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: 220524ko02Sample1
  - J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.raw	DDA
  Experiment/Group: 220524ko03Sample2
  - J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2.raw	DDA
  Experiment/Group: 220524ko05Sample3
  - J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3.raw	DDA
  Experiment/Group: 220524ko06Sample4
  - J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4.raw	DDA
  Experiment/Group: 220524ko08Sample5
  - J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5.raw	DDA
  Experiment/Group: 220524ko09Sample6
  - J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6.raw	DDA
  Experiment/Group: 220524ko11Sample7
  - J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7.raw	DDA
  Experiment/Group: 220524ko12Sample8
  - J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8.raw	DDA
  Experiment/Group: 220524ko14Sample9
  - J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9.raw	DDA
  Experiment/Group: 220524ko15Sample10
  - J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10.raw	DDA
  Experiment/Group: 220524ko17Sample11
  - J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11.raw	DDA
  Experiment/Group: 220524ko18Sample12
  - J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12.raw	DDA


140 commands to execute:
CheckCentroid
java -Xmx68G -cp "D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.raw 15
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
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\c08b9f42-8811-4786-a742-bb732bc81f5d
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
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\7e6bd1f9-656f-4b16-b0fc-01042ee2bdde
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
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\e0e8b951-0ea5-466a-81b5-84aab81decfc
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
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\5321811a-c53c-4ffb-a68b-a4d37ff8586c
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
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\d63bd35b-08c7-4d88-99ef-5bde68050d9f
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
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\a0e04edb-1617-45d9-a91c-68794b01390b
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
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\94002f93-922a-4402-89bb-edde7554a461
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\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\c1e81481-9557-45c8-93f6-d2c71a57ff42
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
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\390dd615-111b-4ae2-93ca-b8dfe8d05493
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
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\ea1bf9bd-bfaa-4681-bbe7-302bb2760aee
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
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\08c73098-5f64-4de9-b762-1ecb0b4febdf
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
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\ba21b2dd-5dec-4ce4-a0e4-64443724570b
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
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\7039bfaf-7992-4cd3-9960-eb94713fc12c
MSFragger [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
java -jar -Dfile.encoding=UTF-8 -Xmx68G D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\fragger.params J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12.raw
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1\220524ko02Sample1.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1\220524ko02Sample1.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2\220524ko03Sample2.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2\220524ko03Sample2.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3\220524ko05Sample3.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3\220524ko05Sample3.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4\220524ko06Sample4.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4\220524ko06Sample4.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5\220524ko08Sample5.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5\220524ko08Sample5.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6\220524ko09Sample6.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6\220524ko09Sample6.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7\220524ko11Sample7.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7\220524ko11Sample7.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8\220524ko12Sample8.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8\220524ko12Sample8.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9\220524ko14Sample9.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9\220524ko14Sample9.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10\220524ko15Sample10.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10\220524ko15Sample10.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11\220524ko17Sample11.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11\220524ko17Sample11.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12\220524ko18Sample12.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12\220524ko18Sample12.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko08Sample5_percolator_target_psms.tsv --decoy-results-psms 220524ko08Sample5_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko08Sample5.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko09Sample6_percolator_target_psms.tsv --decoy-results-psms 220524ko09Sample6_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko09Sample6.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko14Sample9_percolator_target_psms.tsv --decoy-results-psms 220524ko14Sample9_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko14Sample9.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko11Sample7_percolator_target_psms.tsv --decoy-results-psms 220524ko11Sample7_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko11Sample7.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko12Sample8_percolator_target_psms.tsv --decoy-results-psms 220524ko12Sample8_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko12Sample8.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko17Sample11_percolator_target_psms.tsv --decoy-results-psms 220524ko17Sample11_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko17Sample11.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko18Sample12_percolator_target_psms.tsv --decoy-results-psms 220524ko18Sample12_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko18Sample12.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko15Sample10_percolator_target_psms.tsv --decoy-results-psms 220524ko15Sample10_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko15Sample10.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko06Sample4_percolator_target_psms.tsv --decoy-results-psms 220524ko06Sample4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko06Sample4.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko02Sample1_percolator_target_psms.tsv --decoy-results-psms 220524ko02Sample1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko02Sample1.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko03Sample2_percolator_target_psms.tsv --decoy-results-psms 220524ko03Sample2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko03Sample2.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko05Sample3_percolator_target_psms.tsv --decoy-results-psms 220524ko05Sample3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko05Sample3.pin
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko08Sample5.pin 220524ko08Sample5 220524ko08Sample5_percolator_target_psms.tsv 220524ko08Sample5_percolator_decoy_psms.tsv interact-220524ko08Sample5 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5\220524ko08Sample5_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5\220524ko08Sample5_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko09Sample6.pin 220524ko09Sample6 220524ko09Sample6_percolator_target_psms.tsv 220524ko09Sample6_percolator_decoy_psms.tsv interact-220524ko09Sample6 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6\220524ko09Sample6_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6\220524ko09Sample6_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko14Sample9.pin 220524ko14Sample9 220524ko14Sample9_percolator_target_psms.tsv 220524ko14Sample9_percolator_decoy_psms.tsv interact-220524ko14Sample9 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9\220524ko14Sample9_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9\220524ko14Sample9_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko11Sample7.pin 220524ko11Sample7 220524ko11Sample7_percolator_target_psms.tsv 220524ko11Sample7_percolator_decoy_psms.tsv interact-220524ko11Sample7 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7\220524ko11Sample7_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7\220524ko11Sample7_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko12Sample8.pin 220524ko12Sample8 220524ko12Sample8_percolator_target_psms.tsv 220524ko12Sample8_percolator_decoy_psms.tsv interact-220524ko12Sample8 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8\220524ko12Sample8_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8\220524ko12Sample8_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko17Sample11.pin 220524ko17Sample11 220524ko17Sample11_percolator_target_psms.tsv 220524ko17Sample11_percolator_decoy_psms.tsv interact-220524ko17Sample11 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11\220524ko17Sample11_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11\220524ko17Sample11_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko18Sample12.pin 220524ko18Sample12 220524ko18Sample12_percolator_target_psms.tsv 220524ko18Sample12_percolator_decoy_psms.tsv interact-220524ko18Sample12 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12\220524ko18Sample12_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12\220524ko18Sample12_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko15Sample10.pin 220524ko15Sample10 220524ko15Sample10_percolator_target_psms.tsv 220524ko15Sample10_percolator_decoy_psms.tsv interact-220524ko15Sample10 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10\220524ko15Sample10_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10\220524ko15Sample10_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko06Sample4.pin 220524ko06Sample4 220524ko06Sample4_percolator_target_psms.tsv 220524ko06Sample4_percolator_decoy_psms.tsv interact-220524ko06Sample4 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4\220524ko06Sample4_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4\220524ko06Sample4_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko02Sample1.pin 220524ko02Sample1 220524ko02Sample1_percolator_target_psms.tsv 220524ko02Sample1_percolator_decoy_psms.tsv interact-220524ko02Sample1 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1\220524ko02Sample1_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1\220524ko02Sample1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko03Sample2.pin 220524ko03Sample2 220524ko03Sample2_percolator_target_psms.tsv 220524ko03Sample2_percolator_decoy_psms.tsv interact-220524ko03Sample2 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2\220524ko03Sample2_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2\220524ko03Sample2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko05Sample3.pin 220524ko05Sample3 220524ko05Sample3_percolator_target_psms.tsv 220524ko05Sample3_percolator_decoy_psms.tsv interact-220524ko05Sample3 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3\220524ko05Sample3_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3\220524ko05Sample3_percolator_decoy_psms.tsv
ProteinProphet [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
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\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
IonQuant [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
java -Xmx68G -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 0 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 100 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 0 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\filelist_ionquant.txt --modlist J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\modmasses_ionquant.txt
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
    Cmd: [CheckCentroid], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
    Cmd: [MSFragger], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
    Cmd: [Percolator], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
    Cmd: [ProteinProphet], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
    Cmd: [PhilosopherDbAnnotate], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
    Cmd: [PhilosopherFilter], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
    Cmd: [PhilosopherReport], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
    Cmd: [IonQuant], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\220524ko\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=100
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=0
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=false
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=trypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
msfragger.output_report_topN_dia2=3
msfragger.override_charge=false
msfragger.precursor_mass_lower=-50
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=50
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.require_precursor=false
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name=stricttrypsin
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.021465,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,KR,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.write_calibrated_mzml=false
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=4
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 1.0 --ion 1.0 --pep 1.0
phi-report.pep-level-summary=true
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=00.2
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=00.1
ptmshepherd.diagmine_fragMinSpecDiff=00.1
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=00.2
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=2,0.5,0.1
ptmshepherd.prob_dhexY=2,0.5
ptmshepherd.prob_neuacOx=2,0.05,0.2
ptmshepherd.prob_neugcOx=2,0.05,0.2
ptmshepherd.prob_phosphoOx=2,0.05,0.2
ptmshepherd.prob_regY=5,0.5
ptmshepherd.prob_sulfoOx=2,0.05,0.2
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
run-diaumpire=false
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=J\:\\MSFragger_process\\Saitou-lab\\Revision\\220524ko\\MSFragger_iBAQ
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.misc.save-sdrf=true
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=15

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx68G -cp "D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.raw 15
Done in 0.0 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:41] Executing Workspace  v5.0.0                  
INFO[15:58:41] Removing workspace                           
WARN[15:58:41] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:41] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
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\c08b9f42-8811-4786-a742-bb732bc81f5d
INFO[15:58:42] Executing Workspace  v5.0.0                  
INFO[15:58:42] Creating workspace                           
INFO[15:58:42] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:42] Executing Workspace  v5.0.0                  
INFO[15:58:42] Removing workspace                           
WARN[15:58:42] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:42] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
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\7e6bd1f9-656f-4b16-b0fc-01042ee2bdde
INFO[15:58:42] Executing Workspace  v5.0.0                  
INFO[15:58:42] Creating workspace                           
INFO[15:58:42] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:43] Executing Workspace  v5.0.0                  
INFO[15:58:43] Removing workspace                           
WARN[15:58:43] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:43] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
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\e0e8b951-0ea5-466a-81b5-84aab81decfc
INFO[15:58:43] Executing Workspace  v5.0.0                  
INFO[15:58:43] Creating workspace                           
INFO[15:58:43] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:44] Executing Workspace  v5.0.0                  
INFO[15:58:44] Removing workspace                           
WARN[15:58:44] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:44] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
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\5321811a-c53c-4ffb-a68b-a4d37ff8586c
INFO[15:58:44] Executing Workspace  v5.0.0                  
INFO[15:58:44] Creating workspace                           
INFO[15:58:44] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:45] Executing Workspace  v5.0.0                  
INFO[15:58:45] Removing workspace                           
WARN[15:58:45] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:45] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
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\d63bd35b-08c7-4d88-99ef-5bde68050d9f
INFO[15:58:45] Executing Workspace  v5.0.0                  
INFO[15:58:45] Creating workspace                           
INFO[15:58:45] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:45] Executing Workspace  v5.0.0                  
INFO[15:58:45] Removing workspace                           
WARN[15:58:45] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:45] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
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\a0e04edb-1617-45d9-a91c-68794b01390b
INFO[15:58:46] Executing Workspace  v5.0.0                  
INFO[15:58:46] Creating workspace                           
INFO[15:58:46] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:46] Executing Workspace  v5.0.0                  
INFO[15:58:46] Removing workspace                           
WARN[15:58:46] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:46] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
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\94002f93-922a-4402-89bb-edde7554a461
INFO[15:58:47] Executing Workspace  v5.0.0                  
INFO[15:58:47] Creating workspace                           
INFO[15:58:47] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:47] Executing Workspace  v5.0.0                  
INFO[15:58:47] Removing workspace                           
WARN[15:58:47] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:47] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\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\c1e81481-9557-45c8-93f6-d2c71a57ff42
INFO[15:58:47] Executing Workspace  v5.0.0                  
INFO[15:58:47] Creating workspace                           
INFO[15:58:47] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:48] Executing Workspace  v5.0.0                  
INFO[15:58:48] Removing workspace                           
WARN[15:58:48] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:48] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
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\390dd615-111b-4ae2-93ca-b8dfe8d05493
INFO[15:58:48] Executing Workspace  v5.0.0                  
INFO[15:58:48] Creating workspace                           
INFO[15:58:48] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:49] Executing Workspace  v5.0.0                  
INFO[15:58:49] Removing workspace                           
WARN[15:58:49] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:49] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
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\ea1bf9bd-bfaa-4681-bbe7-302bb2760aee
INFO[15:58:49] Executing Workspace  v5.0.0                  
INFO[15:58:49] Creating workspace                           
INFO[15:58:49] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:49] Executing Workspace  v5.0.0                  
INFO[15:58:49] Removing workspace                           
WARN[15:58:50] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:50] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
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\08c73098-5f64-4de9-b762-1ecb0b4febdf
INFO[15:58:50] Executing Workspace  v5.0.0                  
INFO[15:58:50] Creating workspace                           
INFO[15:58:50] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:50] Executing Workspace  v5.0.0                  
INFO[15:58:50] Removing workspace                           
WARN[15:58:50] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:50] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
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\ba21b2dd-5dec-4ce4-a0e4-64443724570b
INFO[15:58:51] Executing Workspace  v5.0.0                  
INFO[15:58:51] Creating workspace                           
INFO[15:58:51] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:58:51] Executing Workspace  v5.0.0                  
INFO[15:58:51] Removing workspace                           
WARN[15:58:51] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:58:51] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
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\7039bfaf-7992-4cd3-9960-eb94713fc12c
INFO[15:58:52] Executing Workspace  v5.0.0                  
INFO[15:58:52] Creating workspace                           
INFO[15:58:52] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
java -jar -Dfile.encoding=UTF-8 -Xmx68G D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\fragger.params J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11.raw J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12.raw
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 68 GB memory
Checking database...
Checking spectral files...
