Dfile.encoding=UTF-8 -Xmx81G D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\fragger.params J:\MSFragger_process\Saitou-lab\240220ko\240120ko08Wapl_IP_1_1_1_40530.d J:\MSFragger_process\Saitou-lab\240220ko\240120ko09Wapl_IP_2_1_1_40531.d J:\MSFragger_process\Saitou-lab\240220ko\240220ko02whole_RAD21_1_1_1_170.d J:\MSFragger_process\Saitou-lab\240220ko\240220ko03whole_RAD21_2_1_1_171.d J:\MSFragger_process\Saitou-lab\240220ko\240220ko05chromatin_RAD21_3_1_1_173.d J:\MSFragger_process\Saitou-lab\240220ko\240220ko06chromatin_RAD21_4_1_1_174.d J:\MSFragger_process\Saitou-lab\240220ko\240220ko08chromatin_WAPL_5_1_1_176.d J:\MSFragger_process\Saitou-lab\240220ko\240220ko09chromatin_WAPL_6_1_1_177.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 81 GB memory
Checking database...
Checking spectral files...
J:\MSFragger_process\Saitou-lab\240220ko\240120ko09Wapl_IP_2_1_1_40531.d: Scans = 60262
J:\MSFragger_process\Saitou-lab\240220ko\240120ko08Wapl_IP_1_1_1_40530.d: Scans = 60078
J:\MSFragger_process\Saitou-lab\240220ko\240220ko02whole_RAD21_1_1_1_170.d: Scans = 60906
J:\MSFragger_process\Saitou-lab\240220ko\240220ko03whole_RAD21_2_1_1_171.d: Scans = 60890
J:\MSFragger_process\Saitou-lab\240220ko\240220ko08chromatin_WAPL_5_1_1_176.d: Scans = 60915
J:\MSFragger_process\Saitou-lab\240220ko\240220ko09chromatin_WAPL_6_1_1_177.d: Scans = 60917
J:\MSFragger_process\Saitou-lab\240220ko\240220ko05chromatin_RAD21_3_1_1_173.d: Scans = 60909
J:\MSFragger_process\Saitou-lab\240220ko\240220ko06chromatin_RAD21_4_1_1_174.d: Scans = 60899
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\240220ko\240120ko08Wapl_IP_1_1_1_40530.d converted with timsdata-2-21-0-4. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\240220ko\240120ko09Wapl_IP_2_1_1_40531.d converted with timsdata-2-21-0-4. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\240220ko\240220ko02whole_RAD21_1_1_1_170.d converted with timsdata-2-21-0-4. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\240220ko\240220ko03whole_RAD21_2_1_1_171.d converted with timsdata-2-21-0-4. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\240220ko\240220ko05chromatin_RAD21_3_1_1_173.d converted with timsdata-2-21-0-4. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\240220ko\240220ko06chromatin_RAD21_4_1_1_174.d converted with timsdata-2-21-0-4. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\240220ko\240220ko08chromatin_WAPL_5_1_1_176.d converted with timsdata-2-21-0-4. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\240220ko\240220ko09chromatin_WAPL_6_1_1_177.d converted with timsdata-2-21-0-4. Will use this mzBIN file.
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 15
database_name = D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas
decoy_prefix = rev_
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 20.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 0
override_charge = 0
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
activation_types = all
group_variable = 0
require_precursor = 1
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.10 Da.
280170470 fragments to be searched in 1 slices (4.17 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 2.69 s
	001. 240120ko08Wapl_IP_1_1_1_40530.mzBIN 26.2 s | deisotoping 1.2 s
		[progress: 127523/127523 (100%) - 42923 spectra/s] 3.0s | postprocessing 0.5 s
	002. 240120ko09Wapl_IP_2_1_1_40531.mzBIN 20.6 s | deisotoping 0.8 s
		[progress: 136128/136128 (100%) - 59915 spectra/s] 2.3s | postprocessing 0.5 s
	003. 240220ko02whole_RAD21_1_1_1_170.mzBIN 34.0 s | deisotoping 1.2 s
		[progress: 193243/193243 (100%) - 52101 spectra/s] 3.7s | postprocessing 0.3 s
	004. 240220ko03whole_RAD21_2_1_1_171.mzBIN 35.6 s | deisotoping 1.4 s
		[progress: 196217/196217 (100%) - 55210 spectra/s] 3.6s | postprocessing 0.3 s
	005. 240220ko05chromatin_RAD21_3_1_1_173.mzBIN 39.1 s | deisotoping 1.4 s
		[progress: 204050/204050 (100%) - 57253 spectra/s] 3.6s | postprocessing 0.3 s
	006. 240220ko06chromatin_RAD21_4_1_1_174.mzBIN 39.9 s | deisotoping 1.5 s
		[progress: 206884/206884 (100%) - 54876 spectra/s] 3.8s | postprocessing 0.3 s
	007. 240220ko08chromatin_WAPL_5_1_1_176.mzBIN 33.6 s | deisotoping 1.2 s
		[progress: 173246/173246 (100%) - 55034 spectra/s] 3.1s | postprocessing 0.2 s
	008. 240220ko09chromatin_WAPL_6_1_1_177.mzBIN 35.5 s | deisotoping 1.4 s
		[progress: 181741/181741 (100%) - 52420 spectra/s] 3.5s | postprocessing 0.3 s
***************************FIRST SEARCH DONE IN 5.210 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |  -5.25   3.84 |   0.06   3.37 |  -5.46   7.03 |  -1.02   7.04  
 002 |  -5.16   3.92 |  -0.11   3.30 |  -5.24   6.90 |  -0.91   6.84  
 003 |  -0.40   5.57 |   0.00   4.28 |  -1.67   7.60 |  -0.40   7.53  
 004 |  -0.17   5.56 |   0.15   4.40 |  -1.57   7.58 |  -0.33   7.54  
 005 |  -0.17   4.44 |  -0.03   3.80 |  -1.13   7.30 |  -0.15   7.23  
 006 |  -0.17   4.42 |   0.03   3.90 |  -1.17   7.36 |  -0.19   7.30  
 007 |  -0.77   4.84 |   0.30   3.88 |  -0.83   7.26 |  -0.10   7.33  
 008 |  -0.82   5.27 |  -0.43   4.44 |  -0.75   7.29 |  -0.14   7.29  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count | skip  | skip  | skip  |  23800|  23914|  23300| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |  23361|  23601|  23663|  23914|  23895| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |  23623
-------|-------
-------|-------
 Rm P. |    0  
-------|-------
 Count |  22690
-------|-------
New fragment_mass_tolerance = 20 PPM
New use_topN_peaks = 150
New minimum_ratio = 0.010000
New intensity_transform = 0
New remove_precursor_peak = 1
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 2.330 MIN*********

************************************MAIN SEARCH************************************
Checking database...
Parameters:
num_threads = 15
database_name = D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas
decoy_prefix = rev_
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 20.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1/2/3
mass_offsets = 0.0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 1
override_charge = 0
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
activation_types = all
group_variable = 0
require_precursor = 1
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.10 Da.
280170470 fragments to be searched in 1 slices (4.17 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 1.94 s
	001. 240120ko08Wapl_IP_1_1_1_40530.mzBIN_calibrated 2.2 s
		[progress: 124917/124917 (100%) - 48455 spectra/s] 2.6s | remapping alternative proteins and postprocessing 4.6 s
	002. 240120ko09Wapl_IP_2_1_1_40531.mzBIN_calibrated 2.4 s
		[progress: 133737/133737 (100%) - 46324 spectra/s] 2.9s | remapping alternative proteins and postprocessing 3.4 s
	003. 240220ko02whole_RAD21_1_1_1_170.mzBIN_calibrated 3.6 s
		[progress: 192122/192122 (100%) - 43359 spectra/s] 4.4s | remapping alternative proteins and postprocessing 2.5 s
	004. 240220ko03whole_RAD21_2_1_1_171.mzBIN_calibrated 3.7 s
		[progress: 195197/195197 (100%) - 42657 spectra/s] 4.6s | remapping alternative proteins and postprocessing 2.7 s
	005. 240220ko05chromatin_RAD21_3_1_1_173.mzBIN_calibrated 3.9 s
		[progress: 202378/202378 (100%) - 43188 spectra/s] 4.7s | remapping alternative proteins and postprocessing 2.2 s
	006. 240220ko06chromatin_RAD21_4_1_1_174.mzBIN_calibrated 4.0 s
		[progress: 205272/205272 (100%) - 41680 spectra/s] 4.9s | remapping alternative proteins and postprocessing 2.4 s
	007. 240220ko08chromatin_WAPL_5_1_1_176.mzBIN_calibrated 3.5 s
		[progress: 172009/172009 (100%) - 42831 spectra/s] 4.0s | remapping alternative proteins and postprocessing 1.6 s
	008. 240220ko09chromatin_WAPL_6_1_1_177.mzBIN_calibrated 3.6 s
		[progress: 180570/180570 (100%) - 43427 spectra/s] 4.2s | remapping alternative proteins and postprocessing 1.7 s
***************************MAIN SEARCH DONE IN 1.429 MIN***************************

*******************************TOTAL TIME 8.969 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\240220ko\240120ko08Wapl_IP_1_1_1_40530.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530\240120ko08Wapl_IP_1_1_1_40530.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\240220ko\240120ko08Wapl_IP_1_1_1_40530.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530\240120ko08Wapl_IP_1_1_1_40530.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\240220ko\240120ko09Wapl_IP_2_1_1_40531.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531\240120ko09Wapl_IP_2_1_1_40531.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\240220ko\240120ko09Wapl_IP_2_1_1_40531.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531\240120ko09Wapl_IP_2_1_1_40531.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\240220ko\240220ko02whole_RAD21_1_1_1_170.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170\240220ko02whole_RAD21_1_1_1_170.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\240220ko\240220ko02whole_RAD21_1_1_1_170.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170\240220ko02whole_RAD21_1_1_1_170.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\240220ko\240220ko03whole_RAD21_2_1_1_171.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171\240220ko03whole_RAD21_2_1_1_171.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\240220ko\240220ko03whole_RAD21_2_1_1_171.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171\240220ko03whole_RAD21_2_1_1_171.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\240220ko\240220ko05chromatin_RAD21_3_1_1_173.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173\240220ko05chromatin_RAD21_3_1_1_173.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\240220ko\240220ko05chromatin_RAD21_3_1_1_173.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173\240220ko05chromatin_RAD21_3_1_1_173.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\240220ko\240220ko06chromatin_RAD21_4_1_1_174.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174\240220ko06chromatin_RAD21_4_1_1_174.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\240220ko\240220ko06chromatin_RAD21_4_1_1_174.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174\240220ko06chromatin_RAD21_4_1_1_174.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\240220ko\240220ko08chromatin_WAPL_5_1_1_176.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\240220ko08chromatin_WAPL_5_1_1_176.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\240220ko\240220ko08chromatin_WAPL_5_1_1_176.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\240220ko08chromatin_WAPL_5_1_1_176.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\240220ko\240220ko09chromatin_WAPL_6_1_1_177.pepXML J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177\240220ko09chromatin_WAPL_6_1_1_177.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\240220ko\240220ko09chromatin_WAPL_6_1_1_177.pin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177\240220ko09chromatin_WAPL_6_1_1_177.pin
Process 'MSFragger move pin' finished, exit code: 0
MSBooster [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
java -Xmx81G -cp "D:\Applications\FragPipe-20.0\fragpipe\tools\msbooster-1.1.11.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar" Features.MainClass --paramsList J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\msbooster_params.txt
MSBooster v1.1.11
Using 15 threads
Generating input file for DIA-NN
111551 unique peptides from 255511 PSMs
Writing DIA-NN input file
Diann input file generation took 1267 milliseconds
Input file at  J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\spectraRT.tsv
111551 unique peptides from 255511 PSMs
createFull input file generation took 603 milliseconds
Input file at  J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\spectraRT_full.tsv
Generating DIA-NN predictions
D:\Applications\FragPipe-20.0\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\spectraRT.tsv --predict --threads 15 --strip-unknown-mods --mod TMT,229.1629 --predict-n-frag 100
DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks)
Compiled on Sep 15 2022 18:28:57
Current date and time: Wed Jan 22 18:31:43 2025
CPU: GenuineIntel Intel(R) Core(TM) i7-7820X CPU @ 3.60GHz
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 16
Predicted spectra will be saved in a binary format
Thread number set to 15
DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option
Modification TMT with mass delta 229.163 added to the list of recognised modifications for spectral library-based search
Deep learning predictor will predict 100 fragments
Cannot find a UniMod modification match for TMT: 73.0618 minimal mass discrepancy; using the original modificaiton name

0 files will be processed
[0:00] Loading spectral library J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\spectraRT.tsv
[0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 111551 precursors in 105935 elution groups.
