System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK .NET Core Info: 6.0.7 Version info: FragPipe version 21.1 MSFragger version 4.0 IonQuant version 1.10.12 Philosopher version 5.1.0 LCMS files: Experiment/Group: 1 (if "spectral library generation" is enabled, all files will be analyzed together) - K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.raw DDA - K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.raw DDA - K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.raw DDA - K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.raw DDA - K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.raw DDA - K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.raw DDA - K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.raw DDA - K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.raw DDA - K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.raw DDA - K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.raw DDA Experiment/Group: 2 (if "spectral library generation" is enabled, all files will be analyzed together) - K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.raw DDA - K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.raw DDA - K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.raw DDA - K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.raw DDA - K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.raw DDA - K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.raw DDA - K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.raw DDA - K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.raw DDA - K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.raw DDA - K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.raw DDA 140 commands to execute: CheckCentroid E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx181G -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;E:\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.raw 20 WorkspaceCleanInit [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\KBHUNI~1\AppData\Local\Temp\81c785d8-1abb-4339-9813-e23812ecd842 WorkspaceCleanInit [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\KBHUNI~1\AppData\Local\Temp\2e32256b-4c4f-4608-9298-a37869e20b59 WorkspaceCleanInit [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\KBHUNI~1\AppData\Local\Temp\cbaede38-4af3-4ab9-9391-d52f8e02a6e4 MSFragger [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx181G E:\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\MSFragger-4.0.jar G:\Juanjuan_2\WDR33i\fragger.params K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.raw MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.pin MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.pepXML MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.pin MSBooster [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx181G -cp E:\FragPipe-jre-21.1\fragpipe\tools\msbooster-1.1.28.jar;E:\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar Features.MainClass --paramsList G:\Juanjuan_2\WDR33i\msbooster_params.txt Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_edited.pin Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_edited.pin Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_uncalibrated.mzML Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_target_psms.tsv Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_decoy_psms.tsv ProteinProphet [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined G:\Juanjuan_2\WDR33i\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate K:\20190404-wjj-phospho-KD-WDR33-Federico\2024-04-10-decoys-contam-HUMAN_2018_06.