J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.raw: Scans = 40962
J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11.raw: Scans = 40203
J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10.raw: Scans = 40954
J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2.raw: Scans = 41685
J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8.raw: Scans = 41031
J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4.raw: Scans = 41990
J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7.raw: Scans = 41462
J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5.raw: Scans = 41570
J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12.raw: Scans = 39882
J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9.raw: Scans = 40714
J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3.raw: Scans = 42712
J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6.raw: Scans = 42055
***********************************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 = 0
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 0
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.021465
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
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 2.43 s
	001. 220524ko02Sample1.raw 16.8 s | deisotoping 0.7 s
		[progress: 36967/36967 (100%) - 13114 spectra/s] 2.8s | postprocessing 0.3 s
	002. 220524ko03Sample2.raw 11.1 s | deisotoping 0.1 s
		[progress: 36961/36961 (100%) - 69086 spectra/s] 0.5s | postprocessing 0.2 s
	003. 220524ko05Sample3.raw 11.1 s | deisotoping 0.0 s
		[progress: 39193/39193 (100%) - 58236 spectra/s] 0.7s | postprocessing 0.2 s
	004. 220524ko06Sample4.raw 10.9 s | deisotoping 0.0 s
		[progress: 38374/38374 (100%) - 57189 spectra/s] 0.7s | postprocessing 0.1 s
	005. 220524ko08Sample5.raw 10.5 s | deisotoping 0.0 s
		[progress: 37391/37391 (100%) - 64802 spectra/s] 0.6s | postprocessing 0.1 s
	006. 220524ko09Sample6.raw 12.2 s | deisotoping 0.0 s
		[progress: 38582/38582 (100%) - 65727 spectra/s] 0.6s | postprocessing 0.1 s
	007. 220524ko11Sample7.raw 10.6 s | deisotoping 0.0 s
		[progress: 37837/37837 (100%) - 66968 spectra/s] 0.6s | postprocessing 0.1 s
	008. 220524ko12Sample8.raw 10.9 s | deisotoping 0.0 s
		[progress: 36504/36504 (100%) - 73895 spectra/s] 0.5s | postprocessing 0.1 s
	009. 220524ko14Sample9.raw 11.6 s | deisotoping 0.0 s
		[progress: 36849/36849 (100%) - 67120 spectra/s] 0.5s | postprocessing 0.1 s
	010. 220524ko15Sample10.raw 11.7 s | deisotoping 0.0 s
		[progress: 37171/37171 (100%) - 75093 spectra/s] 0.5s | postprocessing 0.1 s
	011. 220524ko17Sample11.raw 11.3 s | deisotoping 0.0 s
		[progress: 35834/35834 (100%) - 53805 spectra/s] 0.7s | postprocessing 0.1 s
	012. 220524ko18Sample12.raw 11.1 s | deisotoping 0.0 s
		[progress: 35362/35362 (100%) - 77041 spectra/s] 0.5s | postprocessing 0.1 s
***************************FIRST SEARCH DONE IN 2.899 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |   8.04   1.62 |  -0.01   1.01 |  -5.86   2.62 |  -0.09   2.40  
 002 |   7.64   1.70 |   0.04   0.98 |  -5.28   2.69 |  -0.08   2.49  
 003 |   8.07   1.75 |   0.03   1.00 |  -4.90   2.61 |  -0.03   2.41  
 004 |   8.07   1.91 |   0.02   1.01 |  -4.66   2.63 |  -0.07   2.43  
 005 |   8.59   1.71 |  -0.01   0.99 |  -4.36   2.66 |  -0.04   2.47  
 006 |   7.07   1.72 |   0.03   1.00 |  -3.85   2.59 |  -0.03   2.40  
 007 |   9.63   1.71 |   0.07   1.08 |  -4.27   2.63 |  -0.02   2.41  
 008 |   8.32   1.75 |   0.04   0.97 |  -3.56   2.62 |  -0.02   2.43  
 009 |   8.08   1.62 |   0.05   0.97 |  -3.19   2.57 |   0.00   2.39  
 010 |   8.39   1.62 |   0.01   1.02 |  -3.37   2.58 |  -0.04   2.40  
 011 |   8.31   1.85 |   0.01   0.98 |  -2.83   2.71 |   0.01   2.48  
 012 |   7.38   1.68 |   0.02   0.99 |  -2.72   2.70 |  -0.02   2.51  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count |  23411|  23791|  24095|  23940| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |  24149|  24149|  24149|  24095| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |  24373
-------|-------
-------|-------
 Rm P. |    1  
-------|-------
 Count |  24353
-------|-------
New fragment_mass_tolerance = 10 PPM
New use_topN_peaks = 175
New minimum_ratio = 0.000000
New intensity_transform = 1
New remove_precursor_peak = 0
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 2.145 MIN*********

************************************MAIN SEARCH************************************
output_format = pepXML_pin but report_alternative_proteins = 0. Change report_alternative_proteins to 1.
Checking database...
Parameters:
num_threads = 15
database_name = D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas
decoy_prefix = rev_
precursor_mass_lower = -50.0
precursor_mass_upper = 50.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 10.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1/2
mass_offsets = 0.0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 1
override_charge = 0
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 175
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.0
intensity_transform = 1
activation_types = all
group_variable = 0
require_precursor = 0
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 0
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.021465
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.05 Da.
280170470 fragments to be searched in 1 slices (4.17 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 2.36 s
	001. 220524ko02Sample1.mzBIN_calibrated 0.7 s
		[progress: 36427/36427 (100%) - 41441 spectra/s] 0.9s | remapping alternative proteins and postprocessing 4.1 s
	002. 220524ko03Sample2.mzBIN_calibrated 0.7 s
		[progress: 36407/36407 (100%) - 40999 spectra/s] 0.9s | remapping alternative proteins and postprocessing 3.2 s
	003. 220524ko05Sample3.mzBIN_calibrated 0.8 s
		[progress: 38725/38725 (100%) - 35205 spectra/s] 1.1s | remapping alternative proteins and postprocessing 3.2 s
	004. 220524ko06Sample4.mzBIN_calibrated 0.7 s
		[progress: 37898/37898 (100%) - 34673 spectra/s] 1.1s | remapping alternative proteins and postprocessing 3.2 s
	005. 220524ko08Sample5.mzBIN_calibrated 0.7 s
		[progress: 36898/36898 (100%) - 41930 spectra/s] 0.9s | remapping alternative proteins and postprocessing 3.1 s
	006. 220524ko09Sample6.mzBIN_calibrated 0.8 s
		[progress: 38079/38079 (100%) - 38464 spectra/s] 1.0s | remapping alternative proteins and postprocessing 3.4 s
	007. 220524ko11Sample7.mzBIN_calibrated 0.7 s
		[progress: 37304/37304 (100%) - 37491 spectra/s] 1.0s | remapping alternative proteins and postprocessing 3.1 s
	008. 220524ko12Sample8.mzBIN_calibrated 0.7 s
		[progress: 35960/35960 (100%) - 46340 spectra/s] 0.8s | remapping alternative proteins and postprocessing 3.1 s
	009. 220524ko14Sample9.mzBIN_calibrated 0.7 s
		[progress: 36320/36320 (100%) - 42282 spectra/s] 0.9s | remapping alternative proteins and postprocessing 3.3 s
	010. 220524ko15Sample10.mzBIN_calibrated 0.7 s
		[progress: 36619/36619 (100%) - 41284 spectra/s] 0.9s | remapping alternative proteins and postprocessing 3.2 s
	011. 220524ko17Sample11.mzBIN_calibrated 0.7 s
		[progress: 35270/35270 (100%) - 45334 spectra/s] 0.8s | remapping alternative proteins and postprocessing 2.9 s
	012. 220524ko18Sample12.mzBIN_calibrated 0.6 s
		[progress: 34765/34765 (100%) - 43895 spectra/s] 0.8s | remapping alternative proteins and postprocessing 2.7 s
***************************MAIN SEARCH DONE IN 1.040 MIN***************************

*******************************TOTAL TIME 6.084 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1\220524ko02Sample1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1\220524ko02Sample1.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2\220524ko03Sample2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2\220524ko03Sample2.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3\220524ko05Sample3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3\220524ko05Sample3.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4\220524ko06Sample4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4\220524ko06Sample4.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5\220524ko08Sample5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5\220524ko08Sample5.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6\220524ko09Sample6.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6\220524ko09Sample6.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7\220524ko11Sample7.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7\220524ko11Sample7.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8\220524ko12Sample8.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8\220524ko12Sample8.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9\220524ko14Sample9.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9\220524ko14Sample9.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10\220524ko15Sample10.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10\220524ko15Sample10.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11\220524ko17Sample11.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11\220524ko17Sample11.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12.pepXML J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12\220524ko18Sample12.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12.pin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12\220524ko18Sample12.pin
Process 'MSFragger move pin' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko08Sample5_percolator_target_psms.tsv --decoy-results-psms 220524ko08Sample5_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko08Sample5.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 220524ko08Sample5_percolator_target_psms.tsv --decoy-results-psms 220524ko08Sample5_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko08Sample5.pin
Started Thu Jan 16 16:05:02 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 220524ko08Sample5.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 31506 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 27897 positives and 3609 negatives, size ratio=7.72984 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 15513 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 15538 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 15471 training set positives with q<0.01 in that direction.
Found 23279 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3680 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 23755 PSMs with q<0.01
Iteration 2:	Estimated 23817 PSMs with q<0.01
Iteration 3:	Estimated 23806 PSMs with q<0.01
Iteration 4:	Estimated 23827 PSMs with q<0.01
Iteration 5:	Estimated 23827 PSMs with q<0.01
Iteration 6:	Estimated 23821 PSMs with q<0.01
Iteration 7:	Estimated 23821 PSMs with q<0.01
Iteration 8:	Estimated 23826 PSMs with q<0.01
Iteration 9:	Estimated 23825 PSMs with q<0.01
Iteration 10:	Estimated 23825 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
-0.4066	-0.3976	-0.3865	abs_ppm
-0.1689	-0.1717	-0.1740	isotope_errors
-2.2181	-2.1788	-1.8667	log10_evalue
 0.5368	-0.5052	 0.4292	hyperscore
 0.9922	 0.9455	 0.8789	delta_hyperscore
 1.5294	 2.5584	 1.3781	matched_ion_num
-0.7782	-0.9673	-0.7543	complementary_ions
 0.4068	 0.2726	 0.3515	ion_series
 0.0135	-0.0536	 0.0034	weighted_average_abs_fragment_ppm
-0.0872	-0.0720	-0.0377	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1972	-0.2730	-0.1999	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0811	-0.0517	-0.0694	charge_2
 0.0679	 0.0692	 0.0614	charge_3
 0.0108	-0.0410	 0.0106	charge_4
 0.0591	 0.0197	 0.0303	charge_5
-0.0054	 0.0273	-0.0060	charge_6
-0.0678	-0.0280	-0.0577	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
-0.0424	-0.0342	 0.0255	15.9949M
 3.8070	 3.5926	 3.2394	m0
Found 23768 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 27897 target PSMs and 3609 decoy PSMs.
Calculating q values.
Final list yields 23770 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 6.7460 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko09Sample6_percolator_target_psms.tsv --decoy-results-psms 220524ko09Sample6_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko09Sample6.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 220524ko09Sample6_percolator_target_psms.tsv --decoy-results-psms 220524ko09Sample6_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko09Sample6.pin
Started Thu Jan 16 16:05:10 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 220524ko09Sample6.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 32758 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 29052 positives and 3706 negatives, size ratio=7.83918 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 16122 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 16073 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 16161 training set positives with q<0.01 in that direction.
Found 24179 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3860 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 24724 PSMs with q<0.01
Iteration 2:	Estimated 24745 PSMs with q<0.01
Iteration 3:	Estimated 24729 PSMs with q<0.01
Iteration 4:	Estimated 24734 PSMs with q<0.01
Iteration 5:	Estimated 24733 PSMs with q<0.01
Iteration 6:	Estimated 24733 PSMs with q<0.01
Iteration 7:	Estimated 24733 PSMs with q<0.01
Iteration 8:	Estimated 24733 PSMs with q<0.01
Iteration 9:	Estimated 24730 PSMs with q<0.01
Iteration 10:	Estimated 24728 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
-0.3116	-0.3618	-0.4024	abs_ppm
-0.1075	-0.1323	-0.0822	isotope_errors
-1.3266	-1.4760	-1.7233	log10_evalue
 1.2742	 0.9140	 0.8906	hyperscore
 0.7973	 0.8070	 0.7584	delta_hyperscore
 0.8624	 1.2766	 1.1901	matched_ion_num
-0.7095	-0.8209	-0.7810	complementary_ions
 0.4399	 0.3064	 0.3698	ion_series
 0.0402	 0.0301	 0.0302	weighted_average_abs_fragment_ppm
-0.0077	-0.0629	-0.0448	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1362	-0.1324	-0.1384	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0421	-0.0855	-0.0456	charge_2
 0.0739	 0.0680	 0.0662	charge_3
-0.0677	 0.0429	-0.0389	charge_4
 0.0114	 0.0101	 0.0057	charge_5
 0.0313	-0.0619	-0.0054	charge_6
-0.0071	-0.0326	-0.0106	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
-0.0037	 0.0060	 0.0520	15.9949M
 3.0698	 3.0684	 3.2610	m0
Found 24691 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 29052 target PSMs and 3706 decoy PSMs.
Calculating q values.
Final list yields 24696 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 18.7450 cpu seconds or 19 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko14Sample9_percolator_target_psms.tsv --decoy-results-psms 220524ko14Sample9_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko14Sample9.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 220524ko14Sample9_percolator_target_psms.tsv --decoy-results-psms 220524ko14Sample9_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko14Sample9.pin
Started Thu Jan 16 16:05:29 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 220524ko14Sample9.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 30825 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 27408 positives and 3417 negatives, size ratio=8.02107 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 15330 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 15315 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 15370 training set positives with q<0.01 in that direction.
Found 22997 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3680 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 23502 PSMs with q<0.01
Iteration 2:	Estimated 23483 PSMs with q<0.01
Iteration 3:	Estimated 23469 PSMs with q<0.01
Iteration 4:	Estimated 23489 PSMs with q<0.01
Iteration 5:	Estimated 23487 PSMs with q<0.01
Iteration 6:	Estimated 23495 PSMs with q<0.01
Iteration 7:	Estimated 23503 PSMs with q<0.01
Iteration 8:	Estimated 23502 PSMs with q<0.01
Iteration 9:	Estimated 23502 PSMs with q<0.01
Iteration 10:	Estimated 23497 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
-0.4022	-0.5324	-0.4330	abs_ppm
-0.1993	-0.1374	-0.1427	isotope_errors
-1.7676	-2.0058	-1.6438	log10_evalue
 0.7428	 0.6696	 0.6577	hyperscore
 0.8495	 1.0177	 0.8778	delta_hyperscore
 1.0542	 1.5327	 0.9821	matched_ion_num
-0.7430	-0.8725	-0.6594	complementary_ions
 0.5091	 0.4229	 0.5483	ion_series
-0.0246	-0.0622	 0.0103	weighted_average_abs_fragment_ppm
-0.0241	-0.0667	 0.0192	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1461	-0.0649	-0.1171	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.1180	-0.1091	-0.0641	charge_2
 0.1225	 0.1306	 0.1022	charge_3
 0.0087	-0.0163	-0.0666	charge_4
-0.0447	-0.0466	-0.0048	charge_5
 0.0494	-0.0088	-0.0062	charge_6
-0.0553	-0.0647	-0.0534	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
 0.0665	 0.0347	 0.0154	15.9949M
 3.3028	 3.7846	 3.1239	m0
Found 23431 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 27408 target PSMs and 3417 decoy PSMs.
Calculating q values.
Final list yields 23432 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 6.3440 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko11Sample7_percolator_target_psms.tsv --decoy-results-psms 220524ko11Sample7_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko11Sample7.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 220524ko11Sample7_percolator_target_psms.tsv --decoy-results-psms 220524ko11Sample7_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko11Sample7.pin
Started Thu Jan 16 16:05:37 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 220524ko11Sample7.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 32124 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 28598 positives and 3526 negatives, size ratio=8.11061 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 16186 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 16234 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 16242 training set positives with q<0.01 in that direction.
Found 24320 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3650 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 24751 PSMs with q<0.01
Iteration 2:	Estimated 24755 PSMs with q<0.01
Iteration 3:	Estimated 24753 PSMs with q<0.01
Iteration 4:	Estimated 24755 PSMs with q<0.01
Iteration 5:	Estimated 24753 PSMs with q<0.01
Iteration 6:	Estimated 24746 PSMs with q<0.01
Iteration 7:	Estimated 24751 PSMs with q<0.01
Iteration 8:	Estimated 24751 PSMs with q<0.01
Iteration 9:	Estimated 24752 PSMs with q<0.01
Iteration 10:	Estimated 24752 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
-0.2485	-0.3967	-0.3786	abs_ppm
-0.1770	-0.2212	-0.1490	isotope_errors
-1.6956	-2.3429	-1.8331	log10_evalue
 0.7095	-0.4063	 0.8482	hyperscore
 0.8577	 1.2504	 0.9026	delta_hyperscore
 1.1739	 2.8209	 1.1632	matched_ion_num
-0.6806	-1.0079	-0.7500	complementary_ions
 0.3876	 0.5635	 0.4458	ion_series
 0.0503	 0.0274	 0.0300	weighted_average_abs_fragment_ppm
-0.1382	-0.1297	-0.0239	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1451	-0.2946	-0.1506	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.1102	-0.1599	-0.0715	charge_2
 0.1035	 0.1880	 0.0785	charge_3
 0.0140	-0.0490	-0.0183	charge_4
-0.0079	-0.0017	 0.0010	charge_5
 0.0251	 0.0287	 0.0496	charge_6
 0.0245	-0.0500	 0.0070	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
 0.0765	-0.0399	 0.0373	15.9949M
 2.6997	 4.5527	 3.6000	m0
Found 24669 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 28598 target PSMs and 3526 decoy PSMs.