[0:00] Encoding peptides for spectra and RTs prediction
[0:00] Predicting spectra and IMs
[0:21] Predicting RTs
[0:29] Decoding predicted spectra and IMs
[0:32] Decoding RTs
[0:32] Saving the list of predictions to J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\spectraRT.predicted.bin
Finished
Done generating DIA-NN predictions
Model running took 33687 milliseconds
Generating edited pin with following features: [unweightedSpectralEntropy, deltaRTLOESS]
Loading predicted spectra
Processing 240120ko08Wapl_IP_1_1_1_40530_uncalibrated.mzML
RT regression using 3417 PSMs
Edited pin file at J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530\240120ko08Wapl_IP_1_1_1_40530_edited.pin
Processing 240120ko09Wapl_IP_2_1_1_40531_uncalibrated.mzML
RT regression using 4042 PSMs
Edited pin file at J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531\240120ko09Wapl_IP_2_1_1_40531_edited.pin
Processing 240220ko02whole_RAD21_1_1_1_170_uncalibrated.mzML
RT regression using 1307 PSMs
Edited pin file at J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170\240220ko02whole_RAD21_1_1_1_170_edited.pin
Processing 240220ko03whole_RAD21_2_1_1_171_uncalibrated.mzML
RT regression using 1447 PSMs
Edited pin file at J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171\240220ko03whole_RAD21_2_1_1_171_edited.pin
Processing 240220ko05chromatin_RAD21_3_1_1_173_uncalibrated.mzML
RT regression using 535 PSMs
Edited pin file at J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173\240220ko05chromatin_RAD21_3_1_1_173_edited.pin
Processing 240220ko06chromatin_RAD21_4_1_1_174_uncalibrated.mzML
RT regression using 920 PSMs
Edited pin file at J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174\240220ko06chromatin_RAD21_4_1_1_174_edited.pin
Processing 240220ko08chromatin_WAPL_5_1_1_176_uncalibrated.mzML
RT regression using 246 PSMs
Edited pin file at J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\240220ko08chromatin_WAPL_5_1_1_176_edited.pin
Processing 240220ko09chromatin_WAPL_6_1_1_177_uncalibrated.mzML
RT regression using 321 PSMs
Edited pin file at J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177\240220ko09chromatin_WAPL_6_1_1_177_edited.pin
Done in 63655 ms
Process 'MSBooster' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko09chromatin_WAPL_6_1_1_177_percolator_target_psms.tsv --decoy-results-psms 240220ko09chromatin_WAPL_6_1_1_177_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko09chromatin_WAPL_6_1_1_177_edited.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko09chromatin_WAPL_6_1_1_177_percolator_target_psms.tsv --decoy-results-psms 240220ko09chromatin_WAPL_6_1_1_177_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko09chromatin_WAPL_6_1_1_177_edited.pin
Started Wed Jan 22 18:33:20 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 240220ko09chromatin_WAPL_6_1_1_177_edited.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 19580 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 13504 positives and 6076 negatives, size ratio=2.22251 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 26 as initial direction. Could separate 3717 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 26 as initial direction. Could separate 3442 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 26 as initial direction. Could separate 3476 training set positives with q<0.01 in that direction.
Found 5291 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.2500 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 6833 PSMs with q<0.01
Iteration 2:	Estimated 7058 PSMs with q<0.01
Iteration 3:	Estimated 7091 PSMs with q<0.01
Iteration 4:	Estimated 7132 PSMs with q<0.01
Iteration 5:	Estimated 7137 PSMs with q<0.01
Iteration 6:	Estimated 7136 PSMs with q<0.01
Iteration 7:	Estimated 7137 PSMs with q<0.01
Iteration 8:	Estimated 7138 PSMs with q<0.01
Iteration 9:	Estimated 7141 PSMs with q<0.01
Iteration 10:	Estimated 7141 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
-0.3253	-0.3512	-0.3258	abs_ppm
-0.2855	-0.2388	-0.1720	isotope_errors
-0.7958	-0.6989	-0.7326	log10_evalue
 0.8049	 0.9764	 1.1449	hyperscore
 0.7021	 0.6981	 0.5865	delta_hyperscore
 0.8346	 0.8090	 0.3571	matched_ion_num
-0.6676	-0.6220	-0.5643	complementary_ions
 0.0820	-0.1817	-0.1194	ion_series
-0.3226	-0.3174	-0.2422	weighted_average_abs_fragment_ppm
 0.7731	 0.5965	 0.7067	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.3739	-0.3550	-0.3018	nmc
-0.0255	-0.0451	 0.0510	charge_1
 0.3312	 0.2766	 0.2858	charge_2
-0.2106	-0.1185	-0.1536	charge_3
-0.1469	-0.2054	-0.1905	charge_4
-0.2400	-0.2383	-0.2091	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
 0.0108	 0.0172	-0.0615	15.9949M
 1.8741	 1.6076	 1.6653	unweighted_spectral_entropy
-0.5454	-0.4165	-0.3744	delta_RT_loess
-0.9504	-0.6091	-1.2160	m0
Found 7107 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 13504 target PSMs and 6076 decoy PSMs.
Calculating q values.
Final list yields 7107 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.9900 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240120ko09Wapl_IP_2_1_1_40531_percolator_target_psms.tsv --decoy-results-psms 240120ko09Wapl_IP_2_1_1_40531_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240120ko09Wapl_IP_2_1_1_40531_edited.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240120ko09Wapl_IP_2_1_1_40531_percolator_target_psms.tsv --decoy-results-psms 240120ko09Wapl_IP_2_1_1_40531_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240120ko09Wapl_IP_2_1_1_40531_edited.pin
Started Wed Jan 22 18:33:24 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 240120ko09Wapl_IP_2_1_1_40531_edited.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 44992 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 36538 positives and 8454 negatives, size ratio=4.32198 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 15738 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 15876 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 26 as initial direction. Could separate 15825 training set positives with q<0.01 in that direction.
Found 23378 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.5710 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 27484 PSMs with q<0.01
Iteration 2:	Estimated 27772 PSMs with q<0.01
Iteration 3:	Estimated 27817 PSMs with q<0.01
Iteration 4:	Estimated 27831 PSMs with q<0.01
Iteration 5:	Estimated 27830 PSMs with q<0.01
Iteration 6:	Estimated 27833 PSMs with q<0.01
Iteration 7:	Estimated 27834 PSMs with q<0.01
Iteration 8:	Estimated 27835 PSMs with q<0.01
Iteration 9:	Estimated 27835 PSMs with q<0.01
Iteration 10:	Estimated 27836 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
-0.2322	-0.2263	-0.2240	abs_ppm
-0.2476	-0.2653	-0.1801	isotope_errors
-0.8161	-1.0263	-0.8854	log10_evalue
 0.6967	 0.7888	 0.6856	hyperscore
 0.8924	 0.8600	 0.7897	delta_hyperscore
 1.1916	 0.8235	 0.9974	matched_ion_num
-0.9860	-1.0125	-0.9851	complementary_ions
-0.1137	-0.1164	-0.0644	ion_series
-0.1422	-0.1400	-0.1716	weighted_average_abs_fragment_ppm
 0.2848	 0.2461	 0.3291	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.0886	-0.1309	-0.0363	nmc
 0.0500	 0.0202	 0.0595	charge_1
 0.1269	 0.1297	 0.1286	charge_2
-0.0269	-0.0209	-0.0229	charge_3
-0.1815	-0.2042	-0.1951	charge_4
-0.0962	-0.0397	-0.0980	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
-0.0770	-0.0399	-0.0874	15.9949M
 0.9847	 1.0407	 1.1227	unweighted_spectral_entropy
-0.8065	-0.5958	-0.5740	delta_RT_loess
 1.4105	 1.3934	 1.0282	m0
Found 27710 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 36538 target PSMs and 8454 decoy PSMs.
Calculating q values.
Final list yields 27716 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.9350 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko08chromatin_WAPL_5_1_1_176_percolator_target_psms.tsv --decoy-results-psms 240220ko08chromatin_WAPL_5_1_1_176_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko08chromatin_WAPL_5_1_1_176_edited.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko08chromatin_WAPL_5_1_1_176_percolator_target_psms.tsv --decoy-results-psms 240220ko08chromatin_WAPL_5_1_1_176_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko08chromatin_WAPL_5_1_1_176_edited.pin
Started Wed Jan 22 18:33:31 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 240220ko08chromatin_WAPL_5_1_1_176_edited.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 16858 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 11532 positives and 5326 negatives, size ratio=2.16523 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 26 as initial direction. Could separate 3084 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 26 as initial direction. Could separate 3048 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 26 as initial direction. Could separate 3063 training set positives with q<0.01 in that direction.
Found 4593 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.2030 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 5666 PSMs with q<0.01
Iteration 2:	Estimated 5849 PSMs with q<0.01
Iteration 3:	Estimated 5916 PSMs with q<0.01
Iteration 4:	Estimated 5931 PSMs with q<0.01
Iteration 5:	Estimated 5936 PSMs with q<0.01
Iteration 6:	Estimated 5939 PSMs with q<0.01
Iteration 7:	Estimated 5941 PSMs with q<0.01
Iteration 8:	Estimated 5946 PSMs with q<0.01
Iteration 9:	Estimated 5946 PSMs with q<0.01
Iteration 10:	Estimated 5946 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
-0.3043	-0.3063	-0.3548	abs_ppm
-0.2082	-0.4113	-0.2639	isotope_errors
-1.1488	-0.8189	-0.7579	log10_evalue
 0.8440	 1.0537	 0.8085	hyperscore
 0.9194	 0.9544	 0.4879	delta_hyperscore
 0.7623	 0.8321	 0.9788	matched_ion_num
-0.7893	-0.8034	-0.6080	complementary_ions
-0.0871	 0.0503	 0.0007	ion_series
-0.1991	-0.2099	-0.1583	weighted_average_abs_fragment_ppm
 0.3456	 0.6986	 0.5398	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.2967	-0.4399	-0.4857	nmc
 0.0497	 0.0941	 0.0678	charge_1
 0.1633	 0.2443	 0.2096	charge_2
-0.0409	-0.0431	-0.1363	charge_3
-0.2066	-0.3359	-0.1379	charge_4
-0.1085	-0.1938	-0.0718	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
 0.0886	-0.0029	-0.0117	15.9949M
 1.9455	 2.2913	 1.6721	unweighted_spectral_entropy
-0.3687	-0.5114	-0.5010	delta_RT_loess
-0.9794	-0.9903	-0.8736	m0
Found 5877 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 11532 target PSMs and 5326 decoy PSMs.
Calculating q values.
Final list yields 5885 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.5210 cpu seconds or 3 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko02whole_RAD21_1_1_1_170_percolator_target_psms.tsv --decoy-results-psms 240220ko02whole_RAD21_1_1_1_170_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko02whole_RAD21_1_1_1_170_edited.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko02whole_RAD21_1_1_1_170_percolator_target_psms.tsv --decoy-results-psms 240220ko02whole_RAD21_1_1_1_170_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko02whole_RAD21_1_1_1_170_edited.pin
Started Wed Jan 22 18:33:34 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 240220ko02whole_RAD21_1_1_1_170_edited.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 35321 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 27269 positives and 8052 negatives, size ratio=3.38661 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 9693 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 26 as initial direction. Could separate 9954 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 26 as initial direction. Could separate 9777 training set positives with q<0.01 in that direction.