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml G:\Juanjuan_2\WDR33i\1 --protxml G:\Juanjuan_2\WDR33i\combined.prot.xml --razor PhilosopherFilter [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml G:\Juanjuan_2\WDR33i\2 --dbbin G:\Juanjuan_2\WDR33i\1 --protxml G:\Juanjuan_2\WDR33i\combined.prot.xml --probin G:\Juanjuan_2\WDR33i\1 --razor PhilosopherReport [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PTMShepherd [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx181G -Dlibs.thermo.dir=E:\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp E:\FragPipe-jre-21.1\fragpipe\tools\ptmshepherd-2.0.6.jar;E:\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar;E:\FragPipe-jre-21.1\fragpipe\tools\commons-math3-3.6.1.jar;E:\FragPipe-jre-21.1\fragpipe\tools\hipparchus-1.8\hipparchus-core-1.8.jar;E:\FragPipe-jre-21.1\fragpipe\tools\hipparchus-1.8\hipparchus-stat-1.8.jar edu.umich.andykong.ptmshepherd.PTMShepherd "G:\Juanjuan_2\WDR33i\shepherd.config" WorkspaceClean [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck IonQuant [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx181G -Dlibs.bruker.dir=E:\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=E:\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp E:\FragPipe-jre-21.1\fragpipe\tools\jfreechart-1.5.3.jar;E:\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar;E:\FragPipe-jre-21.1\fragpipe\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 20 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --light K0;R0 --medium K4.025107;R6.020129 --heavy K8.014199;R10.008269 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist G:\Juanjuan_2\WDR33i\filelist_ionquant.txt --modlist G:\Juanjuan_2\WDR33i\modmasses_ionquant.txt ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [G:\Juanjuan_2\WDR33i] Cmd: [CheckCentroid], Work dir: [G:\Juanjuan_2\WDR33i] Cmd: [WorkspaceCleanInit], Work dir: [G:\Juanjuan_2\WDR33i] Cmd: [WorkspaceCleanInit], Work dir: [G:\Juanjuan_2\WDR33i\1] Cmd: [WorkspaceCleanInit], Work dir: [G:\Juanjuan_2\WDR33i\2] Cmd: [MSFragger], Work dir: [G:\Juanjuan_2\WDR33i] Cmd: [MSBooster], Work dir: [G:\Juanjuan_2\WDR33i] Cmd: [Percolator], Work dir: [G:\Juanjuan_2\WDR33i] Cmd: [ProteinProphet], Work dir: [G:\Juanjuan_2\WDR33i] Cmd: [PhilosopherDbAnnotate], Work dir: [G:\Juanjuan_2\WDR33i] Cmd: [PhilosopherFilter], Work dir: [G:\Juanjuan_2\WDR33i] Cmd: [PhilosopherReport], Work dir: [G:\Juanjuan_2\WDR33i] Cmd: [PTMShepherd], Work dir: [G:\Juanjuan_2\WDR33i] Cmd: [WorkspaceClean], Work dir: [G:\Juanjuan_2\WDR33i] Cmd: [WorkspaceClean], Work dir: [G:\Juanjuan_2\WDR33i\1] Cmd: [WorkspaceClean], Work dir: [G:\Juanjuan_2\WDR33i\2] Cmd: [IonQuant], Work dir: [G:\Juanjuan_2\WDR33i] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of K:\20190404-wjj-phospho-KD-WDR33-Federico\2024-04-10-decoys-contam-HUMAN_2018_06.fasta.fas~~~~~~~ >rev_sp|A0A075B6H9|LV469_HUMAN Immunoglobulin lambda variable 4-69 OS=Homo sapiens OX=9606 GN=IGLV4-69 PE=1 SV=1 >rev_sp|P28562|DUS1_HUMAN Dual specificity protein phosphatase 1 OS=Homo sapiens OX=9606 GN=DUSP1 PE=1 SV=3 >rev_sp|Q5JUW0-2|KRBX4_HUMAN Isoform 2 of KRAB domain-containing protein 4 OS=Homo sapiens OX=9606 GN=KRBOX4 >rev_sp|Q8TD26-3|CHD6_HUMAN Isoform 3 of Chromodomain-helicase-DNA-binding protein 6 OS=Homo sapiens OX=9606 GN=CHD6 >rev_sp|Q9NWB6-3|ARGL1_HUMAN Isoform 3 of Arginine and glutamate-rich protein 1 OS=Homo sapiens OX=9606 GN=ARGLU1 >rev_tr|A0A0G2JR26|A0A0G2JR26_HUMAN Mucin-20 OS=Homo sapiens OX=9606 GN=MUC20 PE=1 SV=1 >rev_tr|C9JD82|C9JD82_HUMAN Bromodomain testis-specific protein (Fragment) OS=Homo sapiens OX=9606 GN=BRDT PE=1 SV=1 >rev_tr|E9PPP4|E9PPP4_HUMAN Monocarboxylate transporter 12 (Fragment) OS=Homo sapiens OX=9606 GN=SLC16A12 PE=4 SV=1 >rev_tr|H0YCJ4|H0YCJ4_HUMAN Teneurin-4 (Fragment) OS=Homo sapiens OX=9606 GN=TENM4 PE=1 SV=1 >rev_tr|J3KSD4|J3KSD4_HUMAN Src kinase-associated phosphoprotein 1 (Fragment) OS=Homo sapiens OX=9606 GN=SKAP1 PE=4 SV=1 >rev_tr|X6RLT1|X6RLT1_HUMAN Negative elongation factor C/D (Fragment) OS=Homo sapiens OX=9606 GN=NELFCD PE=1 SV=1 >sp|P28472-2|GBRB3_HUMAN Isoform 2 of Gamma-aminobutyric acid receptor subunit beta-3 OS=Homo sapiens OX=9606 GN=GABRB3 >sp|Q5JUK3-2|KCNT1_HUMAN Isoform 2 of Potassium channel subfamily T member 1 OS=Homo sapiens OX=9606 GN=KCNT1 >sp|Q8TD16|BICD2_HUMAN Protein bicaudal D homolog 2 OS=Homo sapiens OX=9606 GN=BICD2 PE=1 SV=1 >sp|Q9NW97|TMM51_HUMAN Transmembrane protein 51 OS=Homo sapiens OX=9606 GN=TMEM51 PE=1 SV=1 >tr|A0A0G2JQZ4|A0A0G2JQZ4_HUMAN Uncharacterized protein OS=Homo sapiens OX=9606 PE=4 SV=3 >tr|C9JD58|C9JD58_HUMAN WW domain-containing adapter protein with coiled-coil (Fragment) OS=Homo sapiens OX=9606 GN=WAC PE=1 SV=1 >tr|E9PPN2|E9PPN2_HUMAN Phospholipase