Calculating q values.
Final list yields 24669 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.8560 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko12Sample8_percolator_target_psms.tsv --decoy-results-psms 220524ko12Sample8_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko12Sample8.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 220524ko12Sample8_percolator_target_psms.tsv --decoy-results-psms 220524ko12Sample8_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko12Sample8.pin
Started Thu Jan 16 16:05:43 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 220524ko12Sample8.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 30409 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 26957 positives and 3452 negatives, size ratio=7.8091 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 14881 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 14963 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 14941 training set positives with q<0.01 in that direction.
Found 22385 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3590 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 22965 PSMs with q<0.01
Iteration 2:	Estimated 23002 PSMs with q<0.01
Iteration 3:	Estimated 23011 PSMs with q<0.01
Iteration 4:	Estimated 23001 PSMs with q<0.01
Iteration 5:	Estimated 23002 PSMs with q<0.01
Iteration 6:	Estimated 23001 PSMs with q<0.01
Iteration 7:	Estimated 22998 PSMs with q<0.01
Iteration 8:	Estimated 22996 PSMs with q<0.01
Iteration 9:	Estimated 22998 PSMs with q<0.01
Iteration 10:	Estimated 22999 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
-0.4353	-0.4766	-0.4268	abs_ppm
-0.1253	-0.1239	-0.1925	isotope_errors
-1.8332	-2.0981	-1.7415	log10_evalue
 0.5668	 0.5500	 0.4019	hyperscore
 0.8655	 0.9152	 0.8511	delta_hyperscore
 1.0087	 1.4967	 1.5072	matched_ion_num
-0.8103	-0.9104	-0.8474	complementary_ions
 0.6681	 0.4862	 0.4448	ion_series
-0.0011	 0.0203	-0.0119	weighted_average_abs_fragment_ppm
 0.0641	 0.0516	 0.0432	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.2082	-0.1982	-0.1753	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0637	-0.0353	-0.0491	charge_2
 0.0574	 0.0677	 0.0516	charge_3
 0.0181	-0.0458	 0.0100	charge_4
-0.0106	-0.0297	-0.0365	charge_5
 0.0241	-0.0277	 0.0206	charge_6
-0.0439	-0.0559	-0.0495	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
 0.0705	 0.0979	 0.0668	15.9949M
 2.8917	 3.6826	 3.2641	m0
Found 22968 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 26957 target PSMs and 3452 decoy PSMs.
Calculating q values.
Final list yields 22971 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 9.8920 cpu seconds or 10 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko17Sample11_percolator_target_psms.tsv --decoy-results-psms 220524ko17Sample11_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko17Sample11.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 220524ko17Sample11_percolator_target_psms.tsv --decoy-results-psms 220524ko17Sample11_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko17Sample11.pin
Started Thu Jan 16 16:05:54 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 220524ko17Sample11.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 29441 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 26221 positives and 3220 negatives, size ratio=8.14317 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 14492 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 14514 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 14679 training set positives with q<0.01 in that direction.
Found 21834 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3490 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 22435 PSMs with q<0.01
Iteration 2:	Estimated 22469 PSMs with q<0.01
Iteration 3:	Estimated 22469 PSMs with q<0.01
Iteration 4:	Estimated 22465 PSMs with q<0.01
Iteration 5:	Estimated 22462 PSMs with q<0.01
Iteration 6:	Estimated 22462 PSMs with q<0.01
Iteration 7:	Estimated 22460 PSMs with q<0.01
Iteration 8:	Estimated 22461 PSMs with q<0.01
Iteration 9:	Estimated 22462 PSMs with q<0.01
Iteration 10:	Estimated 22463 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
-0.3171	-0.4752	-0.3278	abs_ppm
-0.1801	-0.2175	-0.2348	isotope_errors
-1.4808	-1.5700	-1.5544	log10_evalue
 0.6553	 0.4496	 0.5160	hyperscore
 0.8168	 0.8547	 0.8596	delta_hyperscore
 1.2697	 1.7583	 1.6830	matched_ion_num
-0.7160	-1.0448	-0.7155	complementary_ions
 0.3418	 0.3477	 0.3104	ion_series
-0.0150	-0.0122	-0.0076	weighted_average_abs_fragment_ppm
-0.0700	-0.0512	-0.1147	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1895	-0.2258	-0.1404	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.1053	-0.0908	-0.1615	charge_2
 0.0833	 0.0410	 0.1104	charge_3
 0.0503	 0.0936	 0.1052	charge_4
 0.0029	 0.0293	 0.0148	charge_5
-0.0034	 0.0179	 0.0092	charge_6
-0.0488	-0.0509	-0.0544	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
 0.0533	 0.0321	-0.0093	15.9949M
 2.9583	 3.0892	 3.2973	m0
Found 22383 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 26221 target PSMs and 3220 decoy PSMs.
Calculating q values.
Final list yields 22384 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 6.2910 cpu seconds or 7 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko18Sample12_percolator_target_psms.tsv --decoy-results-psms 220524ko18Sample12_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko18Sample12.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 220524ko18Sample12_percolator_target_psms.tsv --decoy-results-psms 220524ko18Sample12_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko18Sample12.pin
Started Thu Jan 16 16:06:01 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 220524ko18Sample12.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 28963 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 25817 positives and 3146 negatives, size ratio=8.20629 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 14370 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 14316 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 14429 training set positives with q<0.01 in that direction.
Found 21562 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3370 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 22051 PSMs with q<0.01
Iteration 2:	Estimated 22118 PSMs with q<0.01
Iteration 3:	Estimated 22129 PSMs with q<0.01
Iteration 4:	Estimated 22128 PSMs with q<0.01
Iteration 5:	Estimated 22140 PSMs with q<0.01
Iteration 6:	Estimated 22147 PSMs with q<0.01
Iteration 7:	Estimated 22147 PSMs with q<0.01
Iteration 8:	Estimated 22147 PSMs with q<0.01
Iteration 9:	Estimated 22150 PSMs with q<0.01
Iteration 10:	Estimated 22149 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
-0.3563	-0.3571	-0.5018	abs_ppm
-0.2326	-0.2357	-0.2353	isotope_errors
-1.7499	-1.7794	-1.7160	log10_evalue
 0.6700	 0.7094	 0.3482	hyperscore
 0.6773	 0.8764	 0.8525	delta_hyperscore
 1.3362	 1.5182	 1.7450	matched_ion_num
-0.8540	-0.8825	-0.7159	complementary_ions
 0.2831	 0.3436	 0.3501	ion_series
 0.0278	 0.0538	 0.0687	weighted_average_abs_fragment_ppm
-0.0248	-0.0096	-0.0091	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1857	-0.1655	-0.1825	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0893	-0.0589	-0.1057	charge_2
 0.0696	 0.0796	 0.1188	charge_3
 0.0336	-0.0370	-0.0223	charge_4
 0.0215	-0.0101	 0.0070	charge_5
 0.0076	 0.0055	 0.0009	charge_6
 0.0084	 0.0062	-0.0484	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
-0.0177	-0.0031	 0.0386	15.9949M
 3.0559	 3.4148	 3.3606	m0
Found 22063 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 25817 target PSMs and 3146 decoy PSMs.
Calculating q values.
Final list yields 22064 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 20.9140 cpu seconds or 21 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko15Sample10_percolator_target_psms.tsv --decoy-results-psms 220524ko15Sample10_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko15Sample10.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 220524ko15Sample10_percolator_target_psms.tsv --decoy-results-psms 220524ko15Sample10_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko15Sample10.pin
Started Thu Jan 16 16:06:23 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 220524ko15Sample10.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 31108 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 27703 positives and 3405 negatives, size ratio=8.13598 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 15456 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 15511 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 15467 training set positives with q<0.01 in that direction.
Found 23208 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3660 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 23801 PSMs with q<0.01
Iteration 2:	Estimated 23791 PSMs with q<0.01
Iteration 3:	Estimated 23796 PSMs with q<0.01
Iteration 4:	Estimated 23799 PSMs with q<0.01
Iteration 5:	Estimated 23797 PSMs with q<0.01
Iteration 6:	Estimated 23801 PSMs with q<0.01
Iteration 7:	Estimated 23797 PSMs with q<0.01
Iteration 8:	Estimated 23797 PSMs with q<0.01
Iteration 9:	Estimated 23796 PSMs with q<0.01
Iteration 10:	Estimated 23794 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
-0.4537	-0.4296	-0.3781	abs_ppm
-0.2237	-0.0966	-0.1469	isotope_errors
-1.6602	-0.9094	-1.0955	log10_evalue
 0.3625	 1.2820	 0.9283	hyperscore
 1.0224	 1.0292	 1.1805	delta_hyperscore
 2.1430	 1.1855	 1.5852	matched_ion_num
-1.0133	-0.8247	-0.7334	complementary_ions
 0.4358	 0.5333	 0.4747	ion_series
-0.0009	 0.0232	 0.0038	weighted_average_abs_fragment_ppm
 0.0765	 0.0219	 0.0843	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1888	-0.1582	-0.2387	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0444	-0.1198	-0.0641	charge_2
 0.0747	 0.1147	 0.0846	charge_3
-0.0625	 0.0149	-0.0345	charge_4
 0.0119	-0.0078	 0.0077	charge_5
 0.0189	 0.0201	-0.0323	charge_6
-0.0473	-0.0361	-0.0454	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
-0.0081	-0.0221	-0.0604	15.9949M
 3.7328	 3.2882	 3.5789	m0
Found 23768 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 27703 target PSMs and 3405 decoy PSMs.
Calculating q values.
Final list yields 23770 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 6.7450 cpu seconds or 7 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko06Sample4_percolator_target_psms.tsv --decoy-results-psms 220524ko06Sample4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko06Sample4.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 220524ko06Sample4_percolator_target_psms.tsv --decoy-results-psms 220524ko06Sample4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko06Sample4.pin
Started Thu Jan 16 16:06:30 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 220524ko06Sample4.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 32544 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 28400 positives and 4144 negatives, size ratio=6.85328 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 15551 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 15585 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 15473 training set positives with q<0.01 in that direction.
Found 23289 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4030 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 23824 PSMs with q<0.01
Iteration 2:	Estimated 23833 PSMs with q<0.01
Iteration 3:	Estimated 23844 PSMs with q<0.01
Iteration 4:	Estimated 23834 PSMs with q<0.01
Iteration 5:	Estimated 23837 PSMs with q<0.01
Iteration 6:	Estimated 23845 PSMs with q<0.01
Iteration 7:	Estimated 23844 PSMs with q<0.01
Iteration 8:	Estimated 23842 PSMs with q<0.01
Iteration 9:	Estimated 23840 PSMs with q<0.01
Iteration 10:	Estimated 23839 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
-0.5231	-0.4046	-0.4487	abs_ppm
-0.1512	-0.2213	-0.1856	isotope_errors
-2.0846	-2.1086	-1.7817	log10_evalue
 0.2134	-0.1837	 0.8581	hyperscore
 1.0620	 1.1335	 1.0465	delta_hyperscore
 2.0602	 1.9833	 1.1967	matched_ion_num
-1.0103	-0.8405	-0.7976	complementary_ions
 0.3153	 0.6366	 0.5188	ion_series
 0.0177	-0.0549	 0.0134	weighted_average_abs_fragment_ppm
-0.0684	 0.0110	-0.0140	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1360	-0.1637	-0.1973	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0084	-0.0765	-0.0485	charge_2
 0.0585	 0.1002	 0.0660	charge_3
-0.0848	-0.0367	-0.0403	charge_4
 0.0188	 0.0228	 0.0452	charge_5
-0.1035	-0.0706	-0.0626	charge_6
-0.0017	-0.0672	 0.0078	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
 0.0520	 0.0318	 0.0513	15.9949M
 3.5528	 3.6536	 3.4131	m0
Found 23755 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 28400 target PSMs and 4144 decoy PSMs.
Calculating q values.
Final list yields 23756 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 6.3750 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko02Sample1_percolator_target_psms.tsv --decoy-results-psms 220524ko02Sample1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko02Sample1.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 220524ko02Sample1_percolator_target_psms.tsv --decoy-results-psms 220524ko02Sample1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko02Sample1.pin
Started Thu Jan 16 16:06:38 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 220524ko02Sample1.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 30880 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 27073 positives and 3807 negatives, size ratio=7.11137 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 14665 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 14850 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 14667 training set positives with q<0.01 in that direction.
Found 22100 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3650 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 22737 PSMs with q<0.01
Iteration 2:	Estimated 22770 PSMs with q<0.01
Iteration 3:	Estimated 22763 PSMs with q<0.01
Iteration 4:	Estimated 22775 PSMs with q<0.01
Iteration 5:	Estimated 22772 PSMs with q<0.01
Iteration 6:	Estimated 22777 PSMs with q<0.01
Iteration 7:	Estimated 22775 PSMs with q<0.01
Iteration 8:	Estimated 22775 PSMs with q<0.01
Iteration 9:	Estimated 22782 PSMs with q<0.01
Iteration 10:	Estimated 22785 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
-0.3615	-0.2986	-0.3709	abs_ppm
-0.2510	-0.2009	-0.2208	isotope_errors
-2.0382	-1.8911	-1.8004	log10_evalue
 0.4398	 0.7718	 0.7748	hyperscore
 0.9504	 0.7732	 0.9077	delta_hyperscore
 1.7985	 1.1311	 1.1611	matched_ion_num
-0.9923	-0.7660	-0.7759	complementary_ions
 0.3787	 0.4433	 0.4642	ion_series
 0.0483	 0.0010	 0.0037	weighted_average_abs_fragment_ppm
-0.2227	-0.0205	-0.0098	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1937	-0.1778	-0.1695	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.1543	-0.0966	-0.1010	charge_2
 0.0921	 0.0887	 0.0717	charge_3
 0.1133	 0.0352	 0.0638	charge_4
 0.0357	-0.0138	-0.0064	charge_5
 0.0170	-0.0765	 0.0050	charge_6
-0.0205	-0.0447	-0.0226	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
 0.0734	 0.0395	 0.0452	15.9949M
 3.4459	 3.2091	 3.2399	m0
Found 22685 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 27073 target PSMs and 3807 decoy PSMs.
Calculating q values.
Final list yields 22689 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 6.1280 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko03Sample2_percolator_target_psms.tsv --decoy-results-psms 220524ko03Sample2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko03Sample2.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 220524ko03Sample2_percolator_target_psms.tsv --decoy-results-psms 220524ko03Sample2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko03Sample2.pin
Started Thu Jan 16 16:06:45 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 220524ko03Sample2.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 30851 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 27522 positives and 3329 negatives, size ratio=8.26735 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 15450 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 15368 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 15483 training set positives with q<0.01 in that direction.