Found 14162 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4420 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 18091 PSMs with q<0.01
Iteration 2:	Estimated 18411 PSMs with q<0.01
Iteration 3:	Estimated 18451 PSMs with q<0.01
Iteration 4:	Estimated 18455 PSMs with q<0.01
Iteration 5:	Estimated 18462 PSMs with q<0.01
Iteration 6:	Estimated 18459 PSMs with q<0.01
Iteration 7:	Estimated 18467 PSMs with q<0.01
Iteration 8:	Estimated 18464 PSMs with q<0.01
Iteration 9:	Estimated 18467 PSMs with q<0.01
Iteration 10:	Estimated 18469 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
-0.2111	-0.2822	-0.2156	abs_ppm
-0.2831	-0.3783	-0.3622	isotope_errors
-0.5536	-0.8427	-0.5849	log10_evalue
 0.8553	 1.1655	 1.1890	hyperscore
 0.6623	 0.7059	 0.6113	delta_hyperscore
 0.2819	 0.5370	 0.1156	matched_ion_num
-0.6736	-0.7007	-0.7366	complementary_ions
 0.0615	-0.2696	 0.0137	ion_series
-0.2455	-0.2769	-0.2618	weighted_average_abs_fragment_ppm
 0.4421	 0.5249	 0.5376	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1789	-0.1744	-0.2340	nmc
-0.0009	 0.0677	-0.0012	charge_1
 0.1888	 0.2307	 0.2178	charge_2
-0.0701	-0.0601	-0.0956	charge_3
-0.2042	-0.2963	-0.1775	charge_4
-0.1189	-0.1896	-0.2037	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
 0.0462	 0.0178	 0.0392	15.9949M
 1.2683	 1.6213	 1.5404	unweighted_spectral_entropy
-0.6694	-0.7235	-0.5974	delta_RT_loess
-0.0639	 0.4990	 0.2468	m0
Found 18418 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 27269 target PSMs and 8052 decoy PSMs.
Calculating q values.
Final list yields 18421 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.0130 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko06chromatin_RAD21_4_1_1_174_percolator_target_psms.tsv --decoy-results-psms 240220ko06chromatin_RAD21_4_1_1_174_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko06chromatin_RAD21_4_1_1_174_edited.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko06chromatin_RAD21_4_1_1_174_percolator_target_psms.tsv --decoy-results-psms 240220ko06chromatin_RAD21_4_1_1_174_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko06chromatin_RAD21_4_1_1_174_edited.pin
Started Wed Jan 22 18:33:40 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 240220ko06chromatin_RAD21_4_1_1_174_edited.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 32915 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 24172 positives and 8743 negatives, size ratio=2.76473 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 26 as initial direction. Could separate 7538 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 26 as initial direction. Could separate 7447 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 26 as initial direction. Could separate 7414 training set positives with q<0.01 in that direction.
Found 11120 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4120 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 14248 PSMs with q<0.01
Iteration 2:	Estimated 14630 PSMs with q<0.01
Iteration 3:	Estimated 14697 PSMs with q<0.01
Iteration 4:	Estimated 14700 PSMs with q<0.01
Iteration 5:	Estimated 14706 PSMs with q<0.01
Iteration 6:	Estimated 14713 PSMs with q<0.01
Iteration 7:	Estimated 14718 PSMs with q<0.01
Iteration 8:	Estimated 14716 PSMs with q<0.01
Iteration 9:	Estimated 14720 PSMs with q<0.01
Iteration 10:	Estimated 14720 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
-0.3525	-0.3440	-0.3546	abs_ppm
-0.3283	-0.3842	-0.3767	isotope_errors
-0.7976	-0.8075	-1.0175	log10_evalue
 0.8110	 0.7449	 0.6801	hyperscore
 0.7800	 0.8010	 0.8374	delta_hyperscore
 0.9264	 0.8403	 0.9195	matched_ion_num
-0.8662	-0.7163	-0.5980	complementary_ions
-0.0920	-0.0906	-0.1479	ion_series
-0.2882	-0.2530	-0.2719	weighted_average_abs_fragment_ppm
 0.5507	 0.3695	 0.3895	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.2486	-0.1983	-0.2432	nmc
 0.0303	 0.0503	-0.0020	charge_1
 0.2335	 0.2140	 0.1902	charge_2
-0.0901	-0.0978	-0.0608	charge_3
-0.2341	-0.2238	-0.2266	charge_4
-0.1387	-0.0524	-0.0715	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
-0.0358	 0.0189	-0.0009	15.9949M
 1.7924	 1.4385	 1.4964	unweighted_spectral_entropy
-0.8880	-0.7193	-0.7130	delta_RT_loess
-0.1180	-0.0646	 0.0410	m0
Found 14631 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 24172 target PSMs and 8743 decoy PSMs.
Calculating q values.
Final list yields 14633 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 4.4080 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko03whole_RAD21_2_1_1_171_percolator_target_psms.tsv --decoy-results-psms 240220ko03whole_RAD21_2_1_1_171_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko03whole_RAD21_2_1_1_171_edited.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko03whole_RAD21_2_1_1_171_percolator_target_psms.tsv --decoy-results-psms 240220ko03whole_RAD21_2_1_1_171_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko03whole_RAD21_2_1_1_171_edited.pin
Started Wed Jan 22 18:33:45 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 240220ko03whole_RAD21_2_1_1_171_edited.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 36844 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 28768 positives and 8076 negatives, size ratio=3.56216 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 26 as initial direction. Could separate 11086 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 26 as initial direction. Could separate 11149 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 26 as initial direction. Could separate 11277 training set positives with q<0.01 in that direction.
Found 16635 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4510 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 19592 PSMs with q<0.01
Iteration 2:	Estimated 19844 PSMs with q<0.01
Iteration 3:	Estimated 19893 PSMs with q<0.01
Iteration 4:	Estimated 19898 PSMs with q<0.01
Iteration 5:	Estimated 19901 PSMs with q<0.01
Iteration 6:	Estimated 19901 PSMs with q<0.01
Iteration 7:	Estimated 19904 PSMs with q<0.01
Iteration 8:	Estimated 19903 PSMs with q<0.01
Iteration 9:	Estimated 19903 PSMs with q<0.01
Iteration 10:	Estimated 19903 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
-0.2983	-0.2475	-0.3383	abs_ppm
-0.3739	-0.2767	-0.3631	isotope_errors
-0.5833	-0.5037	-0.4519	log10_evalue
 0.5923	 0.7512	 1.2550	hyperscore
 0.6470	 0.5797	 0.6422	delta_hyperscore
 0.7623	 0.6029	 0.4727	matched_ion_num
-0.6543	-0.5600	-0.8152	complementary_ions
-0.0959	-0.0791	-0.1129	ion_series
-0.2453	-0.2770	-0.2693	weighted_average_abs_fragment_ppm
 0.4305	 0.3766	 0.3649	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1725	-0.1713	-0.2476	nmc
 0.0591	 0.0079	 0.0011	charge_1
 0.2030	 0.2019	 0.1956	charge_2
-0.0663	-0.0771	-0.0777	charge_3
-0.2109	-0.1987	-0.1811	charge_4
-0.1966	-0.1517	-0.1566	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
 0.0113	 0.0249	 0.0242	15.9949M
 1.3340	 1.2561	 1.4555	unweighted_spectral_entropy
-0.6633	-0.5635	-0.6510	delta_RT_loess
 0.4585	 0.4514	 0.4038	m0
Found 19845 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 28768 target PSMs and 8076 decoy PSMs.
Calculating q values.
Final list yields 19846 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 4.5190 cpu seconds or 4 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240120ko08Wapl_IP_1_1_1_40530_percolator_target_psms.tsv --decoy-results-psms 240120ko08Wapl_IP_1_1_1_40530_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240120ko08Wapl_IP_1_1_1_40530_edited.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240120ko08Wapl_IP_1_1_1_40530_percolator_target_psms.tsv --decoy-results-psms 240120ko08Wapl_IP_1_1_1_40530_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240120ko08Wapl_IP_1_1_1_40530_edited.pin
Started Wed Jan 22 18:33:51 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 240120ko08Wapl_IP_1_1_1_40530_edited.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 42682 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 34632 positives and 8050 negatives, size ratio=4.30211 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 26 as initial direction. Could separate 14727 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 26 as initial direction. Could separate 15066 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 26 as initial direction. Could separate 14766 training set positives with q<0.01 in that direction.
Found 22274 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.5580 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 25777 PSMs with q<0.01
Iteration 2:	Estimated 26172 PSMs with q<0.01
Iteration 3:	Estimated 26256 PSMs with q<0.01
Iteration 4:	Estimated 26267 PSMs with q<0.01
Iteration 5:	Estimated 26263 PSMs with q<0.01
Iteration 6:	Estimated 26267 PSMs with q<0.01
Iteration 7:	Estimated 26267 PSMs with q<0.01
Iteration 8:	Estimated 26266 PSMs with q<0.01
Iteration 9:	Estimated 26272 PSMs with q<0.01
Iteration 10:	Estimated 26273 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
-0.1618	-0.2159	-0.1754	abs_ppm
-0.2964	-0.2641	-0.3108	isotope_errors
-0.4971	-0.4426	-0.6675	log10_evalue
 0.8148	 0.8297	 0.7236	hyperscore
 0.9574	 0.9482	 0.8922	delta_hyperscore
 0.7567	 0.7723	 1.0051	matched_ion_num
-0.8562	-0.7048	-0.9868	complementary_ions
 0.0570	-0.0409	-0.1214	ion_series
-0.0917	-0.0794	-0.1186	weighted_average_abs_fragment_ppm
 0.3486	 0.3961	 0.3233	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.0785	-0.1087	-0.1285	nmc
 0.0041	-0.0085	-0.0082	charge_1
 0.1950	 0.1801	 0.1649	charge_2
-0.0616	-0.0688	-0.0406	charge_3
-0.2245	-0.1790	-0.2143	charge_4
-0.1072	-0.1065	-0.0653	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
-0.0403	-0.0898	-0.0628	15.9949M
 1.0814	 1.3099	 1.1656	unweighted_spectral_entropy
-0.7211	-0.5208	-0.5168	delta_RT_loess
 1.1141	 1.2581	 1.2468	m0
Found 26221 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 34632 target PSMs and 8050 decoy PSMs.
Calculating q values.
Final list yields 26225 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.2000 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko05chromatin_RAD21_3_1_1_173_percolator_target_psms.tsv --decoy-results-psms 240220ko05chromatin_RAD21_3_1_1_173_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko05chromatin_RAD21_3_1_1_173_edited.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 240220ko05chromatin_RAD21_3_1_1_173_percolator_target_psms.tsv --decoy-results-psms 240220ko05chromatin_RAD21_3_1_1_173_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 240220ko05chromatin_RAD21_3_1_1_173_edited.pin
Started Wed Jan 22 18:33:57 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 240220ko05chromatin_RAD21_3_1_1_173_edited.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 26319 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 18435 positives and 7884 negatives, size ratio=2.33828 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 26 as initial direction. Could separate 5027 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 4945 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 26 as initial direction. Could separate 5060 training set positives with q<0.01 in that direction.
Found 7220 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3190 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 9607 PSMs with q<0.01
Iteration 2:	Estimated 10007 PSMs with q<0.01
Iteration 3:	Estimated 10090 PSMs with q<0.01
Iteration 4:	Estimated 10120 PSMs with q<0.01
Iteration 5:	Estimated 10141 PSMs with q<0.01
Iteration 6:	Estimated 10147 PSMs with q<0.01
Iteration 7:	Estimated 10151 PSMs with q<0.01
Iteration 8:	Estimated 10153 PSMs with q<0.01
Iteration 9:	Estimated 10158 PSMs with q<0.01
Iteration 10:	Estimated 10158 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
-0.2690	-0.2863	-0.2479	abs_ppm
-0.4068	-0.3446	-0.4352	isotope_errors
-0.9808	-1.3190	-1.0962	log10_evalue
 0.7183	 0.5547	 0.4881	hyperscore
 0.7739	 0.7373	 0.7248	delta_hyperscore
 0.6150	 0.8021	 0.8730	matched_ion_num
-0.7574	-0.7197	-0.8145	complementary_ions
-0.2080	-0.0568	-0.1062	ion_series
-0.1562	-0.2443	-0.2907	weighted_average_abs_fragment_ppm
 0.3667	 0.4499	 0.3921	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1059	-0.1731	-0.1637	nmc
 0.0239	 0.0417	 0.0342	charge_1
 0.2013	 0.2610	 0.2421	charge_2
-0.0793	-0.0874	-0.0656	charge_3
-0.2013	-0.2944	-0.3130	charge_4
-0.0842	-0.1006	-0.0646	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
 0.0970	 0.0859	 0.0559	15.9949M
 1.6294	 1.5637	 1.5967	unweighted_spectral_entropy
-0.7219	-0.6238	-0.6622	delta_RT_loess
-0.6582	-0.4078	-0.5173	m0
Found 10073 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 18435 target PSMs and 7884 decoy PSMs.