DDHD2 OS=Homo sapiens OX=9606 GN=DDHD2 PE=1 SV=1 >tr|H0YCI2|H0YCI2_HUMAN 1,5-anhydro-D-fructose reductase (Fragment) OS=Homo sapiens OX=9606 GN=AKR1E2 PE=4 SV=1 >tr|J3KSC3|J3KSC3_HUMAN Uncharacterized protein (Fragment) OS=Homo sapiens OX=9606 PE=4 SV=1 >tr|X6RL83|X6RL83_HUMAN Inactive glycosyltransferase 25 family member 3 (Fragment) OS=Homo sapiens OX=9606 GN=CERCAM PE=1 SV=1 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v21.1ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=K\:\\20190404-wjj-phospho-KD-WDR33-Federico\\2024-04-10-decoys-contam-HUMAN_2018_06.fasta.fas 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="C\:\\Users\\KBH Universitet\\Downloads\\FragPipe-jre-21.1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe" fragpipe-config.bin-ionquant=E\:\\FragPipe-jre-21.1\\fragpipe\\tools\\IonQuant-1.10.12.jar fragpipe-config.bin-msfragger=E\:\\FragPipe-jre-21.1\\fragpipe\\tools\\MSFragger-4.0\\MSFragger-4.0.jar fragpipe-config.bin-philosopher=E\:\\FragPipe-jre-21.1\\fragpipe\\tools\\philosopher_v5.1.0_windows_amd64\\philosopher.exe fragpipe-config.bin-python=C\:\\ProgramData\\Miniconda3\\python freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.heavy=K8.014199;R10.008269 ionquant.imtol=0.05 ionquant.ionfdr=0.01 ionquant.light=K0;R0 ionquant.locprob=0.75 ionquant.maxlfq=1 ionquant.mbr=1 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=10 ionquant.medium=K4.025107;R6.020129 ionquant.minfreq=0 ionquant.minions=2 ionquant.minisotopes=2 ionquant.minscans=3 ionquant.mztol=10 ionquant.normalization=1 ionquant.peptidefdr=1 ionquant.proteinfdr=1 ionquant.requantify=1 ionquant.rttol=0.4 ionquant.run-ionquant=true ionquant.tp=0 ionquant.uniqueness=0 ionquant.use-labeling=true ionquant.use-lfq=false ionquant.writeindex=0 msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.run-msbooster=true msbooster.use-correlated-features=false msfragger.Y_type_masses= msfragger.activation_types=all msfragger.add_topN_complementary=0 msfragger.allowed_missed_cleavage_1=2 msfragger.allowed_missed_cleavage_2=2 msfragger.calibrate_mass=1 msfragger.check_spectral_files=true msfragger.clip_nTerm_M=true msfragger.deisotope=1 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) msfragger.deneutralloss=1 msfragger.diagnostic_fragments= msfragger.diagnostic_intensity_filter=0 msfragger.digest_max_length=40 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=10000 msfragger.max_variable_mods_per_peptide=5 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.00 msfragger.misc.fragger.clear-mz-hi=0 msfragger.misc.fragger.clear-mz-lo=0 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=500 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin msfragger.misc.fragger.enzyme-dropdown-2=null msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=2 msfragger.output_format=pepXML_pin msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.output_report_topN_dda_plus=5 msfragger.output_report_topN_dia1=5 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2= msfragger.search_enzyme_name_1=stricttrypsin msfragger.search_enzyme_name_2=null msfragger.search_enzyme_nocut_1= msfragger.search_enzyme_nocut_2= msfragger.search_enzyme_sense_1=C msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 msfragger.table.var-mods=15.9949,M,true,2; 42.0106,[^,true,1; 79.96633,STY,true,2; 4.025107,K,true,3; 6.020129,R,true,3; 8.014199,K,true,3; 10.008269,R,true,3; 0.0,site_8,false,1; 0.0,site_9,false,1; 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=200 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 0.01 phi-report.pep-level-summary=false phi-report.philosoher-msstats=false phi-report.print-decoys=false phi-report.prot-level-summary=false phi-report.remove-contaminants=false phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 protein-prophet.run-protein-prophet=true ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b STY\:79.966331,n\:42.0106,M\:15.9949,K\:4.025107,K\:8.014199,R\:6.020129,R\:10.008269 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=25 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=00 ptmshepherd.diagmine_fragMinSpecDiff=15 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_mode=false ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=25 ptmshepherd.glyco_adducts= ptmshepherd.glyco_fdr=1.00 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_mode=true ptmshepherd.glyco_ppm_tol=50 ptmshepherd.glycodatabase= ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=false ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=false ptmshepherd.