Found 23111 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3520 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 23661 PSMs with q<0.01
Iteration 2:	Estimated 23671 PSMs with q<0.01
Iteration 3:	Estimated 23655 PSMs with q<0.01
Iteration 4:	Estimated 23657 PSMs with q<0.01
Iteration 5:	Estimated 23647 PSMs with q<0.01
Iteration 6:	Estimated 23644 PSMs with q<0.01
Iteration 7:	Estimated 23644 PSMs with q<0.01
Iteration 8:	Estimated 23647 PSMs with q<0.01
Iteration 9:	Estimated 23649 PSMs with q<0.01
Iteration 10:	Estimated 23644 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
-0.4608	-0.3867	-0.4659	abs_ppm
-0.2154	-0.1710	-0.1394	isotope_errors
-1.5858	-1.6647	-1.6446	log10_evalue
 0.3845	 1.0052	 0.7261	hyperscore
 0.8253	 0.7920	 0.7595	delta_hyperscore
 1.6551	 1.1493	 1.1876	matched_ion_num
-0.7647	-0.8308	-0.7410	complementary_ions
 0.3911	 0.3448	 0.4252	ion_series
 0.0032	-0.0626	-0.0145	weighted_average_abs_fragment_ppm
 0.0604	 0.0781	 0.0546	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1445	-0.1790	-0.1607	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0646	-0.0584	-0.0547	charge_2
 0.0853	 0.0914	 0.0676	charge_3
-0.0256	-0.0607	-0.0163	charge_4
-0.0252	 0.0024	-0.0164	charge_5
-0.0024	 0.0073	 0.0140	charge_6
-0.0462	-0.0419	-0.0444	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
 0.0331	 0.0077	-0.0149	15.9949M
 3.3116	 3.0042	 3.1838	m0
Found 23586 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 27522 target PSMs and 3329 decoy PSMs.
Calculating q values.
Final list yields 23589 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.5860 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 220524ko05Sample3_percolator_target_psms.tsv --decoy-results-psms 220524ko05Sample3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko05Sample3.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 220524ko05Sample3_percolator_target_psms.tsv --decoy-results-psms 220524ko05Sample3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 220524ko05Sample3.pin
Started Thu Jan 16 16:06:51 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 220524ko05Sample3.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 33423 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 29562 positives and 3861 negatives, size ratio=7.65657 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 16375 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 16506 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 16392 training set positives with q<0.01 in that direction.
Found 24608 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3830 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 25076 PSMs with q<0.01
Iteration 2:	Estimated 25069 PSMs with q<0.01
Iteration 3:	Estimated 25084 PSMs with q<0.01
Iteration 4:	Estimated 25094 PSMs with q<0.01
Iteration 5:	Estimated 25094 PSMs with q<0.01
Iteration 6:	Estimated 25090 PSMs with q<0.01
Iteration 7:	Estimated 25094 PSMs with q<0.01
Iteration 8:	Estimated 25095 PSMs with q<0.01
Iteration 9:	Estimated 25094 PSMs with q<0.01
Iteration 10:	Estimated 25092 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
-0.2401	-0.2817	-0.3258	abs_ppm
-0.1426	-0.1010	-0.1268	isotope_errors
-1.6694	-1.7121	-1.9551	log10_evalue
 0.9909	 1.2987	 1.4873	hyperscore
 0.9299	 0.9411	 0.8859	delta_hyperscore
 1.2262	 0.8990	 0.8626	matched_ion_num
-0.8865	-0.7922	-0.9293	complementary_ions
 0.4631	 0.4964	 0.5026	ion_series
 0.0498	-0.0018	 0.0757	weighted_average_abs_fragment_ppm
-0.0812	-0.0190	-0.0608	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.1181	-0.1199	-0.1310	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0478	-0.0885	-0.0740	charge_2
 0.0738	 0.0753	 0.0902	charge_3
-0.0329	 0.0513	-0.0215	charge_4
-0.0203	-0.0404	 0.0043	charge_5
-0.0296	-0.0426	-0.0376	charge_6
-0.0563	-0.0587	-0.0617	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
 0.0762	 0.0292	 0.1238	15.9949M
 3.4300	 3.5750	 3.7588	m0
Found 25033 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 29562 target PSMs and 3861 decoy PSMs.
Calculating q values.
Final list yields 25037 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.9870 cpu seconds or 6 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko08Sample5.pin 220524ko08Sample5 220524ko08Sample5_percolator_target_psms.tsv 220524ko08Sample5_percolator_decoy_psms.tsv interact-220524ko08Sample5 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5\220524ko08Sample5_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5\220524ko08Sample5_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko09Sample6.pin 220524ko09Sample6 220524ko09Sample6_percolator_target_psms.tsv 220524ko09Sample6_percolator_decoy_psms.tsv interact-220524ko09Sample6 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6\220524ko09Sample6_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6\220524ko09Sample6_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko14Sample9.pin 220524ko14Sample9 220524ko14Sample9_percolator_target_psms.tsv 220524ko14Sample9_percolator_decoy_psms.tsv interact-220524ko14Sample9 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9\220524ko14Sample9_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9\220524ko14Sample9_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko11Sample7.pin 220524ko11Sample7 220524ko11Sample7_percolator_target_psms.tsv 220524ko11Sample7_percolator_decoy_psms.tsv interact-220524ko11Sample7 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7\220524ko11Sample7_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7\220524ko11Sample7_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko12Sample8.pin 220524ko12Sample8 220524ko12Sample8_percolator_target_psms.tsv 220524ko12Sample8_percolator_decoy_psms.tsv interact-220524ko12Sample8 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8\220524ko12Sample8_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8\220524ko12Sample8_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko17Sample11.pin 220524ko17Sample11 220524ko17Sample11_percolator_target_psms.tsv 220524ko17Sample11_percolator_decoy_psms.tsv interact-220524ko17Sample11 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11\220524ko17Sample11_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11\220524ko17Sample11_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko18Sample12.pin 220524ko18Sample12 220524ko18Sample12_percolator_target_psms.tsv 220524ko18Sample12_percolator_decoy_psms.tsv interact-220524ko18Sample12 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12\220524ko18Sample12_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12\220524ko18Sample12_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko15Sample10.pin 220524ko15Sample10 220524ko15Sample10_percolator_target_psms.tsv 220524ko15Sample10_percolator_decoy_psms.tsv interact-220524ko15Sample10 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10\220524ko15Sample10_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10\220524ko15Sample10_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko06Sample4.pin 220524ko06Sample4 220524ko06Sample4_percolator_target_psms.tsv 220524ko06Sample4_percolator_decoy_psms.tsv interact-220524ko06Sample4 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4\220524ko06Sample4_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4\220524ko06Sample4_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko02Sample1.pin 220524ko02Sample1 220524ko02Sample1_percolator_target_psms.tsv 220524ko02Sample1_percolator_decoy_psms.tsv interact-220524ko02Sample1 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1\220524ko02Sample1_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1\220524ko02Sample1_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko03Sample2.pin 220524ko03Sample2 220524ko03Sample2_percolator_target_psms.tsv 220524ko03Sample2_percolator_decoy_psms.tsv interact-220524ko03Sample2 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2\220524ko03Sample2_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2\220524ko03Sample2_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 220524ko05Sample3.pin 220524ko05Sample3 220524ko05Sample3_percolator_target_psms.tsv 220524ko05Sample3_percolator_decoy_psms.tsv interact-220524ko05Sample3 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3\220524ko05Sample3_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3\220524ko05Sample3_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
ProteinProphet [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\filelist_proteinprophet.txt
INFO[16:07:25] Executing ProteinProphet  v5.0.0             
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64))
 (no FPKM) (no groups) (using degen pep info)
Reading in J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1\interact-220524ko02Sample1.pep.xml...
...read in 0 1+, 11722 2+, 10129 3+, 1554 4+, 140 5+, 13 6+, 4 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2\interact-220524ko03Sample2.pep.xml...
...read in 0 1+, 11932 2+, 10832 3+, 1698 4+, 166 5+, 21 6+, 4 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3\interact-220524ko05Sample3.pep.xml...
...read in 0 1+, 12543 2+, 11456 3+, 1787 4+, 181 5+, 19 6+, 4 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4\interact-220524ko06Sample4.pep.xml...
...read in 0 1+, 11722 2+, 10966 3+, 1792 4+, 194 5+, 20 6+, 4 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5\interact-220524ko08Sample5.pep.xml...
...read in 0 1+, 12122 2+, 10755 3+, 1628 4+, 176 5+, 16 6+, 4 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6\interact-220524ko09Sample6.pep.xml...
...read in 0 1+, 12499 2+, 11303 3+, 1747 4+, 173 5+, 24 6+, 7 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7\interact-220524ko11Sample7.pep.xml...
...read in 0 1+, 12359 2+, 11231 3+, 1734 4+, 171 5+, 21 6+, 6 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8\interact-220524ko12Sample8.pep.xml...
...read in 0 1+, 11923 2+, 10379 3+, 1485 4+, 123 5+, 14 6+, 3 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9\interact-220524ko14Sample9.pep.xml...
...read in 0 1+, 11951 2+, 10680 3+, 1590 4+, 151 5+, 19 6+, 4 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10\interact-220524ko15Sample10.pep.xml...
...read in 0 1+, 11962 2+, 10984 3+, 1624 4+, 158 5+, 24 6+, 5 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11\interact-220524ko17Sample11.pep.xml...
...read in 0 1+, 11763 2+, 10040 3+, 1422 4+, 126 5+, 19 6+, 3 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12\interact-220524ko18Sample12.pep.xml...
...read in 0 1+, 11685 2+, 9826 3+, 1376 4+, 131 5+, 18 6+, 2 7+ spectra with min prob 0.05

Initializing 35579 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
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry rev_sp|P70274|SEPP1_MOUSE : UUUUUUUUUU
NSHUKUKRTQNDUSUNPNAEMPNMPQNQUAAPPSRCQCSETVKEEAFLGQUSCLSPLNEACQUAIASGSKEFILHRCHCCCSSPAAESEKSLKCLLQNICGRRULKRQALSLHLGESATTDUSELHGQRHQGRHRHHHHLGSPPLTTESPGPQQNESPKSSGLHEQGHKNHHKHHSHAESPEATKNATASTVTKCFDEDELSTLNCNGCREECYAIKIAEEVYPFTLFSYPLGLHYVLRGCRDYILFDDKNGNLLTWVDIGDEEQRYVAIHESVQKKLHSHKLQSPSGQHNVVIYSINFYGQSELKIRLDELRSAQLLCLYUSAQLLAVVTVKGESNLMPNQDGIYWEPAKYCASSQGQSEAGGYPLLCLALALGLSRWM
..:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
......WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9Z1Y9|IOD2_MOUSE : UU
DLIURKSFNKELWSRVEQLNYSFPGKGGLYAIKRRQVICVREFAVGYAVNANNDMRDAVVQCQPPLSFRELLQHAAACRDEQNRHKKVEFSLSSDGPVAWGDSPHAEDIYVLLFDAVSSFEEVLQRFAPLQRTFPPUTASGFNVVLPREASAFDLLHCEAGDATKESAYNNGSEPNSVHVVSSNPADEGLKVQKYADLLFSNWVCRLGESTLMRRWEGRTSKSRSLLLAVHKLLIVSDYLALFLCNSFFVPLIQLTILLDVSLLGM
...:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|P11352|GPX1_MOUSE : U
MCAARLSAAAQSTVYAFSARPLTGGEPVSLGSLRGKVLLIENVASLUGTTIRDYTEMNDLQKRLGPRGLVVLGFPCNQFGHQENGKNEEILNSLKYVRPGGGFEPNFTLFEKCEVNGEKAHPLFTFLRNALPTPSDDPTALMTDPKYIIWSPVCRNDIAWNFEKFLVGPDGVPVRRYSRRFRTIDIEPDIETLLSQQSGNS
.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........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|Q9DBC0|SELO_MOUSE : U
MASVRAAVGASLAVARTRPRCVGLALPSSAPRSAWAAAMEPTPRWLAGLRFDNRALRELPVETPPPGPEDSLATPRPVPGACFSRARPAPLRRPRLVALSEPALALLGLEASEEAEVEAEAALFFSGNALLPGTEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTAAGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGIPTTRAGACVTSESTVMRDVFYDGNPKYEKCTVVLRIAPTFIRFGSFEIFKPPDEHTGRAGPSVGRDDIRVQLLDYVISSFYPEIQAAHTCDTDNIQRNAAFFREVTQRTARMVAEWQCVGFCHGVLNTDNMSIVGLTIDYGPFGFLDRYDPDHICNASDNAGRYTYSKQPQVCKWNLQKLAEALEPELPLALAEAILKEEFDTEFQRHYLQKMRKKLGLIRVEKEEDGTLVAKLLETMHLTGADFTNTFCVLSSFPADLSDSAEFLSRLTSQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALIGTQANVTKELERVEHQSRLEQLSPSDLQRKNRDHWEAWLQEYRDRLDKEKEGVGDTAAWQAERVRVMRANNPKYVLRNYIAQKAIEAAENGDFSEVRRVLKLLESPYHSEEEATGPEAVARSTEEQSSYSNRPPLWAAELCVTUSS
.........:.........:.........:.........:.........:.........33000
.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q9JMH6|TRXR1_MOUSE : U
MPVDDCWLYFPASRGRTFVQTVWVAPTCPNCCWFPGFLPPVPRPPHVPRVLLRGPRGAVLPASRPSKTLPSSSQTPCPTDPCICPPPSTPDSRQEKNTQSELPNKKGQLQKLPTMNGSKDPPGSYDFDLIIIGGGSGGLAAAKEAAKFDKKVLVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALKDSRNYGWKVEDTVKHDWEKMTESVQSHIGSLNWGYRVALREKKVVYENAYGRFIGPHRIVATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPTKIEQIEAGTPGRLRVTAQSTNSEETIEGEFNTVLLAVGRDSCTRTIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSNVKCDYDNVPTTVFTPLEYGCCGLSEEKAVEKFGEENIEVYHSFFWPLEWTVPSRDNNKCYAKIICNLKDDERVVGFHVLGPNAGEVTQGFAAALKCGLTKQQLDSTIGIHPVCAEIFTTLSVTKRSGGDILQSGCUG
.....:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:........  Total: 34386
Computing degenerate peptides for 6148 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 6321 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 6321 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 6321 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 6321 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 6321 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=3.94281e-05, db_size=38845583
Computing MU for 6321 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO[16:07:42] Done                                         
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
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[16:07:42] Executing Database  v5.0.0                   
INFO[16:07:42] Annotating the database                      
INFO[16:07:42] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --razor
INFO[16:07:43] Executing Filter  v5.0.0                     
INFO[16:07:43] Processing peptide identification files      
INFO[16:07:43] Parsing J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1\interact-220524ko02Sample1.pep.xml 
INFO[16:07:44] 1+ Charge profile                             decoy=0 target=0
INFO[16:07:44] 2+ Charge profile                             decoy=250 target=11472
INFO[16:07:44] 3+ Charge profile                             decoy=129 target=10000
INFO[16:07:44] 4+ Charge profile                             decoy=25 target=1529
INFO[16:07:44] 5+ Charge profile                             decoy=2 target=138
INFO[16:07:44] 6+ Charge profile                             decoy=0 target=13
INFO[16:07:44] Database search results                       ions=19454 peptides=16341 psms=23562
INFO[16:07:44] Converged to 1.00 % FDR with 22689 PSMs       decoy=226 threshold=0.693476 total=22915
INFO[16:07:44] Converged to 2.38 % FDR with 15961 Peptides   decoy=380 threshold=0.500027 total=16341
INFO[16:07:44] Converged to 2.02 % FDR with 19068 Ions       decoy=386 threshold=0.500027 total=19454
INFO[16:07:44] Protein inference results                     decoy=1967 target=3907
INFO[16:07:44] Converged to 52.89 % FDR with 3655 Proteins   decoy=1933 threshold=0.4996 total=5588