Calculating q values.
Final list yields 10075 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 3.4020 cpu seconds or 4 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240220ko09chromatin_WAPL_6_1_1_177.pin 240220ko09chromatin_WAPL_6_1_1_177 240220ko09chromatin_WAPL_6_1_1_177_percolator_target_psms.tsv 240220ko09chromatin_WAPL_6_1_1_177_percolator_decoy_psms.tsv interact-240220ko09chromatin_WAPL_6_1_1_177 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240220ko09chromatin_WAPL_6_1_1_177_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\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177\240220ko09chromatin_WAPL_6_1_1_177_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\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177\240220ko09chromatin_WAPL_6_1_1_177_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240120ko09Wapl_IP_2_1_1_40531.pin 240120ko09Wapl_IP_2_1_1_40531 240120ko09Wapl_IP_2_1_1_40531_percolator_target_psms.tsv 240120ko09Wapl_IP_2_1_1_40531_percolator_decoy_psms.tsv interact-240120ko09Wapl_IP_2_1_1_40531 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240120ko09Wapl_IP_2_1_1_40531_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\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531\240120ko09Wapl_IP_2_1_1_40531_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\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531\240120ko09Wapl_IP_2_1_1_40531_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240220ko08chromatin_WAPL_5_1_1_176.pin 240220ko08chromatin_WAPL_5_1_1_176 240220ko08chromatin_WAPL_5_1_1_176_percolator_target_psms.tsv 240220ko08chromatin_WAPL_5_1_1_176_percolator_decoy_psms.tsv interact-240220ko08chromatin_WAPL_5_1_1_176 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240220ko08chromatin_WAPL_5_1_1_176_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\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\240220ko08chromatin_WAPL_5_1_1_176_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\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\240220ko08chromatin_WAPL_5_1_1_176_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240220ko02whole_RAD21_1_1_1_170.pin 240220ko02whole_RAD21_1_1_1_170 240220ko02whole_RAD21_1_1_1_170_percolator_target_psms.tsv 240220ko02whole_RAD21_1_1_1_170_percolator_decoy_psms.tsv interact-240220ko02whole_RAD21_1_1_1_170 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240220ko02whole_RAD21_1_1_1_170_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\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170\240220ko02whole_RAD21_1_1_1_170_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\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170\240220ko02whole_RAD21_1_1_1_170_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240220ko06chromatin_RAD21_4_1_1_174.pin 240220ko06chromatin_RAD21_4_1_1_174 240220ko06chromatin_RAD21_4_1_1_174_percolator_target_psms.tsv 240220ko06chromatin_RAD21_4_1_1_174_percolator_decoy_psms.tsv interact-240220ko06chromatin_RAD21_4_1_1_174 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240220ko06chromatin_RAD21_4_1_1_174_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\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174\240220ko06chromatin_RAD21_4_1_1_174_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\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174\240220ko06chromatin_RAD21_4_1_1_174_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240220ko03whole_RAD21_2_1_1_171.pin 240220ko03whole_RAD21_2_1_1_171 240220ko03whole_RAD21_2_1_1_171_percolator_target_psms.tsv 240220ko03whole_RAD21_2_1_1_171_percolator_decoy_psms.tsv interact-240220ko03whole_RAD21_2_1_1_171 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240220ko03whole_RAD21_2_1_1_171_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\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171\240220ko03whole_RAD21_2_1_1_171_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\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171\240220ko03whole_RAD21_2_1_1_171_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240120ko08Wapl_IP_1_1_1_40530.pin 240120ko08Wapl_IP_1_1_1_40530 240120ko08Wapl_IP_1_1_1_40530_percolator_target_psms.tsv 240120ko08Wapl_IP_1_1_1_40530_percolator_decoy_psms.tsv interact-240120ko08Wapl_IP_1_1_1_40530 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240120ko08Wapl_IP_1_1_1_40530_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\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530\240120ko08Wapl_IP_1_1_1_40530_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\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530\240120ko08Wapl_IP_1_1_1_40530_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 240220ko05chromatin_RAD21_3_1_1_173.pin 240220ko05chromatin_RAD21_3_1_1_173 240220ko05chromatin_RAD21_3_1_1_173_percolator_target_psms.tsv 240220ko05chromatin_RAD21_3_1_1_173_percolator_decoy_psms.tsv interact-240220ko05chromatin_RAD21_3_1_1_173 DDA 0.5 J:\MSFragger_process\Saitou-lab\240220ko\240220ko05chromatin_RAD21_3_1_1_173_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\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173\240220ko05chromatin_RAD21_3_1_1_173_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\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173\240220ko05chromatin_RAD21_3_1_1_173_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
ProteinProphet [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\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\240220ko\MSFragger_iBAQ\filelist_proteinprophet.txt
INFO[18:34:19] 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\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530\interact-240120ko08Wapl_IP_1_1_1_40530.pep.xml...
...read in 136 1+, 19566 2+, 6432 3+, 696 4+, 47 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531\interact-240120ko09Wapl_IP_2_1_1_40531.pep.xml...
...read in 170 1+, 19485 2+, 8018 3+, 752 4+, 58 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170\interact-240220ko02whole_RAD21_1_1_1_170.pep.xml...
...read in 4 1+, 14635 2+, 4371 3+, 334 4+, 55 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171\interact-240220ko03whole_RAD21_2_1_1_171.pep.xml...
...read in 7 1+, 15853 2+, 4477 3+, 355 4+, 81 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173\interact-240220ko05chromatin_RAD21_3_1_1_173.pep.xml...
...read in 6 1+, 8050 2+, 2518 3+, 241 4+, 91 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174\interact-240220ko06chromatin_RAD21_4_1_1_174.pep.xml...
...read in 4 1+, 11945 2+, 3377 3+, 280 4+, 74 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\interact-240220ko08chromatin_WAPL_5_1_1_176.pep.xml...
...read in 9 1+, 4366 2+, 1917 3+, 124 4+, 18 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177\interact-240220ko09chromatin_WAPL_6_1_1_177.pep.xml...
...read in 4 1+, 5429 2+, 2060 3+, 177 4+, 26 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 25918 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\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry rev_sp|P11352|GPX1_MOUSE : U
SNGSQQSLLTEIDPEIDITRFRRSYRRVPVGDPGVLFKEFNWAIDNRCVPSWIIYKPDTMLATPDDSPTPLANRLFTFLPHAKEGNVECKEFLTFNPEFGGGPRVYKLSNLIEENKGNEQHGFQNCPFGLVVLGRPGLRKQLDNMETYDRITTGULSAVNEILLVKGRLSGLSVPEGGTLPRASFAYVTSQAAASLRAACM
........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9BCZ4|SELS_MOUSE : U
NUGGSSPGRRGPRWSCTGGGEGTLPNYGGGRLPKKDSKGKPIVSSTSPGPGDEEQPRGSNRKYSRGEQMSDWMEIKQRRKEEELQRLKEKHKEVQANLDEQMRLRAAALAEQRKVVVDPELVTEAQDLQRQRLARLRLSLRQIVIYLLICSFLIYWGYSALLSGVTVHLFRLSETELAPRASLPEEDRDM
...:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|O70325|GPX4_MOUSE : U
MSWGRLSRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVCLDKYRGFVCIVTNVASQUGKTDVNYTQLVDLHARYAECGLRILAFPCNQFGRQEPGSNQEIKEFAAGYNVKFDMYSKICVNGDDAHPLWKWMKVQPKGRGMLGNAIKWNFTKFLIDKNGCVVKRYGPMEEPQVIEKDLPCYL
......:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|P11352|GPX1_MOUSE : U
MCAARLSAAAQSTVYAFSARPLTGGEPVSLGSLRGKVLLIENVASLUGTTIRDYTEMNDLQKRLGPRGLVVLGFPCNQFGHQENGKNEEILNSLKYVRPGGGFEPNFTLFEKCEVNGEKAHPLFTFLRNALPTPSDDPTALMTDPKYIIWSPVCRNDIAWNFEKFLVGPDGVPVRRYSRRFRTIDIEPDIETLLSQQSGNS
.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:......WARNING: Found the following zero-mass residues in protein entry sp|Q3UQA7|SELH_MOUSE : U
MAPHGRKRKAGAAPMETVDKREKLAEGATVVIEHCTSURVYGRHAAALSQALQLEAPELPVQVNPSKPRRGSFEVTLLRSDNSRVELWTGIKKGPPRKLKFPEPQEVVEELKKYLS
...:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|Q99MD6|TRXR3_MOUSE : U
MEKPPSPPPPPRAQTSPGLGKVGVLPNRRLGAVRGGLMSSPPGRRARLASPGTSRPSSEAREELRRRLRDLIEGNRVMIFSKSYCPHSTRVKELFSSLGVVYNILELDQVDDGASVQEVLTEISNQKTVPNIFVNKVHVGGCDRTFQAHQNGLLQKLLQDDSAHDYDLIIIGGGSGGLSCAKEAANLGKKVMVLDFVVPSPQGTTWGLGGTCVNVGCIPKKLMHQAALLGHALQDAKKYGWEYNQQVKHNWEAMTEAIQSHIGSLNWGYRVTLREKGVTYVNSFGEFVDLHKIKATNKKGQETFYTASKFVIATGERPRYLGIQGDKEYCITSDDLFSLPYCPGCTLVVGASYVGLECAGFLAGLGLDVTVMVRSVLLRGFDQEMAEKVGSYLEQQGVKFQRKFTPILVQQLEKGLPGKLKVVAKSTEGPETVEGIYNTVLLAIGRDSCTRKIGLEKIGVKINEKNGKIPVNDVEQTNVPHVYAIGDILDGKPELTPVAIQAGKLLARRLFGVSLEKCDYINIPTTVFTPLEYGCCGLSEEKAIEMYKKENLEVYHTLFWPLEWTVAGRDNNTCYAKIICNKFDNERVVGFHLLGPNAGEITQGFAAAMKCGLTKQLLDDTIGIHPTCGEVFTTLEITKSSGLDITQKGCUG
..:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........WARNING: Found the following zero-mass residues in protein entry sp|Q9ERR7|SEP15_MOUSE : U
MAAGQGGWLRPALGLRLLLATAFQAVSALGAEFASEACRELGFSSNLLCSSCDLLGQFNLLPLDPVCRGCCQEEAQFETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEELSILKWNTDSVEEFLSEKLERI
:.........:.........33000
.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q9JMH6|TRXR1_MOUSE : U
MPVDDCWLYFPASRGRTFVQTVWVAPTCPNCCWFPGFLPPVPRPPHVPRVLLRGPRGAVLPASRPSKTLPSSSQTPCPTDPCICPPPSTPDSRQEKNTQSELPNKKGQLQKLPTMNGSKDPPGSYDFDLIIIGGGSGGLAAAKEAAKFDKKVLVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALKDSRNYGWKVEDTVKHDWEKMTESVQSHIGSLNWGYRVALREKKVVYENAYGRFIGPHRIVATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPTKIEQIEAGTPGRLRVTAQSTNSEETIEGEFNTVLLAVGRDSCTRTIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSNVKCDYDNVPTTVFTPLEYGCCGLSEEKAVEKFGEENIEVYHSFFWPLEWTVPSRDNNKCYAKIICNLKDDERVVGFHVLGPNAGEVTQGFAAALKCGLTKQQLDSTIGIHPVCAEIFTTLSVTKRSGGDILQSGCUG
.....:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:........  Total: 34386
Computing degenerate peptides for 6384 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 6522 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 6522 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 6522 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 6522 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 6522 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=3.60555e-05, db_size=38845583
Computing MU for 6522 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO[18:34:28] Done                                         
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
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\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas --prefix rev_
INFO[18:34:28] Executing Database  v5.0.0                   
INFO[18:34:28] Annotating the database                      
INFO[18:34:28] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --razor
INFO[18:34:28] Executing Filter  v5.0.0                     
INFO[18:34:28] Processing peptide identification files      
INFO[18:34:28] Parsing J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530\interact-240120ko08Wapl_IP_1_1_1_40530.pep.xml 
INFO[18:34:30] 1+ Charge profile                             decoy=7 target=129
INFO[18:34:30] 2+ Charge profile                             decoy=267 target=19299
INFO[18:34:30] 3+ Charge profile                             decoy=90 target=6342
INFO[18:34:30] 4+ Charge profile                             decoy=17 target=679
INFO[18:34:30] 5+ Charge profile                             decoy=3 target=44
INFO[18:34:30] 6+ Charge profile                             decoy=0 target=0
INFO[18:34:30] Database search results                       ions=14763 peptides=12265 psms=26877
INFO[18:34:30] Converged to 1.00 % FDR with 26225 PSMs       decoy=262 threshold=0.646815 total=26487
INFO[18:34:30] Converged to 1.00 % FDR with 11457 Peptides   decoy=114 threshold=0.885313 total=11571