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=true ptmshepherd.run_diagextract_mode=false ptmshepherd.run_diagmine_mode=true ptmshepherd.run_glyco_mode=false ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses= quantitation.run-label-free-quant=true run-psm-validation=true run-validation-tab=true saintexpress.fragpipe.cmd-opts= saintexpress.max-replicates=3 saintexpress.run-saint-express=true 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=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=false tab-run.delete_calibrated_mzml=false tab-run.delete_temp_files=false tab-run.sub_mzml_prob_threshold=0.5 tab-run.write_sub_mzml=false tmtintegrator.add_Ref=-1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=true tmtintegrator.best_psm=true tmtintegrator.channel_num=TMT-6 tmtintegrator.dont-run-fq-lq=false tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=-1 tmtintegrator.groupby=0 tmtintegrator.log2transformed=true tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.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=G\:\\Juanjuan_2\\WDR33i workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.ram=0 workflow.threads=20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx181G -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;E:\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.raw 20 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[13:00:50] Executing Workspace v5.1.0 INFO[13:00:50] Removing workspace INFO[13:00:50] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\KBHUNI~1\AppData\Local\Temp\81c785d8-1abb-4339-9813-e23812ecd842 INFO[13:00:50] Executing Workspace v5.1.0 INFO[13:00:50] Creating workspace INFO[13:00:50] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[13:00:51] Executing Workspace v5.1.0 INFO[13:00:51] Removing workspace INFO[13:00:51] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\KBHUNI~1\AppData\Local\Temp\2e32256b-4c4f-4608-9298-a37869e20b59 INFO[13:00:51] Executing Workspace v5.1.0 INFO[13:00:51] Creating workspace INFO[13:00:51] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[13:00:51] Executing Workspace v5.1.0 INFO[13:00:51] Removing workspace INFO[13:00:51] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\KBHUNI~1\AppData\Local\Temp\cbaede38-4af3-4ab9-9391-d52f8e02a6e4 INFO[13:00:52] Executing Workspace v5.1.0 INFO[13:00:52] Creating workspace INFO[13:00:52] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx181G E:\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\MSFragger-4.0.jar G:\Juanjuan_2\WDR33i\fragger.params K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.raw K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.raw K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.raw MSFragger version MSFragger-4.0 Batmass-IO version 1.30.0 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 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 181 GB memory Checking database... Checking spectral files... K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.raw: Scans = 38038; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.raw: Scans = 38984; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.raw: Scans = 35160; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.raw: Scans = 34878; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.raw: Scans = 35846; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.raw: Scans = 37453; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.raw: Scans = 36306; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.raw: Scans = 38137; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.raw: Scans = 39607; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.raw: Scans = 37692; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.raw: Scans = 