INFO[16:07:44] Applying sequential FDR estimation            ions=18934 peptides=15850 psms=22915
INFO[16:07:44] Converged to 1.00 % FDR with 22689 PSMs       decoy=226 threshold=0.693476 total=22915
INFO[16:07:44] Converged to 1.36 % FDR with 15637 Peptides   decoy=213 threshold=0.693476 total=15850
INFO[16:07:44] Converged to 1.15 % FDR with 18718 Ions       decoy=216 threshold=0.693476 total=18934
INFO[16:07:44] Post processing identifications              
INFO[16:07:45] Assigning protein identifications to layers  
INFO[16:07:48] Processing protein inference                 
INFO[16:07:48] Synchronizing PSMs and proteins              
INFO[16:07:48] Final report numbers after FDR filtering, and post-processing  ions=18717 peptides=15636 proteins=1887 psms=22688
INFO[16:07:48] Saving                                       
INFO[16:07:49] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
INFO[16:07:49] Executing Filter  v5.0.0                     
INFO[16:07:49] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 
INFO[16:07:49] Processing peptide identification files      
INFO[16:07:49] Parsing J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2\interact-220524ko03Sample2.pep.xml 
INFO[16:07:50] 1+ Charge profile                             decoy=0 target=0
INFO[16:07:50] 2+ Charge profile                             decoy=288 target=11644
INFO[16:07:50] 3+ Charge profile                             decoy=146 target=10686
INFO[16:07:50] 4+ Charge profile                             decoy=16 target=1682
INFO[16:07:50] 5+ Charge profile                             decoy=7 target=159
INFO[16:07:50] 6+ Charge profile                             decoy=1 target=20
INFO[16:07:50] Database search results                       ions=20103 peptides=16591 psms=24653
INFO[16:07:50] Converged to 1.00 % FDR with 23595 PSMs       decoy=235 threshold=0.702996 total=23830
INFO[16:07:50] Converged to 2.66 % FDR with 16161 Peptides   decoy=430 threshold=0.500246 total=16591
INFO[16:07:50] Converged to 2.21 % FDR with 19668 Ions       decoy=435 threshold=0.500246 total=20103
INFO[16:07:50] Protein inference results                     decoy=1967 target=3907
INFO[16:07:50] Converged to 52.89 % FDR with 3655 Proteins   decoy=1933 threshold=0.4996 total=5588
INFO[16:07:50] Applying sequential FDR estimation            ions=19449 peptides=15981 psms=23829
INFO[16:07:50] Converged to 1.00 % FDR with 23594 PSMs       decoy=235 threshold=0.702996 total=23829
INFO[16:07:50] Converged to 1.41 % FDR with 15759 Peptides   decoy=222 threshold=0.702996 total=15981
INFO[16:07:50] Converged to 1.17 % FDR with 19225 Ions       decoy=224 threshold=0.702996 total=19449
INFO[16:07:50] Post processing identifications              
INFO[16:07:51] Assigning protein identifications to layers  
INFO[16:07:54] Processing protein inference                 
INFO[16:07:54] Synchronizing PSMs and proteins              
INFO[16:07:55] Final report numbers after FDR filtering, and post-processing  ions=19223 peptides=15757 proteins=1903 psms=23592
INFO[16:07:55] Saving                                       
INFO[16:07:55] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
INFO[16:07:55] Executing Filter  v5.0.0                     
INFO[16:07:55] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 
INFO[16:07:55] Processing peptide identification files      
INFO[16:07:55] Parsing J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3\interact-220524ko05Sample3.pep.xml 
INFO[16:07:56] 1+ Charge profile                             decoy=0 target=0
INFO[16:07:56] 2+ Charge profile                             decoy=271 target=12272
INFO[16:07:56] 3+ Charge profile                             decoy=147 target=11309
INFO[16:07:56] 4+ Charge profile                             decoy=22 target=1765
INFO[16:07:56] 5+ Charge profile                             decoy=3 target=178
INFO[16:07:56] 6+ Charge profile                             decoy=0 target=19
INFO[16:07:56] Database search results                       ions=21207 peptides=17453 psms=25990
INFO[16:07:56] Converged to 1.00 % FDR with 25045 PSMs       decoy=250 threshold=0.710122 total=25295
INFO[16:07:56] Converged to 2.47 % FDR with 17032 Peptides   decoy=421 threshold=0.500242 total=17453
INFO[16:07:56] Converged to 2.05 % FDR with 20780 Ions       decoy=427 threshold=0.500208 total=21207
INFO[16:07:56] Protein inference results                     decoy=1967 target=3907
INFO[16:07:57] Converged to 52.89 % FDR with 3655 Proteins   decoy=1933 threshold=0.4996 total=5588
INFO[16:07:57] Applying sequential FDR estimation            ions=20626 peptides=16905 psms=25294
INFO[16:07:57] Converged to 1.00 % FDR with 25044 PSMs       decoy=250 threshold=0.710122 total=25294
INFO[16:07:57] Converged to 1.40 % FDR with 16671 Peptides   decoy=234 threshold=0.710122 total=16905
INFO[16:07:57] Converged to 1.17 % FDR with 20388 Ions       decoy=238 threshold=0.710122 total=20626
INFO[16:07:57] Post processing identifications              
INFO[16:07:57] Assigning protein identifications to layers  
INFO[16:08:01] Processing protein inference                 
INFO[16:08:01] Synchronizing PSMs and proteins              
INFO[16:08:01] Final report numbers after FDR filtering, and post-processing  ions=20386 peptides=16669 proteins=1976 psms=25042
INFO[16:08:01] Saving                                       
INFO[16:08:01] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
INFO[16:08:02] Executing Filter  v5.0.0                     
INFO[16:08:02] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 
INFO[16:08:02] Processing peptide identification files      
INFO[16:08:02] Parsing J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4\interact-220524ko06Sample4.pep.xml 
INFO[16:08:03] 1+ Charge profile                             decoy=0 target=0
INFO[16:08:03] 2+ Charge profile                             decoy=258 target=11464
INFO[16:08:03] 3+ Charge profile                             decoy=132 target=10834
INFO[16:08:03] 4+ Charge profile                             decoy=22 target=1770
INFO[16:08:03] 5+ Charge profile                             decoy=5 target=189
INFO[16:08:03] 6+ Charge profile                             decoy=0 target=20
INFO[16:08:03] Database search results                       ions=20183 peptides=16969 psms=24698
INFO[16:08:03] Converged to 1.00 % FDR with 23756 PSMs       decoy=237 threshold=0.697929 total=23993
INFO[16:08:03] Converged to 2.41 % FDR with 16570 Peptides   decoy=399 threshold=0.500504 total=16969
INFO[16:08:03] Converged to 2.03 % FDR with 19782 Ions       decoy=401 threshold=0.500504 total=20183
INFO[16:08:03] Protein inference results                     decoy=1967 target=3907
INFO[16:08:03] Converged to 52.89 % FDR with 3655 Proteins   decoy=1933 threshold=0.4996 total=5588
INFO[16:08:03] Applying sequential FDR estimation            ions=19627 peptides=16433 psms=23993
INFO[16:08:03] Converged to 1.00 % FDR with 23756 PSMs       decoy=237 threshold=0.697929 total=23993
INFO[16:08:03] Converged to 1.38 % FDR with 16209 Peptides   decoy=224 threshold=0.697929 total=16433
INFO[16:08:03] Converged to 1.16 % FDR with 19401 Ions       decoy=226 threshold=0.697929 total=19627
INFO[16:08:03] Post processing identifications              
INFO[16:08:04] Assigning protein identifications to layers  
INFO[16:08:07] Processing protein inference                 
INFO[16:08:07] Synchronizing PSMs and proteins              
INFO[16:08:08] Final report numbers after FDR filtering, and post-processing  ions=19398 peptides=16206 proteins=1962 psms=23753
INFO[16:08:08] Saving                                       
INFO[16:08:08] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
INFO[16:08:08] Executing Filter  v5.0.0                     
INFO[16:08:08] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 
INFO[16:08:08] Processing peptide identification files      
INFO[16:08:08] Parsing J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5\interact-220524ko08Sample5.pep.xml 
INFO[16:08:09] 1+ Charge profile                             decoy=0 target=0
INFO[16:08:09] 2+ Charge profile                             decoy=279 target=11843
INFO[16:08:09] 3+ Charge profile                             decoy=138 target=10617
INFO[16:08:09] 4+ Charge profile                             decoy=16 target=1612
INFO[16:08:09] 5+ Charge profile                             decoy=4 target=172
INFO[16:08:09] 6+ Charge profile                             decoy=0 target=16
INFO[16:08:09] Database search results                       ions=20304 peptides=16880 psms=24701
INFO[16:08:09] Converged to 1.00 % FDR with 23771 PSMs       decoy=237 threshold=0.683685 total=24008
INFO[16:08:09] Converged to 2.50 % FDR with 16469 Peptides   decoy=411 threshold=0.500732 total=16880
INFO[16:08:09] Converged to 2.09 % FDR with 19889 Ions       decoy=415 threshold=0.500732 total=20304
INFO[16:08:09] Protein inference results                     decoy=1967 target=3907
INFO[16:08:09] Converged to 52.89 % FDR with 3655 Proteins   decoy=1933 threshold=0.4996 total=5588
INFO[16:08:10] Applying sequential FDR estimation            ions=19751 peptides=16353 psms=24007
INFO[16:08:10] Converged to 1.00 % FDR with 23770 PSMs       decoy=237 threshold=0.683685 total=24007
INFO[16:08:10] Converged to 1.37 % FDR with 16132 Peptides   decoy=221 threshold=0.683685 total=16353
INFO[16:08:10] Converged to 1.15 % FDR with 19527 Ions       decoy=224 threshold=0.683685 total=19751
INFO[16:08:10] Post processing identifications              
INFO[16:08:10] Assigning protein identifications to layers  
INFO[16:08:14] Processing protein inference                 
INFO[16:08:14] Synchronizing PSMs and proteins              
INFO[16:08:14] Final report numbers after FDR filtering, and post-processing  ions=19527 peptides=16132 proteins=1900 psms=23770
INFO[16:08:14] Saving                                       
INFO[16:08:14] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
INFO[16:08:14] Executing Filter  v5.0.0                     
INFO[16:08:14] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 
INFO[16:08:14] Processing peptide identification files      
INFO[16:08:14] Parsing J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6\interact-220524ko09Sample6.pep.xml 
INFO[16:08:16] 1+ Charge profile                             decoy=0 target=0
INFO[16:08:16] 2+ Charge profile                             decoy=290 target=12209
INFO[16:08:16] 3+ Charge profile                             decoy=163 target=11140
INFO[16:08:16] 4+ Charge profile                             decoy=17 target=1730
INFO[16:08:16] 5+ Charge profile                             decoy=4 target=169
INFO[16:08:16] 6+ Charge profile                             decoy=1 target=23
INFO[16:08:16] Database search results                       ions=21051 peptides=17553 psms=25753
INFO[16:08:16] Converged to 1.00 % FDR with 24713 PSMs       decoy=247 threshold=0.703445 total=24960
INFO[16:08:16] Converged to 2.66 % FDR with 17099 Peptides   decoy=454 threshold=0.500411 total=17553
INFO[16:08:16] Converged to 2.22 % FDR with 20593 Ions       decoy=458 threshold=0.500411 total=21051
INFO[16:08:16] Protein inference results                     decoy=1967 target=3907
INFO[16:08:16] Converged to 52.89 % FDR with 3655 Proteins   decoy=1933 threshold=0.4996 total=5588
INFO[16:08:16] Applying sequential FDR estimation            ions=20407 peptides=16938 psms=24959
INFO[16:08:16] Converged to 1.00 % FDR with 24712 PSMs       decoy=247 threshold=0.703445 total=24959
INFO[16:08:16] Converged to 1.39 % FDR with 16706 Peptides   decoy=232 threshold=0.703445 total=16938
INFO[16:08:16] Converged to 1.17 % FDR with 20171 Ions       decoy=236 threshold=0.703445 total=20407
INFO[16:08:16] Post processing identifications              
INFO[16:08:17] Assigning protein identifications to layers  
INFO[16:08:20] Processing protein inference                 
INFO[16:08:20] Synchronizing PSMs and proteins              
INFO[16:08:21] Final report numbers after FDR filtering, and post-processing  ions=20169 peptides=16704 proteins=1913 psms=24710
INFO[16:08:21] Saving                                       
INFO[16:08:21] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
INFO[16:08:21] Executing Filter  v5.0.0                     
INFO[16:08:21] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 
INFO[16:08:21] Processing peptide identification files      
INFO[16:08:21] Parsing J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7\interact-220524ko11Sample7.pep.xml 
INFO[16:08:22] 1+ Charge profile                             decoy=0 target=0
INFO[16:08:22] 2+ Charge profile                             decoy=273 target=12086
INFO[16:08:22] 3+ Charge profile                             decoy=131 target=11100
INFO[16:08:22] 4+ Charge profile                             decoy=16 target=1718
INFO[16:08:22] 5+ Charge profile                             decoy=4 target=167
INFO[16:08:22] 6+ Charge profile                             decoy=1 target=20
INFO[16:08:22] Database search results                       ions=21068 peptides=17726 psms=25522
INFO[16:08:22] Converged to 1.00 % FDR with 24671 PSMs       decoy=246 threshold=0.650804 total=24917
INFO[16:08:22] Converged to 2.32 % FDR with 17324 Peptides   decoy=402 threshold=0.500215 total=17726
INFO[16:08:22] Converged to 1.98 % FDR with 20658 Ions       decoy=410 threshold=0.500215 total=21068
INFO[16:08:22] Protein inference results                     decoy=1967 target=3907
INFO[16:08:23] Converged to 52.89 % FDR with 3655 Proteins   decoy=1933 threshold=0.4996 total=5588
INFO[16:08:23] Applying sequential FDR estimation            ions=20568 peptides=17259 psms=24917
INFO[16:08:23] Converged to 1.00 % FDR with 24671 PSMs       decoy=246 threshold=0.650804 total=24917
INFO[16:08:23] Converged to 1.35 % FDR with 17029 Peptides   decoy=230 threshold=0.651278 total=17259
INFO[16:08:23] Converged to 1.15 % FDR with 20334 Ions       decoy=234 threshold=0.651278 total=20568
INFO[16:08:23] Post processing identifications              
INFO[16:08:23] Assigning protein identifications to layers  
INFO[16:08:27] Processing protein inference                 
INFO[16:08:27] Synchronizing PSMs and proteins              
INFO[16:08:27] Final report numbers after FDR filtering, and post-processing  ions=20332 peptides=17027 proteins=1970 psms=24669
INFO[16:08:27] Saving                                       
INFO[16:08:27] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
INFO[16:08:28] Executing Filter  v5.0.0                     
INFO[16:08:28] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 
INFO[16:08:28] Processing peptide identification files      
INFO[16:08:28] Parsing J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8\interact-220524ko12Sample8.pep.xml 
INFO[16:08:29] 1+ Charge profile                             decoy=0 target=0
INFO[16:08:29] 2+ Charge profile                             decoy=276 target=11647
INFO[16:08:29] 3+ Charge profile                             decoy=139 target=10240
INFO[16:08:29] 4+ Charge profile                             decoy=15 target=1470
INFO[16:08:29] 5+ Charge profile                             decoy=3 target=120
INFO[16:08:29] 6+ Charge profile                             decoy=3 target=11
INFO[16:08:29] Database search results                       ions=19657 peptides=16334 psms=23927
INFO[16:08:29] Converged to 1.00 % FDR with 22972 PSMs       decoy=229 threshold=0.715524 total=23201
INFO[16:08:29] Converged to 2.61 % FDR with 15919 Peptides   decoy=415 threshold=0.500304 total=16334