INFO[18:34:30] Converged to 0.99 % FDR with 13979 Ions       decoy=139 threshold=0.835407 total=14118
INFO[18:34:30] Protein inference results                     decoy=1877 target=4221
INFO[18:34:30] Converged to 0.96 % FDR with 2186 Proteins    decoy=21 threshold=0.9943 total=2207
INFO[18:34:30] Applying sequential FDR estimation            ions=13962 peptides=11481 psms=25922
INFO[18:34:30] Converged to 0.06 % FDR with 25906 PSMs       decoy=16 threshold=0.646876 total=25922
INFO[18:34:30] Converged to 0.10 % FDR with 11469 Peptides   decoy=12 threshold=0.647229 total=11481
INFO[18:34:30] Converged to 0.09 % FDR with 13950 Ions       decoy=12 threshold=0.647229 total=13962
INFO[18:34:30] Post processing identifications              
INFO[18:34:31] Assigning protein identifications to layers  
INFO[18:34:33] Processing protein inference                 
INFO[18:34:33] Synchronizing PSMs and proteins              
INFO[18:34:33] Final report numbers after FDR filtering, and post-processing  ions=13949 peptides=11468 proteins=1772 psms=25904
INFO[18:34:33] Saving                                       
INFO[18:34:34] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
INFO[18:34:34] Executing Filter  v5.0.0                     
INFO[18:34:34] Fetching protein inference from J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 
INFO[18:34:34] Processing peptide identification files      
INFO[18:34:34] Parsing J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531\interact-240120ko09Wapl_IP_2_1_1_40531.pep.xml 
INFO[18:34:35] 1+ Charge profile                             decoy=11 target=159
INFO[18:34:35] 2+ Charge profile                             decoy=276 target=19209
INFO[18:34:35] 3+ Charge profile                             decoy=113 target=7905
INFO[18:34:35] 4+ Charge profile                             decoy=21 target=731
INFO[18:34:35] 5+ Charge profile                             decoy=3 target=55
INFO[18:34:35] 6+ Charge profile                             decoy=0 target=0
INFO[18:34:35] Database search results                       ions=15499 peptides=12744 psms=28483
INFO[18:34:35] Converged to 1.00 % FDR with 27719 PSMs       decoy=277 threshold=0.66144 total=27996
INFO[18:34:36] Converged to 0.99 % FDR with 11967 Peptides   decoy=119 threshold=0.840119 total=12086
INFO[18:34:36] Converged to 1.00 % FDR with 14700 Ions       decoy=147 threshold=0.803453 total=14847
INFO[18:34:36] Protein inference results                     decoy=1877 target=4221
INFO[18:34:36] Converged to 0.96 % FDR with 2186 Proteins    decoy=21 threshold=0.9943 total=2207
INFO[18:34:36] Applying sequential FDR estimation            ions=14623 peptides=11900 psms=27405
INFO[18:34:36] Converged to 0.04 % FDR with 27393 PSMs       decoy=12 threshold=0.66144 total=27405
INFO[18:34:36] Converged to 0.08 % FDR with 11890 Peptides   decoy=10 threshold=0.665111 total=11900
INFO[18:34:36] Converged to 0.07 % FDR with 14613 Ions       decoy=10 threshold=0.665111 total=14623
INFO[18:34:36] Post processing identifications              
INFO[18:34:36] Assigning protein identifications to layers  
INFO[18:34:39] Processing protein inference                 
INFO[18:34:39] Synchronizing PSMs and proteins              
INFO[18:34:39] Final report numbers after FDR filtering, and post-processing  ions=14612 peptides=11889 proteins=1802 psms=27392
INFO[18:34:39] Saving                                       
INFO[18:34:39] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
INFO[18:34:39] Executing Filter  v5.0.0                     
INFO[18:34:39] Fetching protein inference from J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 
INFO[18:34:39] Processing peptide identification files      
INFO[18:34:39] Parsing J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170\interact-240220ko02whole_RAD21_1_1_1_170.pep.xml 
INFO[18:34:41] 1+ Charge profile                             decoy=1 target=3
INFO[18:34:41] 2+ Charge profile                             decoy=292 target=14343
INFO[18:34:41] 3+ Charge profile                             decoy=110 target=4261
INFO[18:34:41] 4+ Charge profile                             decoy=16 target=318
INFO[18:34:41] 5+ Charge profile                             decoy=2 target=53
INFO[18:34:41] 6+ Charge profile                             decoy=0 target=0
INFO[18:34:41] Database search results                       ions=7944 peptides=7112 psms=19399
INFO[18:34:41] Converged to 1.00 % FDR with 18422 PSMs       decoy=184 threshold=0.757508 total=18606
INFO[18:34:41] Converged to 0.99 % FDR with 6264 Peptides    decoy=62 threshold=0.90138 total=6326
INFO[18:34:41] Converged to 0.99 % FDR with 7063 Ions        decoy=70 threshold=0.889568 total=7133
INFO[18:34:41] Protein inference results                     decoy=1877 target=4221
INFO[18:34:41] Converged to 0.96 % FDR with 2186 Proteins    decoy=21 threshold=0.9943 total=2207
INFO[18:34:41] Applying sequential FDR estimation            ions=7117 peptides=6315 psms=18244
INFO[18:34:41] Converged to 0.07 % FDR with 18232 PSMs       decoy=12 threshold=0.7577 total=18244
INFO[18:34:41] Converged to 0.13 % FDR with 6307 Peptides    decoy=8 threshold=0.761803 total=6315
INFO[18:34:41] Converged to 0.11 % FDR with 7109 Ions        decoy=8 threshold=0.7577 total=7117
INFO[18:34:41] Post processing identifications              
INFO[18:34:41] Assigning protein identifications to layers  
INFO[18:34:43] Processing protein inference                 
INFO[18:34:43] Synchronizing PSMs and proteins              
INFO[18:34:43] Final report numbers after FDR filtering, and post-processing  ions=7108 peptides=6306 proteins=1232 psms=18231
INFO[18:34:43] Saving                                       
INFO[18:34:43] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
INFO[18:34:43] Executing Filter  v5.0.0                     
INFO[18:34:43] Fetching protein inference from J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 
INFO[18:34:43] Processing peptide identification files      
INFO[18:34:43] Parsing J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171\interact-240220ko03whole_RAD21_2_1_1_171.pep.xml 
INFO[18:34:45] 1+ Charge profile                             decoy=2 target=5
INFO[18:34:45] 2+ Charge profile                             decoy=291 target=15562
INFO[18:34:45] 3+ Charge profile                             decoy=99 target=4378
INFO[18:34:45] 4+ Charge profile                             decoy=11 target=344
INFO[18:34:45] 5+ Charge profile                             decoy=3 target=78
INFO[18:34:45] 6+ Charge profile                             decoy=0 target=0
INFO[18:34:45] Database search results                       ions=8747 peptides=7861 psms=20773
INFO[18:34:45] Converged to 1.00 % FDR with 19848 PSMs       decoy=198 threshold=0.734809 total=20046
INFO[18:34:45] Converged to 0.99 % FDR with 6976 Peptides    decoy=69 threshold=0.920709 total=7045
INFO[18:34:45] Converged to 0.99 % FDR with 7842 Ions        decoy=78 threshold=0.902741 total=7920
INFO[18:34:45] Protein inference results                     decoy=1877 target=4221
INFO[18:34:45] Converged to 0.96 % FDR with 2186 Proteins    decoy=21 threshold=0.9943 total=2207
INFO[18:34:45] Applying sequential FDR estimation            ions=7913 peptides=7050 psms=19632
INFO[18:34:45] Converged to 0.06 % FDR with 19621 PSMs       decoy=11 threshold=0.736759 total=19632
INFO[18:34:45] Converged to 0.11 % FDR with 7042 Peptides    decoy=8 threshold=0.740438 total=7050
INFO[18:34:45] Converged to 0.10 % FDR with 7905 Ions        decoy=8 threshold=0.737903 total=7913
INFO[18:34:45] Post processing identifications              
INFO[18:34:45] Assigning protein identifications to layers  
INFO[18:34:47] Processing protein inference                 
INFO[18:34:47] Synchronizing PSMs and proteins              
INFO[18:34:47] Final report numbers after FDR filtering, and post-processing  ions=7904 peptides=7041 proteins=1303 psms=19619
INFO[18:34:47] Saving                                       
INFO[18:34:47] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
INFO[18:34:47] Executing Filter  v5.0.0                     
INFO[18:34:47] Fetching protein inference from J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 
INFO[18:34:47] Processing peptide identification files      
INFO[18:34:47] Parsing J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173\interact-240220ko05chromatin_RAD21_3_1_1_173.pep.xml 
INFO[18:34:48] 1+ Charge profile                             decoy=2 target=4
INFO[18:34:48] 2+ Charge profile                             decoy=240 target=7810
INFO[18:34:48] 3+ Charge profile                             decoy=61 target=2457
INFO[18:34:48] 4+ Charge profile                             decoy=8 target=233
INFO[18:34:48] 5+ Charge profile                             decoy=5 target=86
INFO[18:34:48] 6+ Charge profile                             decoy=0 target=0
INFO[18:34:48] Database search results                       ions=3898 peptides=3508 psms=10906
INFO[18:34:48] Converged to 1.00 % FDR with 10101 PSMs       decoy=101 threshold=0.773496 total=10202
INFO[18:34:48] Converged to 0.99 % FDR with 2841 Peptides    decoy=28 threshold=0.91915 total=2869
INFO[18:34:48] Converged to 0.97 % FDR with 3191 Ions        decoy=31 threshold=0.91609 total=3222
INFO[18:34:48] Protein inference results                     decoy=1877 target=4221
INFO[18:34:48] Converged to 0.96 % FDR with 2186 Proteins    decoy=21 threshold=0.9943 total=2207
INFO[18:34:48] Applying sequential FDR estimation            ions=3296 peptides=2925 psms=9995
INFO[18:34:48] Converged to 0.04 % FDR with 9991 PSMs        decoy=4 threshold=0.773496 total=9995
INFO[18:34:48] Converged to 0.14 % FDR with 2921 Peptides    decoy=4 threshold=0.774711 total=2925
INFO[18:34:48] Converged to 0.12 % FDR with 3292 Ions        decoy=4 threshold=0.774711 total=3296
INFO[18:34:48] Post processing identifications              
INFO[18:34:48] Assigning protein identifications to layers  
INFO[18:34:49] Processing protein inference                 
INFO[18:34:49] Synchronizing PSMs and proteins              
INFO[18:34:50] Final report numbers after FDR filtering, and post-processing  ions=3292 peptides=2921 proteins=607 psms=9991
INFO[18:34:50] Saving                                       
INFO[18:34:50] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
INFO[18:34:50] Executing Filter  v5.0.0                     
INFO[18:34:50] Fetching protein inference from J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 
INFO[18:34:50] Processing peptide identification files      
INFO[18:34:50] Parsing J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174\interact-240220ko06chromatin_RAD21_4_1_1_174.pep.xml 
INFO[18:34:51] 1+ Charge profile                             decoy=2 target=2
INFO[18:34:51] 2+ Charge profile                             decoy=302 target=11643
INFO[18:34:51] 3+ Charge profile                             decoy=88 target=3289
INFO[18:34:51] 4+ Charge profile                             decoy=12 target=268
INFO[18:34:51] 5+ Charge profile                             decoy=4 target=70
INFO[18:34:51] 6+ Charge profile                             decoy=0 target=0
INFO[18:34:51] Database search results                       ions=6101 peptides=5474 psms=15680
INFO[18:34:51] Converged to 1.00 % FDR with 14638 PSMs       decoy=146 threshold=0.776317 total=14784
INFO[18:34:51] Converged to 0.99 % FDR with 4640 Peptides    decoy=46 threshold=0.908383 total=4686
INFO[18:34:51] Converged to 0.99 % FDR with 5235 Ions        decoy=52 threshold=0.899218 total=5287
INFO[18:34:51] Protein inference results                     decoy=1877 target=4221
INFO[18:34:51] Converged to 0.96 % FDR with 2186 Proteins    decoy=21 threshold=0.9943 total=2207
INFO[18:34:51] Applying sequential FDR estimation            ions=5295 peptides=4691 psms=14503
INFO[18:34:51] Converged to 0.05 % FDR with 14496 PSMs       decoy=7 threshold=0.776317 total=14503
INFO[18:34:51] Converged to 0.06 % FDR with 4688 Peptides    decoy=3 threshold=0.777256 total=4691