37822; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.raw: Scans = 38351; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.raw: Scans = 39012; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.raw: Scans = 39335; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.raw: Scans = 39620; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.raw: Scans = 40524; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.raw: Scans = 39004; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.raw: Scans = 40231; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.raw: Scans = 39897; Isolation sizes = [2.6] K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.raw: Scans = 40535; Isolation sizes = [2.6] ***********************************FIRST SEARCH************************************ Parameters: num_threads = 20 database_name = K:\20190404-wjj-phospho-KD-WDR33-Federico\2024-04-10-decoys-contam-HUMAN_2018_06.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 1 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 = 2 precursor_charge_high = 3 digest_min_length = 7 digest_max_length = 40 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 200 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 2 variable_mod_02 = 42.0106 [^ 1 variable_mod_03 = 79.96633 STY 2 variable_mod_04 = 4.025107 K 3 variable_mod_05 = 6.020129 R 3 variable_mod_06 = 8.014199 K 3 variable_mod_07 = 10.008269 R 3 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.10 Da. 29535337760 fragments to be searched in 4 slices (440.11 GB total) Operating on slice 1 of 4: Fragment index slice generated in 100.32 s 001. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.raw 30.4 s | deisotoping 1.8 s [progress: 38976/38976 (100%) - 6026 spectra/s] 6.5s 002. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.raw 54.0 s | deisotoping 1.3 s [progress: 40514/40514 (100%) - 6109 spectra/s] 6.6s 003. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.raw 23.6 s | deisotoping 0.2 s [progress: 36274/36274 (100%) - 9144 spectra/s] 4.0s 004. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.raw 28.8 s | deisotoping 0.5 s [progress: 39304/39304 (100%) - 7406 spectra/s] 5.3s 005. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.raw 33.7 s | deisotoping 1.5 s [progress: 40530/40530 (100%) - 5336 spectra/s] 7.6s 006. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.raw 35.2 s | deisotoping 1.5 s [progress: 38108/38108 (100%) - 6120 spectra/s] 6.2s 007. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.raw 40.4 s | deisotoping 1.7 s [progress: 39603/39603 (100%) - 6267 spectra/s] 6.3s 008. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.raw 22.8 s | deisotoping 0.4 s [progress: 34970/34970 (100%) - 7720 spectra/s] 4.5s 009. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.raw 29.9 s | deisotoping 0.6 s [progress: 37781/37781 (100%) - 5764 spectra/s] 6.6s 010. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.raw 33.8 s | deisotoping 1.4 s [progress: 39892/39892 (100%) - 4954 spectra/s] 8.1s 011. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.raw 32.2 s | deisotoping 0.9 s [progress: 38022/38022 (100%) - 5450 spectra/s] 7.0s 012. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.raw 45.6 s | deisotoping 0.8 s [progress: 39598/39598 (100%) - 5606 spectra/s] 7.1s 013. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.raw 33.2 s | deisotoping 0.2 s [progress: 35797/35797 (100%) - 6992 spectra/s] 5.1s 014. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.raw 40.3 s | deisotoping 0.5 s [progress: 38317/38317 (100%) - 5786 spectra/s] 6.6s 015. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.raw 43.8 s | deisotoping 1.5 s [progress: 40221/40221 (100%) - 4686 spectra/s] 8.6s 016. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.raw 50.0 s | deisotoping 1.7 s [progress: 37423/37423 (100%) - 3484 spectra/s] 10.7s 017. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.raw 36.2 s | 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[progress: 39304/39304 (100%) - 32672 spectra/s] 1.2s | postprocessing 0.4 s 005. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.raw 9.6 s | deisotoping 2.2 s [progress: 40530/40530 (100%) - 9747 spectra/s] 4.2s | postprocessing 0.5 s 006. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.raw 8.6 s | deisotoping 2.1 s [progress: 38108/38108 (100%) - 9878 spectra/s] 3.9s | postprocessing 0.2 s 007. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.raw 12.3 s | deisotoping 2.3 s [progress: 39603/39603 (100%) - 7625 spectra/s] 5.2s | postprocessing 0.7 s 008. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.raw 7.8 s | deisotoping 0.3 s [progress: 34970/34970 (100%) - 15257 spectra/s] 2.3s | postprocessing 0.6 s 009. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.raw 8.7 s | deisotoping 1.0 s [progress: 37781/37781 (100%) - 9668 spectra/s] 3.9s | postprocessing 0.7 s 010. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.raw 10.4 s | deisotoping 2.0 s [progress: 39892/39892 (100%) - 7898 spectra/s] 5.1s | postprocessing 0.7 s 011. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.raw 9.1 s | deisotoping 1.3 s [progress: 38022/38022 (100%) - 11525 spectra/s] 3.3s | postprocessing 0.5 s 012. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.raw 15.0 s | deisotoping 0.9 s [progress: 39598/39598 (100%) - 17292 spectra/s] 2.3s | postprocessing 0.4 s 013. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.raw 7.3 s | deisotoping 0.2 s [progress: 35797/35797 (100%) - 36086 spectra/s] 1.0s | postprocessing 0.2 s 014. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.raw 7.9 s | deisotoping 0.4 s [progress: 38317/38317 (100%) - 20915 spectra/s] 1.8s | postprocessing 0.2 s 015. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.raw 9.1 s | deisotoping 0.9 s [progress: 40221/40221 (100%) - 21532 spectra/s] 1.9s | postprocessing 0.8 s 016. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.raw 8.3 s | deisotoping 0.8 s [progress: 37423/37423 (100%) - 18730 spectra/s] 2.0s | postprocessing 0.2 s 017. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.raw 9.6 s | deisotoping 2.2 s [progress: 38976/38976 (100%) - 7034 spectra/s] 5.5s | postprocessing 0.3 s 018. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.raw 19.6 s | deisotoping 0.3 s [progress: 34716/34716 (100%) - 18195 spectra/s] 1.9s | postprocessing 0.2 s 019. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.raw 10.8 s | deisotoping 1.3 s [progress: 37632/37632 (100%) - 19975 spectra/s] 1.9s | postprocessing 1.0 s 020. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.raw 9.4 s | deisotoping 1.2 s [progress: 38987/38987 (100%) - 9197 spectra/s] 4.2s | postprocessing 0.6 s ***************************FIRST SEARCH DONE IN 34.865 MIN************************** *********************************MASS CALIBRATION********************************** -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | 0.97 1.84 | -0.13 1.32 | 0.28 1.11 | -0.08 1.10 002 | 1.53 2.31 | -0.07 1.50 | 0.23 1.13 | -0.08 1.12 003 | 0.53 1.58 | -0.09 1.23 | 0.15 1.23 | -0.04 1.21 004 | 0.50 1.54 | -0.02 1.09 | 0.19 1.09 | -0.07 1.08 005 | 2.03 2.77 | -0.14 1.47 | 0.41 1.14 | -0.09 1.13 006 | 1.18 2.20 | -0.10 1.32 | 0.26 1.13 | -0.07 1.13 007 | 2.10 2.69 | -0.03 1.61 | 0.44 1.15 | -0.10 1.14 008 | 0.55 1.35 | -0.06 0.94 | 0.30 1.34 | -0.03 1.34 009 | 0.91 1.47 | -0.21 1.16 | 0.43 1.18 | -0.07 1.16 010 | 2.03 2.74 | -0.23 1.62 | 0.68 1.23 | -0.08 1.20 011 | 1.20 2.08 | -0.05 1.30 | 0.56 1.14 | -0.08 1.11 012 | 1.39 2.09 | -0.06 1.40 | 0.40 1.18 | -0.09 1.16 013 | 0.62 1.46 | -0.16 1.11 | 0.37 1.26 | -0.05 1.23 014 | 0.79 1.69 | -0.17 1.15 | 0.41 1.16 | -0.09 1.13 015 | 1.65 2.61 | -0.20 1.44 | 0.35 1.19 | -0.06 1.18 016 | 1.37 2.19 | -0.10 1.35 | 0.49 1.18 | -0.12 1.15 017 | 1.53 2.08 | -0.15 1.41 | 0.40 1.19 | -0.09 1.18 018 | 0.62 1.61 | -0.18 1.27 | 0.19 1.36 | -0.04 1.36 019 | 0.70 1.53 | -0.30 1.13 | 0.24 1.19 | -0.08 1.20 020 | 1.66 2.46 | -0.20 1.46 | 0.49 1.24 | -0.10 1.22 -----|---------------|---------------|---------------|--------------- **************************MASS CALIBRATION DONE IN 4.520 MIN*********************** ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 20 database_name = K:\20190404-wjj-phospho-KD-WDR33-Federico\2024-04-10-decoys-contam-HUMAN_2018_06.