INFO[16:08:29] Converged to 2.18 % FDR with 19238 Ions       decoy=419 threshold=0.500304 total=19657
INFO[16:08:29] Protein inference results                     decoy=1967 target=3907
INFO[16:08:29] Converged to 52.89 % FDR with 3655 Proteins   decoy=1933 threshold=0.4996 total=5588
INFO[16:08:29] Applying sequential FDR estimation            ions=19071 peptides=15780 psms=23201
INFO[16:08:29] Converged to 1.00 % FDR with 22972 PSMs       decoy=229 threshold=0.715524 total=23201
INFO[16:08:29] Converged to 1.41 % FDR with 15561 Peptides   decoy=219 threshold=0.715573 total=15780
INFO[16:08:29] Converged to 1.17 % FDR with 18850 Ions       decoy=221 threshold=0.715573 total=19071
INFO[16:08:29] Post processing identifications              
INFO[16:08:30] Assigning protein identifications to layers  
INFO[16:08:33] Processing protein inference                 
INFO[16:08:33] Synchronizing PSMs and proteins              
INFO[16:08:33] Final report numbers after FDR filtering, and post-processing  ions=18847 peptides=15558 proteins=1922 psms=22969
INFO[16:08:33] Saving                                       
INFO[16:08:34] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
INFO[16:08:34] Executing Filter  v5.0.0                     
INFO[16:08:34] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 
INFO[16:08:34] Processing peptide identification files      
INFO[16:08:34] Parsing J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9\interact-220524ko14Sample9.pep.xml 
INFO[16:08:35] 1+ Charge profile                             decoy=0 target=0
INFO[16:08:35] 2+ Charge profile                             decoy=276 target=11675
INFO[16:08:35] 3+ Charge profile                             decoy=137 target=10543
INFO[16:08:35] 4+ Charge profile                             decoy=20 target=1570
INFO[16:08:35] 5+ Charge profile                             decoy=3 target=148
INFO[16:08:35] 6+ Charge profile                             decoy=2 target=17
INFO[16:08:35] Database search results                       ions=20141 peptides=16807 psms=24395
INFO[16:08:35] Converged to 1.00 % FDR with 23436 PSMs       decoy=234 threshold=0.690561 total=23670
INFO[16:08:35] Converged to 2.56 % FDR with 16387 Peptides   decoy=420 threshold=0.500056 total=16807
INFO[16:08:35] Converged to 2.14 % FDR with 19719 Ions       decoy=422 threshold=0.500056 total=20141
INFO[16:08:35] Protein inference results                     decoy=1967 target=3907
INFO[16:08:35] Converged to 52.89 % FDR with 3655 Proteins   decoy=1933 threshold=0.4996 total=5588
INFO[16:08:35] Applying sequential FDR estimation            ions=19550 peptides=16244 psms=23670
INFO[16:08:35] Converged to 1.00 % FDR with 23436 PSMs       decoy=234 threshold=0.690561 total=23670
INFO[16:08:35] Converged to 1.39 % FDR with 16022 Peptides   decoy=222 threshold=0.692043 total=16244
INFO[16:08:35] Converged to 1.16 % FDR with 19326 Ions       decoy=224 threshold=0.691506 total=19550
INFO[16:08:35] Post processing identifications              
INFO[16:08:36] Assigning protein identifications to layers  
INFO[16:08:39] Processing protein inference                 
INFO[16:08:39] Synchronizing PSMs and proteins              
INFO[16:08:39] Final report numbers after FDR filtering, and post-processing  ions=19325 peptides=16021 proteins=1889 psms=23435
INFO[16:08:39] Saving                                       
INFO[16:08:39] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
INFO[16:08:40] Executing Filter  v5.0.0                     
INFO[16:08:40] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 
INFO[16:08:40] Processing peptide identification files      
INFO[16:08:40] Parsing J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10\interact-220524ko15Sample10.pep.xml 
INFO[16:08:41] 1+ Charge profile                             decoy=0 target=0
INFO[16:08:41] 2+ Charge profile                             decoy=282 target=11680
INFO[16:08:41] 3+ Charge profile                             decoy=160 target=10824
INFO[16:08:41] 4+ Charge profile                             decoy=12 target=1612
INFO[16:08:41] 5+ Charge profile                             decoy=4 target=154
INFO[16:08:41] 6+ Charge profile                             decoy=0 target=24
INFO[16:08:41] Database search results                       ions=20331 peptides=16914 psms=24757
INFO[16:08:41] Converged to 1.00 % FDR with 23779 PSMs       decoy=237 threshold=0.711323 total=24016
INFO[16:08:41] Converged to 2.62 % FDR with 16482 Peptides   decoy=432 threshold=0.500478 total=16914
INFO[16:08:41] Converged to 2.20 % FDR with 19893 Ions       decoy=438 threshold=0.500478 total=20331
INFO[16:08:41] Protein inference results                     decoy=1967 target=3907
INFO[16:08:41] Converged to 52.89 % FDR with 3655 Proteins   decoy=1933 threshold=0.4996 total=5588
INFO[16:08:41] Applying sequential FDR estimation            ions=19722 peptides=16348 psms=24015
INFO[16:08:41] Converged to 1.00 % FDR with 23778 PSMs       decoy=237 threshold=0.711323 total=24015
INFO[16:08:41] Converged to 1.38 % FDR with 16125 Peptides   decoy=223 threshold=0.711323 total=16348
INFO[16:08:41] Converged to 1.15 % FDR with 19497 Ions       decoy=225 threshold=0.711323 total=19722
INFO[16:08:41] Post processing identifications              
INFO[16:08:42] Assigning protein identifications to layers  
INFO[16:08:45] Processing protein inference                 
INFO[16:08:45] Synchronizing PSMs and proteins              
INFO[16:08:45] Final report numbers after FDR filtering, and post-processing  ions=19494 peptides=16122 proteins=1911 psms=23775
INFO[16:08:45] Saving                                       
INFO[16:08:46] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
INFO[16:08:46] Executing Filter  v5.0.0                     
INFO[16:08:46] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 
INFO[16:08:46] Processing peptide identification files      
INFO[16:08:46] Parsing J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11\interact-220524ko17Sample11.pep.xml 
INFO[16:08:47] 1+ Charge profile                             decoy=0 target=0
INFO[16:08:47] 2+ Charge profile                             decoy=277 target=11486
INFO[16:08:47] 3+ Charge profile                             decoy=129 target=9911
INFO[16:08:47] 4+ Charge profile                             decoy=27 target=1395
INFO[16:08:47] 5+ Charge profile                             decoy=4 target=122
INFO[16:08:47] 6+ Charge profile                             decoy=1 target=18
INFO[16:08:47] Database search results                       ions=19523 peptides=16281 psms=23373
INFO[16:08:47] Converged to 1.00 % FDR with 22384 PSMs       decoy=223 threshold=0.756667 total=22607
INFO[16:08:47] Converged to 2.64 % FDR with 15863 Peptides   decoy=418 threshold=0.50126 total=16281
INFO[16:08:47] Converged to 2.21 % FDR with 19101 Ions       decoy=422 threshold=0.50126 total=19523
INFO[16:08:47] Protein inference results                     decoy=1967 target=3907
INFO[16:08:47] Converged to 52.89 % FDR with 3655 Proteins   decoy=1933 threshold=0.4996 total=5588
INFO[16:08:47] Applying sequential FDR estimation            ions=18877 peptides=15674 psms=22605
INFO[16:08:47] Converged to 1.00 % FDR with 22382 PSMs       decoy=223 threshold=0.756667 total=22605
INFO[16:08:47] Converged to 1.36 % FDR with 15463 Peptides   decoy=211 threshold=0.756667 total=15674
INFO[16:08:47] Converged to 1.14 % FDR with 18664 Ions       decoy=213 threshold=0.756667 total=18877
INFO[16:08:47] Post processing identifications              
INFO[16:08:48] Assigning protein identifications to layers  
INFO[16:08:51] Processing protein inference                 
INFO[16:08:51] Synchronizing PSMs and proteins              
INFO[16:08:52] Final report numbers after FDR filtering, and post-processing  ions=18664 peptides=15463 proteins=1841 psms=22382
INFO[16:08:52] Saving                                       
INFO[16:08:52] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12 --protxml J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 --razor
INFO[16:08:52] Executing Filter  v5.0.0                     
INFO[16:08:52] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1 
INFO[16:08:52] Processing peptide identification files      
INFO[16:08:52] Parsing J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12\interact-220524ko18Sample12.pep.xml 
INFO[16:08:53] 1+ Charge profile                             decoy=0 target=0
INFO[16:08:53] 2+ Charge profile                             decoy=264 target=11421
INFO[16:08:53] 3+ Charge profile                             decoy=131 target=9695
INFO[16:08:53] 4+ Charge profile                             decoy=15 target=1361
INFO[16:08:53] 5+ Charge profile                             decoy=3 target=128
INFO[16:08:53] 6+ Charge profile                             decoy=1 target=17
INFO[16:08:53] Database search results                       ions=19251 peptides=16090 psms=23038
INFO[16:08:53] Converged to 1.00 % FDR with 22066 PSMs       decoy=220 threshold=0.747567 total=22286
INFO[16:08:53] Converged to 2.50 % FDR with 15697 Peptides   decoy=393 threshold=0.500061 total=16090
INFO[16:08:53] Converged to 2.12 % FDR with 18851 Ions       decoy=400 threshold=0.500061 total=19251
INFO[16:08:53] Protein inference results                     decoy=1967 target=3907
INFO[16:08:53] Converged to 52.89 % FDR with 3655 Proteins   decoy=1933 threshold=0.4996 total=5588
INFO[16:08:53] Applying sequential FDR estimation            ions=18628 peptides=15502 psms=22286
INFO[16:08:53] Converged to 1.00 % FDR with 22066 PSMs       decoy=220 threshold=0.747567 total=22286
INFO[16:08:53] Converged to 1.36 % FDR with 15294 Peptides   decoy=208 threshold=0.747567 total=15502
INFO[16:08:53] Converged to 1.15 % FDR with 18417 Ions       decoy=211 threshold=0.747567 total=18628
INFO[16:08:53] Post processing identifications              
INFO[16:08:54] Assigning protein identifications to layers  
INFO[16:08:57] Processing protein inference                 
INFO[16:08:57] Synchronizing PSMs and proteins              
INFO[16:08:57] Final report numbers after FDR filtering, and post-processing  ions=18417 peptides=15294 proteins=1886 psms=22066
INFO[16:08:57] Saving                                       
INFO[16:08:57] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:08:58] Executing Report  v5.0.0                     
INFO[16:08:58] Creating reports                             
INFO[16:08:58] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:08:58] Executing Report  v5.0.0                     
INFO[16:08:58] Creating reports                             
INFO[16:08:58] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:08:58] Executing Report  v5.0.0                     
INFO[16:08:58] Creating reports                             
INFO[16:08:59] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:08:59] Executing Report  v5.0.0                     
INFO[16:08:59] Creating reports                             
INFO[16:08:59] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:08:59] Executing Report  v5.0.0                     
INFO[16:08:59] Creating reports                             
INFO[16:08:59] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:09:00] Executing Report  v5.0.0                     
INFO[16:09:00] Creating reports                             
INFO[16:09:00] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:09:00] Executing Report  v5.0.0                     
INFO[16:09:00] Creating reports                             
INFO[16:09:00] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:09:00] Executing Report  v5.0.0                     
INFO[16:09:00] Creating reports                             
INFO[16:09:01] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:09:01] Executing Report  v5.0.0                     
INFO[16:09:01] Creating reports                             
INFO[16:09:01] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:09:01] Executing Report  v5.0.0                     
INFO[16:09:01] Creating reports                             
INFO[16:09:02] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:09:02] Executing Report  v5.0.0                     
INFO[16:09:02] Creating reports                             
INFO[16:09:02] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[16:09:02] Executing Report  v5.0.0                     
INFO[16:09:02] Creating reports                             
INFO[16:09:03] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:03] Executing Workspace  v5.0.0                  
INFO[16:09:03] Removing workspace                           
INFO[16:09:03] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:03] Executing Workspace  v5.0.0                  
INFO[16:09:03] Removing workspace                           
INFO[16:09:03] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:04] Executing Workspace  v5.0.0                  
INFO[16:09:04] Removing workspace                           
INFO[16:09:04] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:04] Executing Workspace  v5.0.0                  
INFO[16:09:04] Removing workspace                           
INFO[16:09:04] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:05] Executing Workspace  v5.0.0                  
INFO[16:09:05] Removing workspace                           
INFO[16:09:05] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:05] Executing Workspace  v5.0.0                  
INFO[16:09:05] Removing workspace                           
INFO[16:09:05] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:05] Executing Workspace  v5.0.0                  
INFO[16:09:05] Removing workspace                           
INFO[16:09:05] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:06] Executing Workspace  v5.0.0                  
INFO[16:09:06] Removing workspace                           
INFO[16:09:06] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:06] Executing Workspace  v5.0.0                  
INFO[16:09:06] Removing workspace                           
INFO[16:09:06] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:07] Executing Workspace  v5.0.0                  
INFO[16:09:07] Removing workspace                           
INFO[16:09:07] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:07] Executing Workspace  v5.0.0                  
INFO[16:09:07] Removing workspace                           
INFO[16:09:07] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:08] Executing Workspace  v5.0.0                  
INFO[16:09:08] Removing workspace                           
INFO[16:09:08] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[16:09:08] Executing Workspace  v5.0.0                  
INFO[16:09:08] Removing workspace                           
INFO[16:09:08] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
IonQuant [Work dir: J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ]
java -Xmx68G -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 0 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 100 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 0 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\filelist_ionquant.txt --modlist J:\MSFragger_process\Saitou-lab\Revision\220524ko\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 68 GB memory
2025-01-16 16:09:08 [INFO] - Collecting variable modifications from all psm.tsv files...
2025-01-16 16:09:09 [INFO] - Loading and indexing all psm.tsv files...
2025-01-16 16:09:09 [INFO] - Collecting all compensation voltages if applicable...