INFO[18:34:51] Converged to 0.06 % FDR with 5292 Ions        decoy=3 threshold=0.777256 total=5295
INFO[18:34:51] Post processing identifications              
INFO[18:34:51] Assigning protein identifications to layers  
INFO[18:34:53] Processing protein inference                 
INFO[18:34:53] Synchronizing PSMs and proteins              
INFO[18:34:53] Final report numbers after FDR filtering, and post-processing  ions=5292 peptides=4688 proteins=794 psms=14496
INFO[18:34:53] Saving                                       
INFO[18:34:53] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
INFO[18:34:53] Executing Filter  v5.0.0                     
INFO[18:34:53] Fetching protein inference from J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 
INFO[18:34:53] Processing peptide identification files      
INFO[18:34:53] Parsing J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\interact-240220ko08chromatin_WAPL_5_1_1_176.pep.xml 
INFO[18:34:54] 1+ Charge profile                             decoy=1 target=8
INFO[18:34:54] 2+ Charge profile                             decoy=140 target=4226
INFO[18:34:54] 3+ Charge profile                             decoy=54 target=1863
INFO[18:34:54] 4+ Charge profile                             decoy=5 target=119
INFO[18:34:54] 5+ Charge profile                             decoy=1 target=17
INFO[18:34:54] 6+ Charge profile                             decoy=0 target=0
INFO[18:34:54] Database search results                       ions=1789 peptides=1612 psms=6434
INFO[18:34:54] Converged to 0.99 % FDR with 5887 PSMs        decoy=58 threshold=0.781202 total=5945
INFO[18:34:54] Converged to 0.94 % FDR with 1176 Peptides    decoy=11 threshold=0.919097 total=1187
INFO[18:34:54] Converged to 0.98 % FDR with 1327 Ions        decoy=13 threshold=0.916057 total=1340
INFO[18:34:54] Protein inference results                     decoy=1877 target=4221
INFO[18:34:54] Converged to 0.96 % FDR with 2186 Proteins    decoy=21 threshold=0.9943 total=2207
INFO[18:34:54] Applying sequential FDR estimation            ions=1372 peptides=1215 psms=5830
INFO[18:34:54] Converged to 0.02 % FDR with 5829 PSMs        decoy=1 threshold=0.781202 total=5830
INFO[18:34:54] Converged to 0.08 % FDR with 1214 Peptides    decoy=1 threshold=0.782825 total=1215
INFO[18:34:54] Converged to 0.07 % FDR with 1371 Ions        decoy=1 threshold=0.782825 total=1372
INFO[18:34:54] Post processing identifications              
INFO[18:34:54] Assigning protein identifications to layers  
INFO[18:34:54] Processing protein inference                 
INFO[18:34:54] Synchronizing PSMs and proteins              
INFO[18:34:55] Final report numbers after FDR filtering, and post-processing  ions=1371 peptides=1214 proteins=300 psms=5829
INFO[18:34:55] Saving                                       
INFO[18:34:55] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177 --protxml J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 --razor
INFO[18:34:55] Executing Filter  v5.0.0                     
INFO[18:34:55] Fetching protein inference from J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530 
INFO[18:34:55] Processing peptide identification files      
INFO[18:34:55] Parsing J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177\interact-240220ko09chromatin_WAPL_6_1_1_177.pep.xml 
INFO[18:34:55] 1+ Charge profile                             decoy=1 target=3
INFO[18:34:55] 2+ Charge profile                             decoy=166 target=5263
INFO[18:34:55] 3+ Charge profile                             decoy=62 target=1998
INFO[18:34:55] 4+ Charge profile                             decoy=10 target=167
INFO[18:34:55] 5+ Charge profile                             decoy=2 target=24
INFO[18:34:55] 6+ Charge profile                             decoy=0 target=0
INFO[18:34:55] Database search results                       ions=2232 peptides=1998 psms=7696
INFO[18:34:55] Converged to 1.00 % FDR with 7111 PSMs        decoy=71 threshold=0.763902 total=7182
INFO[18:34:55] Converged to 0.99 % FDR with 1510 Peptides    decoy=15 threshold=0.915387 total=1525
INFO[18:34:55] Converged to 1.00 % FDR with 1708 Ions        decoy=17 threshold=0.912568 total=1725
INFO[18:34:55] Protein inference results                     decoy=1877 target=4221
INFO[18:34:55] Converged to 0.96 % FDR with 2186 Proteins    decoy=21 threshold=0.9943 total=2207
INFO[18:34:55] Applying sequential FDR estimation            ions=1762 peptides=1545 psms=7035
INFO[18:34:55] Converged to 0.04 % FDR with 7032 PSMs        decoy=3 threshold=0.763902 total=7035
INFO[18:34:55] Converged to 0.06 % FDR with 1544 Peptides    decoy=1 threshold=0.764185 total=1545
INFO[18:34:55] Converged to 0.06 % FDR with 1761 Ions        decoy=1 threshold=0.764185 total=1762
INFO[18:34:55] Post processing identifications              
INFO[18:34:56] Assigning protein identifications to layers  
INFO[18:34:56] Processing protein inference                 
INFO[18:34:56] Synchronizing PSMs and proteins              
INFO[18:34:56] Final report numbers after FDR filtering, and post-processing  ions=1761 peptides=1544 proteins=357 psms=7032
INFO[18:34:56] Saving                                       
INFO[18:34:56] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[18:34:57] Executing Report  v5.0.0                     
INFO[18:34:57] Creating reports                             
INFO[18:34:57] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[18:34:57] Executing Report  v5.0.0                     
INFO[18:34:57] Creating reports                             
INFO[18:34:57] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[18:34:57] Executing Report  v5.0.0                     
INFO[18:34:57] Creating reports                             
INFO[18:34:57] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[18:34:58] Executing Report  v5.0.0                     
INFO[18:34:58] Creating reports                             
INFO[18:34:58] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[18:34:58] Executing Report  v5.0.0                     
INFO[18:34:58] Creating reports                             
INFO[18:34:58] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[18:34:59] Executing Report  v5.0.0                     
INFO[18:34:59] Creating reports                             
INFO[18:34:59] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[18:34:59] Executing Report  v5.0.0                     
INFO[18:34:59] Creating reports                             
INFO[18:34:59] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[18:34:59] Executing Report  v5.0.0                     
INFO[18:34:59] Creating reports                             
INFO[18:35:00] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:35:00] Executing Workspace  v5.0.0                  
INFO[18:35:00] Removing workspace                           
INFO[18:35:00] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:35:00] Executing Workspace  v5.0.0                  
INFO[18:35:00] Removing workspace                           
INFO[18:35:00] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:35:01] Executing Workspace  v5.0.0                  
INFO[18:35:01] Removing workspace                           
INFO[18:35:01] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:35:01] Executing Workspace  v5.0.0                  
INFO[18:35:01] Removing workspace                           
INFO[18:35:01] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:35:02] Executing Workspace  v5.0.0                  
INFO[18:35:02] Removing workspace                           
INFO[18:35:02] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:35:02] Executing Workspace  v5.0.0                  
INFO[18:35:02] Removing workspace                           
INFO[18:35:02] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:35:02] Executing Workspace  v5.0.0                  
INFO[18:35:02] Removing workspace                           
INFO[18:35:02] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:35:03] Executing Workspace  v5.0.0                  
INFO[18:35:03] Removing workspace                           
INFO[18:35:03] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[18:35:03] Executing Workspace  v5.0.0                  
INFO[18:35:03] Removing workspace                           
INFO[18:35:03] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
IonQuant [Work dir: J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ]
java -Xmx81G -Dlibs.bruker.dir="D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\bruker" -Dlibs.thermo.dir="D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\thermo" -cp "D:\Applications\FragPipe-20.0\fragpipe\tools\jfreechart-1.5.3.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\IonQuant-1.9.8.jar" ionquant.IonQuant --threads 15 --ionmobility 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\filelist_ionquant.txt --modlist J:\MSFragger_process\Saitou-lab\240220ko\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 81 GB memory
2025-01-22 18:35:04 [INFO] - Collecting variable modifications from all psm.tsv files...
2025-01-22 18:35:04 [INFO] - Loading and indexing all psm.tsv files...
2025-01-22 18:35:07 [INFO] - Parameters:
2025-01-22 18:35:07 [INFO] - threads = 15
2025-01-22 18:35:07 [INFO] - mztol = 10.0
2025-01-22 18:35:07 [INFO] - rttol = 0.4
2025-01-22 18:35:07 [INFO] - imtol = 0.05
2025-01-22 18:35:07 [INFO] - minisotopes = 2
2025-01-22 18:35:07 [INFO] - minscans = 3
2025-01-22 18:35:07 [INFO] - psm = J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko08Wapl_IP_1_1_1_40530\psm.tsv
2025-01-22 18:35:07 [INFO] - psm = J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240120ko09Wapl_IP_2_1_1_40531\psm.tsv
2025-01-22 18:35:07 [INFO] - psm = J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko02whole_RAD21_1_1_1_170\psm.tsv
2025-01-22 18:35:07 [INFO] - psm = J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko03whole_RAD21_2_1_1_171\psm.tsv
2025-01-22 18:35:07 [INFO] - psm = J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko05chromatin_RAD21_3_1_1_173\psm.tsv
2025-01-22 18:35:07 [INFO] - psm = J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko06chromatin_RAD21_4_1_1_174\psm.tsv
2025-01-22 18:35:07 [INFO] - psm = J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko08chromatin_WAPL_5_1_1_176\psm.tsv
2025-01-22 18:35:07 [INFO] - psm = J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\240220ko09chromatin_WAPL_6_1_1_177\psm.tsv
2025-01-22 18:35:07 [INFO] - multidir = J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\.\
2025-01-22 18:35:07 [INFO] - excludemods = 
2025-01-22 18:35:07 [INFO] - minions = 2
2025-01-22 18:35:07 [INFO] - maxlfq = 1
2025-01-22 18:35:07 [INFO] - ibaq = 0
2025-01-22 18:35:07 [INFO] - normalization = 1
2025-01-22 18:35:07 [INFO] - minexps = 1
2025-01-22 18:35:07 [INFO] - minfreq = 0.0
2025-01-22 18:35:07 [INFO] - tp = 0
2025-01-22 18:35:07 [INFO] - mbr = 1
2025-01-22 18:35:07 [INFO] - mbrrttol = 1.0
2025-01-22 18:35:07 [INFO] - mbrimtol = 0.05
2025-01-22 18:35:07 [INFO] - mbrtoprun = 10
2025-01-22 18:35:07 [INFO] - mbrmincorr = 0.0
2025-01-22 18:35:07 [INFO] - ionmobility = 1
2025-01-22 18:35:07 [INFO] - ionfdr = 0.01
2025-01-22 18:35:07 [INFO] - peptidefdr = 1.0
2025-01-22 18:35:07 [INFO] - proteinfdr = 1.0
2025-01-22 18:35:07 [INFO] - light = 
2025-01-22 18:35:07 [INFO] - medium = 
2025-01-22 18:35:07 [INFO] - heavy = 
2025-01-22 18:35:07 [INFO] - requantify = 0
2025-01-22 18:35:07 [INFO] - writeindex = 0
2025-01-22 18:35:07 [INFO] - locprob = 0.75
2025-01-22 18:35:07 [INFO] - uniqueness = 0
2025-01-22 18:35:07 [INFO] - filelist = J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\filelist_ionquant.txt
2025-01-22 18:35:07 [INFO] - specdir = J:\MSFragger_process\Saitou-lab\240220ko
2025-01-22 18:35:07 [INFO] - modlist = J:\MSFragger_process\Saitou-lab\240220ko\MSFragger_iBAQ\modmasses_ionquant.txt
2025-01-22 18:35:07 [INFO] - mod masses:
2025-01-22 18:35:07 [INFO] - 15.9949
2025-01-22 18:35:07 [INFO] - 42.0106
2025-01-22 18:35:07 [INFO] - 57.02146
2025-01-22 18:35:07 [INFO] - Checking J:\MSFragger_process\Saitou-lab\240220ko\240120ko08Wapl_IP_1_1_1_40530.d...