2025-01-16 16:10:07 [INFO] - There are in total 3 compensation voltages: -80, -60, -40
2025-01-16 16:10:10 [INFO] - Parameters:
2025-01-16 16:10:10 [INFO] - threads = 15
2025-01-16 16:10:10 [INFO] - mztol = 10.0
2025-01-16 16:10:10 [INFO] - rttol = 0.4
2025-01-16 16:10:10 [INFO] - imtol = 0.05
2025-01-16 16:10:10 [INFO] - minisotopes = 2
2025-01-16 16:10:10 [INFO] - minscans = 3
2025-01-16 16:10:10 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko02Sample1\psm.tsv
2025-01-16 16:10:10 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko03Sample2\psm.tsv
2025-01-16 16:10:10 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko05Sample3\psm.tsv
2025-01-16 16:10:10 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko06Sample4\psm.tsv
2025-01-16 16:10:10 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko08Sample5\psm.tsv
2025-01-16 16:10:10 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko09Sample6\psm.tsv
2025-01-16 16:10:10 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko11Sample7\psm.tsv
2025-01-16 16:10:10 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko12Sample8\psm.tsv
2025-01-16 16:10:10 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko14Sample9\psm.tsv
2025-01-16 16:10:10 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko15Sample10\psm.tsv
2025-01-16 16:10:10 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko17Sample11\psm.tsv
2025-01-16 16:10:10 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\220524ko18Sample12\psm.tsv
2025-01-16 16:10:10 [INFO] - multidir = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\.\
2025-01-16 16:10:10 [INFO] - excludemods = 
2025-01-16 16:10:10 [INFO] - minions = 2
2025-01-16 16:10:10 [INFO] - maxlfq = 1
2025-01-16 16:10:10 [INFO] - ibaq = 0
2025-01-16 16:10:10 [INFO] - normalization = 0
2025-01-16 16:10:10 [INFO] - minexps = 1
2025-01-16 16:10:10 [INFO] - minfreq = 0.0
2025-01-16 16:10:10 [INFO] - tp = 0
2025-01-16 16:10:10 [INFO] - mbr = 1
2025-01-16 16:10:10 [INFO] - mbrrttol = 1.0
2025-01-16 16:10:10 [INFO] - mbrimtol = 0.05
2025-01-16 16:10:10 [INFO] - mbrtoprun = 100
2025-01-16 16:10:10 [INFO] - mbrmincorr = 0.0
2025-01-16 16:10:10 [INFO] - ionmobility = 0
2025-01-16 16:10:10 [INFO] - ionfdr = 0.01
2025-01-16 16:10:10 [INFO] - peptidefdr = 1.0
2025-01-16 16:10:10 [INFO] - proteinfdr = 1.0
2025-01-16 16:10:10 [INFO] - light = 
2025-01-16 16:10:10 [INFO] - medium = 
2025-01-16 16:10:10 [INFO] - heavy = 
2025-01-16 16:10:10 [INFO] - requantify = 0
2025-01-16 16:10:10 [INFO] - writeindex = 0
2025-01-16 16:10:10 [INFO] - locprob = 0.75
2025-01-16 16:10:10 [INFO] - uniqueness = 0
2025-01-16 16:10:10 [INFO] - filelist = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\filelist_ionquant.txt
2025-01-16 16:10:10 [INFO] - specdir = J:\MSFragger_process\Saitou-lab\Revision\220524ko
2025-01-16 16:10:10 [INFO] - modlist = J:\MSFragger_process\Saitou-lab\Revision\220524ko\MSFragger_iBAQ\modmasses_ionquant.txt
2025-01-16 16:10:10 [INFO] - mod masses:
2025-01-16 16:10:10 [INFO] - 15.9949
2025-01-16 16:10:10 [INFO] - 42.0106
2025-01-16 16:10:10 [INFO] - 57.021465
2025-01-16 16:10:10 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.raw...
2025-01-16 16:10:15 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2.raw...
2025-01-16 16:10:20 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3.raw...
2025-01-16 16:10:25 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4.raw...
2025-01-16 16:10:30 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5.raw...
2025-01-16 16:10:35 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6.raw...
2025-01-16 16:10:40 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7.raw...
2025-01-16 16:10:45 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8.raw...
2025-01-16 16:10:49 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9.raw...
2025-01-16 16:10:54 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10.raw...
2025-01-16 16:10:59 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11.raw...
2025-01-16 16:11:03 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12.raw...
2025-01-16 16:11:08 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.raw...
2025-01-16 16:11:15 [INFO] - 220524ko02Sample1 has 3 compensation voltages: -80, -60, -40
2025-01-16 16:11:15 [INFO] - Building index...
2025-01-16 16:11:15 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.quantindex
2025-01-16 16:11:16 [INFO] - Loading 220524ko02Sample1....
2025-01-16 16:11:16 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 16:11:16 [INFO] - Quantifying...
2025-01-16 16:11:16 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2.raw...
2025-01-16 16:11:23 [INFO] - 220524ko03Sample2 has 3 compensation voltages: -80, -60, -40
2025-01-16 16:11:23 [INFO] - Building index...
2025-01-16 16:11:23 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2.quantindex
2025-01-16 16:11:23 [INFO] - Loading 220524ko03Sample2....
2025-01-16 16:11:24 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 16:11:24 [INFO] - Quantifying...
2025-01-16 16:11:24 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3.raw...
2025-01-16 16:11:31 [INFO] - 220524ko05Sample3 has 3 compensation voltages: -80, -60, -40
2025-01-16 16:11:31 [INFO] - Building index...
2025-01-16 16:11:31 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3.quantindex
2025-01-16 16:11:31 [INFO] - Loading 220524ko05Sample3....
2025-01-16 16:11:31 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 16:11:31 [INFO] - Quantifying...
2025-01-16 16:11:31 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4.raw...
2025-01-16 16:11:38 [INFO] - 220524ko06Sample4 has 3 compensation voltages: -80, -60, -40
2025-01-16 16:11:38 [INFO] - Building index...
2025-01-16 16:11:38 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4.quantindex
2025-01-16 16:11:38 [INFO] - Loading 220524ko06Sample4....
2025-01-16 16:11:38 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 16:11:38 [INFO] - Quantifying...
2025-01-16 16:11:39 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5.raw...
2025-01-16 16:11:45 [INFO] - 220524ko08Sample5 has 3 compensation voltages: -80, -60, -40
2025-01-16 16:11:45 [INFO] - Building index...
2025-01-16 16:11:46 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5.quantindex
2025-01-16 16:11:46 [INFO] - Loading 220524ko08Sample5....
2025-01-16 16:11:46 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 16:11:46 [INFO] - Quantifying...
2025-01-16 16:11:46 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6.raw...
2025-01-16 16:11:53 [INFO] - 220524ko09Sample6 has 3 compensation voltages: -80, -60, -40
2025-01-16 16:11:53 [INFO] - Building index...
2025-01-16 16:11:53 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6.quantindex
2025-01-16 16:11:53 [INFO] - Loading 220524ko09Sample6....
2025-01-16 16:11:53 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 16:11:53 [INFO] - Quantifying...
2025-01-16 16:11:53 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7.raw...
2025-01-16 16:12:00 [INFO] - 220524ko11Sample7 has 3 compensation voltages: -80, -60, -40
2025-01-16 16:12:00 [INFO] - Building index...
2025-01-16 16:12:00 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7.quantindex
2025-01-16 16:12:00 [INFO] - Loading 220524ko11Sample7....
2025-01-16 16:12:00 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 16:12:00 [INFO] - Quantifying...
2025-01-16 16:12:00 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8.raw...
2025-01-16 16:12:07 [INFO] - 220524ko12Sample8 has 3 compensation voltages: -80, -60, -40
2025-01-16 16:12:07 [INFO] - Building index...
2025-01-16 16:12:07 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8.quantindex
2025-01-16 16:12:07 [INFO] - Loading 220524ko12Sample8....
2025-01-16 16:12:07 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 16:12:07 [INFO] - Quantifying...
2025-01-16 16:12:07 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9.raw...
2025-01-16 16:12:13 [INFO] - 220524ko14Sample9 has 3 compensation voltages: -80, -60, -40
2025-01-16 16:12:13 [INFO] - Building index...
2025-01-16 16:12:14 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9.quantindex
2025-01-16 16:12:14 [INFO] - Loading 220524ko14Sample9....
2025-01-16 16:12:14 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 16:12:14 [INFO] - Quantifying...
2025-01-16 16:12:14 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10.raw...
2025-01-16 16:12:21 [INFO] - 220524ko15Sample10 has 3 compensation voltages: -80, -60, -40
2025-01-16 16:12:21 [INFO] - Building index...
2025-01-16 16:12:21 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10.quantindex
2025-01-16 16:12:21 [INFO] - Loading 220524ko15Sample10....
2025-01-16 16:12:21 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 16:12:21 [INFO] - Quantifying...
2025-01-16 16:12:21 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11.raw...
2025-01-16 16:12:28 [INFO] - 220524ko17Sample11 has 3 compensation voltages: -80, -60, -40
2025-01-16 16:12:28 [INFO] - Building index...
2025-01-16 16:12:28 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11.quantindex
2025-01-16 16:12:28 [INFO] - Loading 220524ko17Sample11....
2025-01-16 16:12:28 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 16:12:28 [INFO] - Quantifying...
2025-01-16 16:12:28 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12.raw...
2025-01-16 16:12:34 [INFO] - 220524ko18Sample12 has 3 compensation voltages: -80, -60, -40
2025-01-16 16:12:34 [INFO] - Building index...
2025-01-16 16:12:35 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12.quantindex
2025-01-16 16:12:35 [INFO] - Loading 220524ko18Sample12....
2025-01-16 16:12:35 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 16:12:35 [INFO] - Quantifying...
2025-01-16 16:12:35 [INFO] - Updating Philosopher's tables...
2025-01-16 16:12:41 [INFO] - Matching-between-runs: 220524ko02Sample1...
2025-01-16 16:12:41 [INFO] - Calculating correlations between all other runs...
2025-01-16 16:12:42 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko02Sample1.quantindex
2025-01-16 16:12:42 [INFO] - Transferring 220524ko03Sample2...
2025-01-16 16:12:43 [INFO] - Transferring 220524ko05Sample3...
2025-01-16 16:12:43 [INFO] - Transferring 220524ko06Sample4...
2025-01-16 16:12:43 [INFO] - Transferring 220524ko08Sample5...
2025-01-16 16:12:43 [INFO] - Transferring 220524ko09Sample6...
2025-01-16 16:12:44 [INFO] - Transferring 220524ko11Sample7...
2025-01-16 16:12:44 [INFO] - Transferring 220524ko12Sample8...
2025-01-16 16:12:44 [INFO] - Transferring 220524ko14Sample9...
2025-01-16 16:12:44 [INFO] - Transferring 220524ko15Sample10...
2025-01-16 16:12:44 [INFO] - Transferring 220524ko17Sample11...
2025-01-16 16:12:44 [INFO] - Transferring 220524ko18Sample12...
2025-01-16 16:12:44 [INFO] - Training LDA models for all matched features.
2025-01-16 16:12:44 [INFO] - #{+1} = 5877, #{-1} = 506, #{+2} = 9385, #{-2} = 815
2025-01-16 16:12:45 [INFO] - Standardized coefficients:
2025-01-16 16:12:45 [INFO] - log10(intensity): 0.7500571259577835
2025-01-16 16:12:45 [INFO] - log10(KL): -0.25185752781691745
2025-01-16 16:12:45 [INFO] - abs(ppm): -0.5323964183231029
2025-01-16 16:12:45 [INFO] - RT diff: -0.30089225187537094
2025-01-16 16:12:45 [INFO] - Fitting a mixture model...
2025-01-16 16:12:48 [INFO] - Matching-between-runs: 220524ko03Sample2...
2025-01-16 16:12:48 [INFO] - Calculating correlations between all other runs...
2025-01-16 16:12:48 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko03Sample2.quantindex
2025-01-16 16:12:48 [INFO] - Transferring 220524ko02Sample1...
2025-01-16 16:12:48 [INFO] - Transferring 220524ko05Sample3...
2025-01-16 16:12:49 [INFO] - Transferring 220524ko06Sample4...
2025-01-16 16:12:49 [INFO] - Transferring 220524ko08Sample5...
2025-01-16 16:12:49 [INFO] - Transferring 220524ko09Sample6...
2025-01-16 16:12:49 [INFO] - Transferring 220524ko11Sample7...
2025-01-16 16:12:49 [INFO] - Transferring 220524ko12Sample8...
2025-01-16 16:12:49 [INFO] - Transferring 220524ko14Sample9...
2025-01-16 16:12:49 [INFO] - Transferring 220524ko15Sample10...
2025-01-16 16:12:49 [INFO] - Transferring 220524ko17Sample11...
2025-01-16 16:12:50 [INFO] - Transferring 220524ko18Sample12...
2025-01-16 16:12:50 [INFO] - Training LDA models for all matched features.
2025-01-16 16:12:50 [INFO] - #{+1} = 5643, #{-1} = 490, #{+2} = 9801, #{-2} = 806
2025-01-16 16:12:50 [INFO] - Standardized coefficients:
2025-01-16 16:12:50 [INFO] - log10(intensity): 0.7356467677899723
2025-01-16 16:12:50 [INFO] - log10(KL): -0.30684909091456536
2025-01-16 16:12:50 [INFO] - abs(ppm): -0.5598945630499603
2025-01-16 16:12:50 [INFO] - RT diff: -0.3036587038120096
2025-01-16 16:12:50 [INFO] - Fitting a mixture model...
2025-01-16 16:12:50 [INFO] - Matching-between-runs: 220524ko05Sample3...
2025-01-16 16:12:50 [INFO] - Calculating correlations between all other runs...
2025-01-16 16:12:50 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko05Sample3.quantindex
2025-01-16 16:12:50 [INFO] - Transferring 220524ko02Sample1...
2025-01-16 16:12:51 [INFO] - Transferring 220524ko03Sample2...
2025-01-16 16:12:51 [INFO] - Transferring 220524ko06Sample4...
2025-01-16 16:12:51 [INFO] - Transferring 220524ko08Sample5...
2025-01-16 16:12:51 [INFO] - Transferring 220524ko09Sample6...
2025-01-16 16:12:51 [INFO] - Transferring 220524ko11Sample7...
2025-01-16 16:12:51 [INFO] - Transferring 220524ko12Sample8...
2025-01-16 16:12:51 [INFO] - Transferring 220524ko14Sample9...
2025-01-16 16:12:51 [INFO] - Transferring 220524ko15Sample10...
2025-01-16 16:12:52 [INFO] - Transferring 220524ko17Sample11...
2025-01-16 16:12:52 [INFO] - Transferring 220524ko18Sample12...
2025-01-16 16:12:52 [INFO] - Training LDA models for all matched features.
2025-01-16 16:12:52 [INFO] - #{+1} = 5317, #{-1} = 489, #{+2} = 10233, #{-2} = 866
2025-01-16 16:12:52 [INFO] - Standardized coefficients:
2025-01-16 16:12:52 [INFO] - log10(intensity): 0.7573578269523569
2025-01-16 16:12:52 [INFO] - log10(KL): -0.2823792433744495
2025-01-16 16:12:52 [INFO] - abs(ppm): -0.5133896592682471
2025-01-16 16:12:52 [INFO] - RT diff: -0.35862759053032345
2025-01-16 16:12:52 [INFO] - Fitting a mixture model...
2025-01-16 16:12:52 [INFO] - Matching-between-runs: 220524ko06Sample4...
2025-01-16 16:12:52 [INFO] - Calculating correlations between all other runs...
2025-01-16 16:12:52 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko06Sample4.quantindex
2025-01-16 16:12:52 [INFO] - Transferring 220524ko02Sample1...
2025-01-16 16:12:53 [INFO] - Transferring 220524ko03Sample2...
2025-01-16 16:12:53 [INFO] - Transferring 220524ko05Sample3...
2025-01-16 16:12:53 [INFO] - Transferring 220524ko08Sample5...
2025-01-16 16:12:53 [INFO] - Transferring 220524ko09Sample6...
2025-01-16 16:12:53 [INFO] - Transferring 220524ko11Sample7...
2025-01-16 16:12:53 [INFO] - Transferring 220524ko12Sample8...
2025-01-16 16:12:53 [INFO] - Transferring 220524ko14Sample9...
2025-01-16 16:12:53 [INFO] - Transferring 220524ko15Sample10...
2025-01-16 16:12:53 [INFO] - Transferring 220524ko17Sample11...
2025-01-16 16:12:54 [INFO] - Transferring 220524ko18Sample12...
2025-01-16 16:12:54 [INFO] - Training LDA models for all matched features.
2025-01-16 16:12:54 [INFO] - #{+1} = 5025, #{-1} = 505, #{+2} = 9195, #{-2} = 758
2025-01-16 16:12:54 [INFO] - Standardized coefficients:
2025-01-16 16:12:54 [INFO] - log10(intensity): 0.7454578682126385
2025-01-16 16:12:54 [INFO] - log10(KL): -0.31166754465063784
2025-01-16 16:12:54 [INFO] - abs(ppm): -0.46912864670470183
2025-01-16 16:12:54 [INFO] - RT diff: -0.4065946999091133
2025-01-16 16:12:54 [INFO] - Fitting a mixture model...
2025-01-16 16:12:54 [INFO] - Matching-between-runs: 220524ko08Sample5...