2025-01-22 18:35:08 [INFO] - Checking J:\MSFragger_process\Saitou-lab\240220ko\240120ko09Wapl_IP_2_1_1_40531.d...
2025-01-22 18:35:08 [INFO] - Checking J:\MSFragger_process\Saitou-lab\240220ko\240220ko02whole_RAD21_1_1_1_170.d...
2025-01-22 18:35:08 [INFO] - Checking J:\MSFragger_process\Saitou-lab\240220ko\240220ko03whole_RAD21_2_1_1_171.d...
2025-01-22 18:35:08 [INFO] - Checking J:\MSFragger_process\Saitou-lab\240220ko\240220ko05chromatin_RAD21_3_1_1_173.d...
2025-01-22 18:35:08 [INFO] - Checking J:\MSFragger_process\Saitou-lab\240220ko\240220ko06chromatin_RAD21_4_1_1_174.d...
2025-01-22 18:35:08 [INFO] - Checking J:\MSFragger_process\Saitou-lab\240220ko\240220ko08chromatin_WAPL_5_1_1_176.d...
2025-01-22 18:35:08 [INFO] - Checking J:\MSFragger_process\Saitou-lab\240220ko\240220ko09chromatin_WAPL_6_1_1_177.d...
2025-01-22 18:35:08 [INFO] - Loading J:\MSFragger_process\Saitou-lab\240220ko\240120ko08Wapl_IP_1_1_1_40530.d...
2025-01-22 18:35:09 [INFO] - ...20%...40%...60%...80%...100%
2025-01-22 18:35:38 [INFO] - Building index...
2025-01-22 18:36:17 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\240220ko\240120ko08Wapl_IP_1_1_1_40530.quantindex
2025-01-22 18:36:19 [INFO] - Loading 240120ko08Wapl_IP_1_1_1_40530....
2025-01-22 18:36:19 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-22 18:36:19 [INFO] - Quantifying...
2025-01-22 18:36:21 [INFO] - Loading J:\MSFragger_process\Saitou-lab\240220ko\240120ko09Wapl_IP_2_1_1_40531.d...
2025-01-22 18:36:22 [INFO] - ...20%...40%...60%...80%...100%
2025-01-22 18:36:54 [INFO] - Building index...
2025-01-22 18:37:32 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\240220ko\240120ko09Wapl_IP_2_1_1_40531.quantindex
2025-01-22 18:37:34 [INFO] - Loading 240120ko09Wapl_IP_2_1_1_40531....
2025-01-22 18:37:34 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-22 18:37:34 [INFO] - Quantifying...
2025-01-22 18:37:35 [INFO] - Loading J:\MSFragger_process\Saitou-lab\240220ko\240220ko02whole_RAD21_1_1_1_170.d...
2025-01-22 18:37:35 [INFO] - ...20%...40%...60%...80%...100%
2025-01-22 18:39:30 [INFO] - Building index...
2025-01-22 18:40:09 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\240220ko\240220ko02whole_RAD21_1_1_1_170.quantindex
2025-01-22 18:40:14 [INFO] - Loading 240220ko02whole_RAD21_1_1_1_170....
2025-01-22 18:40:14 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-22 18:40:14 [INFO] - Quantifying...
2025-01-22 18:40:15 [INFO] - Loading J:\MSFragger_process\Saitou-lab\240220ko\240220ko03whole_RAD21_2_1_1_171.d...
2025-01-22 18:40:15 [INFO] - ...20%...40%...60%...80%...100%
2025-01-22 18:42:47 [INFO] - Building index...
2025-01-22 18:43:25 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\240220ko\240220ko03whole_RAD21_2_1_1_171.quantindex
2025-01-22 18:43:30 [INFO] - Loading 240220ko03whole_RAD21_2_1_1_171....
2025-01-22 18:43:30 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-22 18:43:30 [INFO] - Quantifying...
2025-01-22 18:43:31 [INFO] - Loading J:\MSFragger_process\Saitou-lab\240220ko\240220ko05chromatin_RAD21_3_1_1_173.d...
2025-01-22 18:43:32 [INFO] - ...20%...40%...60%...80%...100%
2025-01-22 18:45:56 [INFO] - Building index...
2025-01-22 18:46:35 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\240220ko\240220ko05chromatin_RAD21_3_1_1_173.quantindex
2025-01-22 18:46:40 [INFO] - Loading 240220ko05chromatin_RAD21_3_1_1_173....
2025-01-22 18:46:40 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-22 18:46:40 [INFO] - Quantifying...
2025-01-22 18:46:40 [INFO] - Loading J:\MSFragger_process\Saitou-lab\240220ko\240220ko06chromatin_RAD21_4_1_1_174.d...
2025-01-22 18:46:41 [INFO] - ...20%...40%...60%...80%...100%
2025-01-22 18:48:59 [INFO] - Building index...
2025-01-22 18:49:38 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\240220ko\240220ko06chromatin_RAD21_4_1_1_174.quantindex
2025-01-22 18:49:44 [INFO] - Loading 240220ko06chromatin_RAD21_4_1_1_174....
2025-01-22 18:49:44 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-22 18:49:44 [INFO] - Quantifying...
2025-01-22 18:49:44 [INFO] - Loading J:\MSFragger_process\Saitou-lab\240220ko\240220ko08chromatin_WAPL_5_1_1_176.d...
2025-01-22 18:49:45 [INFO] - ...20%...40%...60%...80%...100%
2025-01-22 18:52:07 [INFO] - Building index...
2025-01-22 18:52:45 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\240220ko\240220ko08chromatin_WAPL_5_1_1_176.quantindex
2025-01-22 18:52:50 [INFO] - Loading 240220ko08chromatin_WAPL_5_1_1_176....
2025-01-22 18:52:50 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-22 18:52:50 [INFO] - Quantifying...
2025-01-22 18:52:51 [INFO] - Loading J:\MSFragger_process\Saitou-lab\240220ko\240220ko09chromatin_WAPL_6_1_1_177.d...
2025-01-22 18:52:51 [INFO] - ...20%...40%...60%...80%...100%
2025-01-22 18:55:21 [INFO] - Building index...
2025-01-22 18:55:59 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\240220ko\240220ko09chromatin_WAPL_6_1_1_177.quantindex
2025-01-22 18:56:05 [INFO] - Loading 240220ko09chromatin_WAPL_6_1_1_177....
2025-01-22 18:56:05 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-22 18:56:05 [INFO] - Quantifying...
2025-01-22 18:56:05 [INFO] - Updating Philosopher's tables...
2025-01-22 18:56:08 [INFO] - Matching-between-runs: 240120ko08Wapl_IP_1_1_1_40530...
2025-01-22 18:56:09 [INFO] - Calculating correlations between all other runs...
2025-01-22 18:56:09 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\240220ko\240120ko08Wapl_IP_1_1_1_40530.quantindex
2025-01-22 18:56:12 [INFO] - Transferring 240120ko09Wapl_IP_2_1_1_40531...
2025-01-22 18:56:13 [INFO] - Transferring 240220ko02whole_RAD21_1_1_1_170...
2025-01-22 18:56:13 [INFO] - Transferring 240220ko03whole_RAD21_2_1_1_171...
2025-01-22 18:56:14 [INFO] - Transferring 240220ko05chromatin_RAD21_3_1_1_173...
2025-01-22 18:56:14 [INFO] - Transferring 240220ko06chromatin_RAD21_4_1_1_174...
2025-01-22 18:56:14 [INFO] - Transferring 240220ko08chromatin_WAPL_5_1_1_176...
2025-01-22 18:56:14 [INFO] - Transferring 240220ko09chromatin_WAPL_6_1_1_177...
2025-01-22 18:56:14 [INFO] - Training LDA models for all matched features.
2025-01-22 18:56:14 [INFO] - #{+1} = 1283, #{-1} = 32, #{+2} = 7626, #{-2} = 150
2025-01-22 18:56:14 [INFO] - Standardized coefficients:
2025-01-22 18:56:14 [INFO] - log10(intensity): 0.3290235733330715
2025-01-22 18:56:14 [INFO] - log10(KL): -0.19778944359528722
2025-01-22 18:56:14 [INFO] - abs(ppm): -0.6805291599738554
2025-01-22 18:56:14 [INFO] - IM diff: -0.5607962076774039
2025-01-22 18:56:14 [INFO] - RT diff: -0.2746792376888871
2025-01-22 18:56:14 [INFO] - Fitting a mixture model...
2025-01-22 18:56:16 [INFO] - Matching-between-runs: 240120ko09Wapl_IP_2_1_1_40531...
2025-01-22 18:56:16 [INFO] - Calculating correlations between all other runs...
2025-01-22 18:56:16 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\240220ko\240120ko09Wapl_IP_2_1_1_40531.quantindex
2025-01-22 18:56:19 [INFO] - Transferring 240120ko08Wapl_IP_1_1_1_40530...
2025-01-22 18:56:20 [INFO] - Transferring 240220ko02whole_RAD21_1_1_1_170...
2025-01-22 18:56:20 [INFO] - Transferring 240220ko03whole_RAD21_2_1_1_171...
2025-01-22 18:56:20 [INFO] - Transferring 240220ko05chromatin_RAD21_3_1_1_173...
2025-01-22 18:56:21 [INFO] - Transferring 240220ko06chromatin_RAD21_4_1_1_174...
2025-01-22 18:56:21 [INFO] - Transferring 240220ko08chromatin_WAPL_5_1_1_176...
2025-01-22 18:56:21 [INFO] - Transferring 240220ko09chromatin_WAPL_6_1_1_177...
2025-01-22 18:56:21 [INFO] - Training LDA models for all matched features.
2025-01-22 18:56:21 [INFO] - #{+1} = 1137, #{-1} = 34, #{+2} = 7807, #{-2} = 160
2025-01-22 18:56:21 [INFO] - Standardized coefficients:
2025-01-22 18:56:21 [INFO] - log10(intensity): 0.4614482808339363
2025-01-22 18:56:21 [INFO] - log10(KL): -0.1487905313340768
2025-01-22 18:56:21 [INFO] - abs(ppm): -0.5444591783555944
2025-01-22 18:56:21 [INFO] - IM diff: -0.6019645370834658
2025-01-22 18:56:21 [INFO] - RT diff: -0.33107240034732754
2025-01-22 18:56:21 [INFO] - Fitting a mixture model...