2025-01-16 16:12:54 [INFO] - Calculating correlations between all other runs...
2025-01-16 16:12:54 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko08Sample5.quantindex
2025-01-16 16:12:54 [INFO] - Transferring 220524ko02Sample1...
2025-01-16 16:12:54 [INFO] - Transferring 220524ko03Sample2...
2025-01-16 16:12:55 [INFO] - Transferring 220524ko05Sample3...
2025-01-16 16:12:55 [INFO] - Transferring 220524ko06Sample4...
2025-01-16 16:12:55 [INFO] - Transferring 220524ko09Sample6...
2025-01-16 16:12:55 [INFO] - Transferring 220524ko11Sample7...
2025-01-16 16:12:55 [INFO] - Transferring 220524ko12Sample8...
2025-01-16 16:12:55 [INFO] - Transferring 220524ko14Sample9...
2025-01-16 16:12:55 [INFO] - Transferring 220524ko15Sample10...
2025-01-16 16:12:55 [INFO] - Transferring 220524ko17Sample11...
2025-01-16 16:12:55 [INFO] - Transferring 220524ko18Sample12...
2025-01-16 16:12:56 [INFO] - Training LDA models for all matched features.
2025-01-16 16:12:56 [INFO] - #{+1} = 5499, #{-1} = 518, #{+2} = 9884, #{-2} = 838
2025-01-16 16:12:56 [INFO] - Standardized coefficients:
2025-01-16 16:12:56 [INFO] - log10(intensity): 0.7049022603911381
2025-01-16 16:12:56 [INFO] - log10(KL): -0.2902334273774804
2025-01-16 16:12:56 [INFO] - abs(ppm): -0.5083212251362422
2025-01-16 16:12:56 [INFO] - RT diff: -0.4006081539411981
2025-01-16 16:12:56 [INFO] - Fitting a mixture model...
2025-01-16 16:12:56 [INFO] - Matching-between-runs: 220524ko09Sample6...
2025-01-16 16:12:56 [INFO] - Calculating correlations between all other runs...
2025-01-16 16:12:56 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko09Sample6.quantindex
2025-01-16 16:12:56 [INFO] - Transferring 220524ko02Sample1...
2025-01-16 16:12:56 [INFO] - Transferring 220524ko03Sample2...
2025-01-16 16:12:56 [INFO] - Transferring 220524ko05Sample3...
2025-01-16 16:12:57 [INFO] - Transferring 220524ko06Sample4...
2025-01-16 16:12:57 [INFO] - Transferring 220524ko08Sample5...
2025-01-16 16:12:57 [INFO] - Transferring 220524ko11Sample7...
2025-01-16 16:12:57 [INFO] - Transferring 220524ko12Sample8...
2025-01-16 16:12:57 [INFO] - Transferring 220524ko14Sample9...
2025-01-16 16:12:57 [INFO] - Transferring 220524ko15Sample10...
2025-01-16 16:12:57 [INFO] - Transferring 220524ko17Sample11...
2025-01-16 16:12:57 [INFO] - Transferring 220524ko18Sample12...
2025-01-16 16:12:58 [INFO] - Training LDA models for all matched features.
2025-01-16 16:12:58 [INFO] - #{+1} = 5655, #{-1} = 556, #{+2} = 10343, #{-2} = 899
2025-01-16 16:12:58 [INFO] - Standardized coefficients:
2025-01-16 16:12:58 [INFO] - log10(intensity): 0.7816544787795494
2025-01-16 16:12:58 [INFO] - log10(KL): -0.17661593203745135
2025-01-16 16:12:58 [INFO] - abs(ppm): -0.4803677979479023
2025-01-16 16:12:58 [INFO] - RT diff: -0.402443095382522
2025-01-16 16:12:58 [INFO] - Fitting a mixture model...
2025-01-16 16:12:58 [INFO] - Matching-between-runs: 220524ko11Sample7...
2025-01-16 16:12:58 [INFO] - Calculating correlations between all other runs...
2025-01-16 16:12:58 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko11Sample7.quantindex
2025-01-16 16:12:58 [INFO] - Transferring 220524ko02Sample1...
2025-01-16 16:12:58 [INFO] - Transferring 220524ko03Sample2...
2025-01-16 16:12:58 [INFO] - Transferring 220524ko05Sample3...
2025-01-16 16:12:59 [INFO] - Transferring 220524ko06Sample4...
2025-01-16 16:12:59 [INFO] - Transferring 220524ko08Sample5...
2025-01-16 16:12:59 [INFO] - Transferring 220524ko09Sample6...
2025-01-16 16:12:59 [INFO] - Transferring 220524ko12Sample8...
2025-01-16 16:12:59 [INFO] - Transferring 220524ko14Sample9...
2025-01-16 16:12:59 [INFO] - Transferring 220524ko15Sample10...
2025-01-16 16:12:59 [INFO] - Transferring 220524ko17Sample11...
2025-01-16 16:12:59 [INFO] - Transferring 220524ko18Sample12...
2025-01-16 16:12:59 [INFO] - Training LDA models for all matched features.
2025-01-16 16:13:00 [INFO] - #{+1} = 4959, #{-1} = 498, #{+2} = 10514, #{-2} = 896
2025-01-16 16:13:00 [INFO] - Standardized coefficients:
2025-01-16 16:13:00 [INFO] - log10(intensity): 0.7482186915484152
2025-01-16 16:13:00 [INFO] - log10(KL): -0.2131276164529808
2025-01-16 16:13:00 [INFO] - abs(ppm): -0.5414626401075505
2025-01-16 16:13:00 [INFO] - RT diff: -0.38134550814146523
2025-01-16 16:13:00 [INFO] - Fitting a mixture model...
2025-01-16 16:13:00 [INFO] - Matching-between-runs: 220524ko12Sample8...
2025-01-16 16:13:00 [INFO] - Calculating correlations between all other runs...
2025-01-16 16:13:00 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko12Sample8.quantindex
2025-01-16 16:13:00 [INFO] - Transferring 220524ko02Sample1...
2025-01-16 16:13:00 [INFO] - Transferring 220524ko03Sample2...
2025-01-16 16:13:00 [INFO] - Transferring 220524ko05Sample3...
2025-01-16 16:13:00 [INFO] - Transferring 220524ko06Sample4...
2025-01-16 16:13:01 [INFO] - Transferring 220524ko08Sample5...
2025-01-16 16:13:01 [INFO] - Transferring 220524ko09Sample6...
2025-01-16 16:13:01 [INFO] - Transferring 220524ko11Sample7...
2025-01-16 16:13:01 [INFO] - Transferring 220524ko14Sample9...
2025-01-16 16:13:01 [INFO] - Transferring 220524ko15Sample10...
2025-01-16 16:13:01 [INFO] - Transferring 220524ko17Sample11...
2025-01-16 16:13:01 [INFO] - Transferring 220524ko18Sample12...
2025-01-16 16:13:01 [INFO] - Training LDA models for all matched features.
2025-01-16 16:13:01 [INFO] - #{+1} = 6121, #{-1} = 550, #{+2} = 9464, #{-2} = 786
2025-01-16 16:13:01 [INFO] - Standardized coefficients:
2025-01-16 16:13:01 [INFO] - log10(intensity): 0.7393851872386928
2025-01-16 16:13:01 [INFO] - log10(KL): -0.2331432028125082
2025-01-16 16:13:01 [INFO] - abs(ppm): -0.5140355500922729
2025-01-16 16:13:01 [INFO] - RT diff: -0.424267502716579
2025-01-16 16:13:01 [INFO] - Fitting a mixture model...
2025-01-16 16:13:02 [INFO] - Matching-between-runs: 220524ko14Sample9...
2025-01-16 16:13:02 [INFO] - Calculating correlations between all other runs...
2025-01-16 16:13:02 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko14Sample9.quantindex
2025-01-16 16:13:02 [INFO] - Transferring 220524ko02Sample1...
2025-01-16 16:13:02 [INFO] - Transferring 220524ko03Sample2...
2025-01-16 16:13:02 [INFO] - Transferring 220524ko05Sample3...
2025-01-16 16:13:02 [INFO] - Transferring 220524ko06Sample4...
2025-01-16 16:13:02 [INFO] - Transferring 220524ko08Sample5...
2025-01-16 16:13:02 [INFO] - Transferring 220524ko09Sample6...
2025-01-16 16:13:03 [INFO] - Transferring 220524ko11Sample7...
2025-01-16 16:13:03 [INFO] - Transferring 220524ko12Sample8...
2025-01-16 16:13:03 [INFO] - Transferring 220524ko15Sample10...
2025-01-16 16:13:03 [INFO] - Transferring 220524ko17Sample11...
2025-01-16 16:13:03 [INFO] - Transferring 220524ko18Sample12...
2025-01-16 16:13:03 [INFO] - Training LDA models for all matched features.
2025-01-16 16:13:03 [INFO] - #{+1} = 5918, #{-1} = 531, #{+2} = 9984, #{-2} = 873
2025-01-16 16:13:03 [INFO] - Standardized coefficients:
2025-01-16 16:13:03 [INFO] - log10(intensity): 0.7855970563135727
2025-01-16 16:13:03 [INFO] - log10(KL): -0.19805084271615256
2025-01-16 16:13:03 [INFO] - abs(ppm): -0.48587649528770616
2025-01-16 16:13:03 [INFO] - RT diff: -0.41271458798356725
2025-01-16 16:13:03 [INFO] - Fitting a mixture model...
2025-01-16 16:13:03 [INFO] - Matching-between-runs: 220524ko15Sample10...
2025-01-16 16:13:03 [INFO] - Calculating correlations between all other runs...
2025-01-16 16:13:04 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko15Sample10.quantindex
2025-01-16 16:13:04 [INFO] - Transferring 220524ko02Sample1...
2025-01-16 16:13:04 [INFO] - Transferring 220524ko03Sample2...
2025-01-16 16:13:04 [INFO] - Transferring 220524ko05Sample3...
2025-01-16 16:13:04 [INFO] - Transferring 220524ko06Sample4...
2025-01-16 16:13:04 [INFO] - Transferring 220524ko08Sample5...
2025-01-16 16:13:04 [INFO] - Transferring 220524ko09Sample6...
2025-01-16 16:13:04 [INFO] - Transferring 220524ko11Sample7...
2025-01-16 16:13:04 [INFO] - Transferring 220524ko12Sample8...
2025-01-16 16:13:05 [INFO] - Transferring 220524ko14Sample9...
2025-01-16 16:13:05 [INFO] - Transferring 220524ko17Sample11...
2025-01-16 16:13:05 [INFO] - Transferring 220524ko18Sample12...
2025-01-16 16:13:05 [INFO] - Training LDA models for all matched features.
2025-01-16 16:13:05 [INFO] - #{+1} = 5345, #{-1} = 449, #{+2} = 10153, #{-2} = 860
2025-01-16 16:13:05 [INFO] - Standardized coefficients:
2025-01-16 16:13:05 [INFO] - log10(intensity): 0.7528653494554911
2025-01-16 16:13:05 [INFO] - log10(KL): -0.2362518518842069
2025-01-16 16:13:05 [INFO] - abs(ppm): -0.5279105962757957
2025-01-16 16:13:05 [INFO] - RT diff: -0.38978194981326747
2025-01-16 16:13:05 [INFO] - Fitting a mixture model...
2025-01-16 16:13:05 [INFO] - Matching-between-runs: 220524ko17Sample11...
2025-01-16 16:13:05 [INFO] - Calculating correlations between all other runs...
2025-01-16 16:13:05 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko17Sample11.quantindex
2025-01-16 16:13:05 [INFO] - Transferring 220524ko02Sample1...
2025-01-16 16:13:06 [INFO] - Transferring 220524ko03Sample2...
2025-01-16 16:13:06 [INFO] - Transferring 220524ko05Sample3...
2025-01-16 16:13:06 [INFO] - Transferring 220524ko06Sample4...
2025-01-16 16:13:06 [INFO] - Transferring 220524ko08Sample5...
2025-01-16 16:13:06 [INFO] - Transferring 220524ko09Sample6...
2025-01-16 16:13:06 [INFO] - Transferring 220524ko11Sample7...
2025-01-16 16:13:06 [INFO] - Transferring 220524ko12Sample8...
2025-01-16 16:13:06 [INFO] - Transferring 220524ko14Sample9...
2025-01-16 16:13:07 [INFO] - Transferring 220524ko15Sample10...
2025-01-16 16:13:07 [INFO] - Transferring 220524ko18Sample12...
2025-01-16 16:13:07 [INFO] - Training LDA models for all matched features.
2025-01-16 16:13:07 [INFO] - #{+1} = 6164, #{-1} = 569, #{+2} = 9513, #{-2} = 773
2025-01-16 16:13:07 [INFO] - Standardized coefficients:
2025-01-16 16:13:07 [INFO] - log10(intensity): 0.7568613855131248
2025-01-16 16:13:07 [INFO] - log10(KL): -0.21269770241370825
2025-01-16 16:13:07 [INFO] - abs(ppm): -0.4778860979134815
2025-01-16 16:13:07 [INFO] - RT diff: -0.44865740078448924
2025-01-16 16:13:07 [INFO] - Fitting a mixture model...
2025-01-16 16:13:07 [INFO] - Matching-between-runs: 220524ko18Sample12...
2025-01-16 16:13:07 [INFO] - Calculating correlations between all other runs...
2025-01-16 16:13:07 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\220524ko\220524ko18Sample12.quantindex
2025-01-16 16:13:07 [INFO] - Transferring 220524ko02Sample1...
2025-01-16 16:13:07 [INFO] - Transferring 220524ko03Sample2...
2025-01-16 16:13:08 [INFO] - Transferring 220524ko05Sample3...
2025-01-16 16:13:08 [INFO] - Transferring 220524ko06Sample4...
2025-01-16 16:13:08 [INFO] - Transferring 220524ko08Sample5...
2025-01-16 16:13:08 [INFO] - Transferring 220524ko09Sample6...
2025-01-16 16:13:08 [INFO] - Transferring 220524ko11Sample7...
2025-01-16 16:13:08 [INFO] - Transferring 220524ko12Sample8...
2025-01-16 16:13:08 [INFO] - Transferring 220524ko14Sample9...
2025-01-16 16:13:08 [INFO] - Transferring 220524ko15Sample10...
2025-01-16 16:13:09 [INFO] - Transferring 220524ko17Sample11...
2025-01-16 16:13:09 [INFO] - Training LDA models for all matched features.
2025-01-16 16:13:09 [INFO] - #{+1} = 8172, #{-1} = 745, #{+2} = 11476, #{-2} = 1011
2025-01-16 16:13:09 [INFO] - Standardized coefficients:
2025-01-16 16:13:09 [INFO] - log10(intensity): 0.8311721515989546
2025-01-16 16:13:09 [INFO] - log10(KL): -0.12852319746369714
2025-01-16 16:13:09 [INFO] - abs(ppm): -0.22831924757431218
2025-01-16 16:13:09 [INFO] - RT diff: -0.4904130537691385
2025-01-16 16:13:09 [INFO] - Fitting a mixture model...
2025-01-16 16:13:09 [INFO] - Estimating match-between-runs FDR...
2025-01-16 16:13:11 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.963100
2025-01-16 16:13:11 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100
2025-01-16 16:13:11 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100
2025-01-16 16:13:11 [INFO] - Updating Philosopher's tables...
2025-01-16 16:13:14 [WARNING] - Could not find protein sp|A2AKX3|SETX_MOUSE from the protein index.
2025-01-16 16:13:17 [INFO] - Combining experiments and estimating protein intensity...
2025-01-16 16:13:25 [INFO] - Done!
Process 'IonQuant' finished, exit code: 0

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

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