2025-01-22 18:56:21 [INFO] - Matching-between-runs: 240220ko02whole_RAD21_1_1_1_170...
2025-01-22 18:56:22 [INFO] - Calculating correlations between all other runs...
2025-01-22 18:56:22 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\240220ko\240220ko02whole_RAD21_1_1_1_170.quantindex
2025-01-22 18:56:27 [INFO] - Transferring 240120ko08Wapl_IP_1_1_1_40530...
2025-01-22 18:56:27 [INFO] - Transferring 240120ko09Wapl_IP_2_1_1_40531...
2025-01-22 18:56:28 [INFO] - Transferring 240220ko03whole_RAD21_2_1_1_171...
2025-01-22 18:56:28 [INFO] - Transferring 240220ko05chromatin_RAD21_3_1_1_173...
2025-01-22 18:56:28 [INFO] - Transferring 240220ko06chromatin_RAD21_4_1_1_174...
2025-01-22 18:56:29 [INFO] - Transferring 240220ko08chromatin_WAPL_5_1_1_176...
2025-01-22 18:56:29 [INFO] - Transferring 240220ko09chromatin_WAPL_6_1_1_177...
2025-01-22 18:56:29 [INFO] - Training LDA models for all matched features.
2025-01-22 18:56:29 [INFO] - #{+1} = 1558, #{-1} = 83, #{+2} = 3430, #{-2} = 122
2025-01-22 18:56:29 [INFO] - Standardized coefficients:
2025-01-22 18:56:29 [INFO] - log10(intensity): 0.5489839985551205
2025-01-22 18:56:29 [INFO] - log10(KL): -0.10723564295062918
2025-01-22 18:56:29 [INFO] - abs(ppm): -0.47116580864039964
2025-01-22 18:56:29 [INFO] - IM diff: -0.653011960418405
2025-01-22 18:56:29 [INFO] - RT diff: -0.21087280564318064
2025-01-22 18:56:29 [INFO] - Fitting a mixture model...
2025-01-22 18:56:29 [INFO] - Matching-between-runs: 240220ko03whole_RAD21_2_1_1_171...
2025-01-22 18:56:30 [INFO] - Calculating correlations between all other runs...
2025-01-22 18:56:30 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\240220ko\240220ko03whole_RAD21_2_1_1_171.quantindex
2025-01-22 18:56:35 [INFO] - Transferring 240120ko08Wapl_IP_1_1_1_40530...
2025-01-22 18:56:36 [INFO] - Transferring 240120ko09Wapl_IP_2_1_1_40531...
2025-01-22 18:56:36 [INFO] - Transferring 240220ko02whole_RAD21_1_1_1_170...
2025-01-22 18:56:37 [INFO] - Transferring 240220ko05chromatin_RAD21_3_1_1_173...
2025-01-22 18:56:37 [INFO] - Transferring 240220ko06chromatin_RAD21_4_1_1_174...
2025-01-22 18:56:38 [INFO] - Transferring 240220ko08chromatin_WAPL_5_1_1_176...
2025-01-22 18:56:38 [INFO] - Transferring 240220ko09chromatin_WAPL_6_1_1_177...
2025-01-22 18:56:38 [INFO] - Training LDA models for all matched features.
2025-01-22 18:56:38 [INFO] - #{+1} = 1345, #{-1} = 84, #{+2} = 3619, #{-2} = 124
2025-01-22 18:56:38 [INFO] - Standardized coefficients:
2025-01-22 18:56:38 [INFO] - log10(intensity): 0.5936607154305924
2025-01-22 18:56:38 [INFO] - log10(KL): -0.0996580846091645
2025-01-22 18:56:38 [INFO] - abs(ppm): -0.45373106995167756
2025-01-22 18:56:38 [INFO] - IM diff: -0.5997088761852583
2025-01-22 18:56:38 [INFO] - RT diff: -0.27649508419647745
2025-01-22 18:56:38 [INFO] - Fitting a mixture model...
2025-01-22 18:56:39 [INFO] - Matching-between-runs: 240220ko05chromatin_RAD21_3_1_1_173...
2025-01-22 18:56:39 [INFO] - Calculating correlations between all other runs...
2025-01-22 18:56:39 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\240220ko\240220ko05chromatin_RAD21_3_1_1_173.quantindex
2025-01-22 18:56:44 [INFO] - Transferring 240120ko08Wapl_IP_1_1_1_40530...
2025-01-22 18:56:45 [INFO] - Transferring 240120ko09Wapl_IP_2_1_1_40531...
2025-01-22 18:56:45 [INFO] - Transferring 240220ko02whole_RAD21_1_1_1_170...
2025-01-22 18:56:46 [INFO] - Transferring 240220ko03whole_RAD21_2_1_1_171...
2025-01-22 18:56:47 [INFO] - Transferring 240220ko06chromatin_RAD21_4_1_1_174...
2025-01-22 18:56:48 [INFO] - Transferring 240220ko08chromatin_WAPL_5_1_1_176...
2025-01-22 18:56:48 [INFO] - Transferring 240220ko09chromatin_WAPL_6_1_1_177...
2025-01-22 18:56:48 [INFO] - Training LDA models for all matched features.
2025-01-22 18:56:48 [INFO] - #{+1} = 1219, #{-1} = 83, #{+2} = 1707, #{-2} = 41
2025-01-22 18:56:48 [INFO] - Standardized coefficients:
2025-01-22 18:56:48 [INFO] - log10(intensity): 0.5487541077924031
2025-01-22 18:56:48 [INFO] - log10(KL): -0.07893617729685465
2025-01-22 18:56:48 [INFO] - abs(ppm): -0.45304634008709693
2025-01-22 18:56:48 [INFO] - IM diff: -0.6893184835767174
2025-01-22 18:56:48 [INFO] - RT diff: -0.11242791571963859
2025-01-22 18:56:48 [INFO] - Fitting a mixture model...
2025-01-22 18:56:48 [INFO] - Matching-between-runs: 240220ko06chromatin_RAD21_4_1_1_174...
2025-01-22 18:56:48 [INFO] - Calculating correlations between all other runs...
2025-01-22 18:56:49 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\240220ko\240220ko06chromatin_RAD21_4_1_1_174.quantindex
2025-01-22 18:56:54 [INFO] - Transferring 240120ko08Wapl_IP_1_1_1_40530...
2025-01-22 18:56:54 [INFO] - Transferring 240120ko09Wapl_IP_2_1_1_40531...
2025-01-22 18:56:55 [INFO] - Transferring 240220ko02whole_RAD21_1_1_1_170...
2025-01-22 18:56:55 [INFO] - Transferring 240220ko03whole_RAD21_2_1_1_171...
2025-01-22 18:56:55 [INFO] - Transferring 240220ko05chromatin_RAD21_3_1_1_173...
2025-01-22 18:56:56 [INFO] - Transferring 240220ko08chromatin_WAPL_5_1_1_176...
2025-01-22 18:56:56 [INFO] - Transferring 240220ko09chromatin_WAPL_6_1_1_177...
2025-01-22 18:56:56 [INFO] - Training LDA models for all matched features.
2025-01-22 18:56:56 [INFO] - #{+1} = 1257, #{-1} = 92, #{+2} = 2480, #{-2} = 73
2025-01-22 18:56:56 [INFO] - Standardized coefficients:
2025-01-22 18:56:56 [INFO] - log10(intensity): 0.7159132087723266
2025-01-22 18:56:56 [INFO] - log10(KL): -0.09049859131683564
2025-01-22 18:56:56 [INFO] - abs(ppm): -0.36590280633868144
2025-01-22 18:56:56 [INFO] - IM diff: -0.558023633268553
2025-01-22 18:56:56 [INFO] - RT diff: -0.18439914181530412
2025-01-22 18:56:56 [INFO] - Fitting a mixture model...
2025-01-22 18:56:56 [INFO] - Matching-between-runs: 240220ko08chromatin_WAPL_5_1_1_176...
2025-01-22 18:56:56 [INFO] - Calculating correlations between all other runs...
2025-01-22 18:56:56 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\240220ko\240220ko08chromatin_WAPL_5_1_1_176.quantindex
2025-01-22 18:57:01 [INFO] - Transferring 240120ko08Wapl_IP_1_1_1_40530...
2025-01-22 18:57:02 [INFO] - Transferring 240120ko09Wapl_IP_2_1_1_40531...
2025-01-22 18:57:02 [INFO] - Transferring 240220ko02whole_RAD21_1_1_1_170...
2025-01-22 18:57:02 [INFO] - Transferring 240220ko03whole_RAD21_2_1_1_171...
2025-01-22 18:57:02 [INFO] - Transferring 240220ko05chromatin_RAD21_3_1_1_173...
2025-01-22 18:57:03 [INFO] - Transferring 240220ko06chromatin_RAD21_4_1_1_174...
2025-01-22 18:57:03 [INFO] - Transferring 240220ko09chromatin_WAPL_6_1_1_177...
2025-01-22 18:57:03 [INFO] - Training LDA models for all matched features.
2025-01-22 18:57:03 [INFO] - #{+1} = 509, #{-1} = 29, #{+2} = 638, #{-2} = 13
2025-01-22 18:57:03 [INFO] - Standardized coefficients:
2025-01-22 18:57:03 [INFO] - log10(intensity): 0.6024215290870243
2025-01-22 18:57:03 [INFO] - log10(KL): -0.47647130335723625
2025-01-22 18:57:03 [INFO] - abs(ppm): 0.03219315446678296
2025-01-22 18:57:03 [INFO] - IM diff: -0.6746426693801796
2025-01-22 18:57:03 [INFO] - RT diff: 0.00517718660088494
2025-01-22 18:57:03 [INFO] - Fitting a mixture model...
2025-01-22 18:57:03 [INFO] - Matching-between-runs: 240220ko09chromatin_WAPL_6_1_1_177...
2025-01-22 18:57:03 [INFO] - Calculating correlations between all other runs...
2025-01-22 18:57:03 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\240220ko\240220ko09chromatin_WAPL_6_1_1_177.quantindex
2025-01-22 18:57:09 [INFO] - Transferring 240120ko08Wapl_IP_1_1_1_40530...
2025-01-22 18:57:09 [INFO] - Transferring 240120ko09Wapl_IP_2_1_1_40531...
2025-01-22 18:57:09 [INFO] - Transferring 240220ko02whole_RAD21_1_1_1_170...
2025-01-22 18:57:09 [INFO] - Transferring 240220ko03whole_RAD21_2_1_1_171...
2025-01-22 18:57:10 [INFO] - Transferring 240220ko05chromatin_RAD21_3_1_1_173...
2025-01-22 18:57:10 [INFO] - Transferring 240220ko06chromatin_RAD21_4_1_1_174...
2025-01-22 18:57:10 [INFO] - Transferring 240220ko08chromatin_WAPL_5_1_1_176...
2025-01-22 18:57:10 [INFO] - Training LDA models for all matched features.
2025-01-22 18:57:10 [INFO] - #{+1} = 629, #{-1} = 45, #{+2} = 842, #{-2} = 17
2025-01-22 18:57:10 [INFO] - Standardized coefficients:
2025-01-22 18:57:10 [INFO] - log10(intensity): 0.502259728727267
2025-01-22 18:57:10 [INFO] - log10(KL): -0.2715822580225905
2025-01-22 18:57:10 [INFO] - abs(ppm): 0.1213538360463403
2025-01-22 18:57:10 [INFO] - IM diff: -0.7587544503250369
2025-01-22 18:57:10 [INFO] - RT diff: -0.28903835837990777
2025-01-22 18:57:10 [INFO] - Fitting a mixture model...
2025-01-22 18:57:10 [INFO] - Estimating match-between-runs FDR...
2025-01-22 18:57:12 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.967400
2025-01-22 18:57:12 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100
2025-01-22 18:57:12 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100
2025-01-22 18:57:12 [INFO] - Updating Philosopher's tables...
2025-01-22 18:57:15 [INFO] - Combining experiments and estimating protein intensity...
2025-01-22 18:57:19 [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 34.9 MINUTES=============================================================