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 1 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 = 5 max_variable_mods_combinations = 10000 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 = 40 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 200 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 2 variable_mod_02 = 42.0106 [^ 1 variable_mod_03 = 79.96633 STY 2 variable_mod_04 = 4.025107 K 3 variable_mod_05 = 6.020129 R 3 variable_mod_06 = 8.014199 K 3 variable_mod_07 = 10.008269 R 3 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.10 Da. 77993797528 fragments to be searched in 9 slices (1162.20 GB total) Operating on slice 1 of 9: Fragment index slice generated in 87.57 s 001. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.mzBIN_calibrated 1.5 s [progress: 38967/38967 (100%) - 3004 spectra/s] 13.0s 002. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.mzBIN_calibrated 0.6 s [progress: 40508/40508 (100%) - 3234 spectra/s] 12.5s 003. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.mzBIN_calibrated 0.4 s [progress: 36256/36256 (100%) - 4093 spectra/s] 8.9s 004. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.mzBIN_calibrated 0.5 s [progress: 39294/39294 (100%) - 3877 spectra/s] 10.1s 005. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.mzBIN_calibrated 0.7 s [progress: 40522/40522 (100%) - 2826 spectra/s] 14.3s 006. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.mzBIN_calibrated 1.3 s [progress: 38087/38087 (100%) - 2871 spectra/s] 13.3s 007. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.mzBIN_calibrated 0.6 s [progress: 39586/39586 (100%) - 2669 spectra/s] 14.8s 008. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.mzBIN_calibrated 0.4 s [progress: 34934/34934 (100%) - 4188 spectra/s] 8.3s 009. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.mzBIN_calibrated 0.4 s [progress: 37762/37762 (100%) - 2574 spectra/s] 14.7s 010. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.mzBIN_calibrated 1.3 s [progress: 39884/39884 (100%) - 2130 spectra/s] 18.7s 011. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.mzBIN_calibrated 0.5 s [progress: 38014/38014 (100%) - 3119 spectra/s] 12.2s 012. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.mzBIN_calibrated 0.5 s [progress: 39590/39590 (100%) - 4554 spectra/s] 8.7s 013. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.mzBIN_calibrated 0.4 s [progress: 35781/35781 (100%) - 4609 spectra/s] 7.8s 014. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.mzBIN_calibrated 0.5 s [progress: 38309/38309 (100%) - 4589 spectra/s] 8.3s 015. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.mzBIN_calibrated 0.6 s [progress: 40218/40218 (100%) - 3193 spectra/s] 12.6s 016. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.mzBIN_calibrated 0.5 s [progress: 37400/37400 (100%) - 4572 spectra/s] 8.2s 017. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.mzBIN_calibrated 0.5 s [progress: 38969/38969 (100%) - 4700 spectra/s] 8.3s 018. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.mzBIN_calibrated 0.3 s [progress: 34666/34666 (100%) - 3265 spectra/s] 10.6s 019. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.mzBIN_calibrated 0.6 s [progress: 37618/37618 (100%) - 3209 spectra/s] 11.7s 020. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.mzBIN_calibrated 1.0 s [progress: 38981/38981 (100%) - 2429 spectra/s] 16.0s Operating on slice 2 of 9: Fragment index slice generated in 70.00 s 001. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.mzBIN_calibrated 1.0 s [progress: 38967/38967 (100%) - 5241 spectra/s] 7.4s 002. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.mzBIN_calibrated 0.7 s [progress: 40508/40508 (100%) - 5392 spectra/s] 7.5s 003. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.mzBIN_calibrated 0.5 s [progress: 36256/36256 (100%) - 9311 spectra/s] 3.9s 004. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.mzBIN_calibrated 1.0 s [progress: 39294/39294 (100%) - 7706 spectra/s] 5.1s 005. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.mzBIN_calibrated 0.7 s [progress: 40522/40522 (100%) - 4308 spectra/s] 9.4s 006. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.mzBIN_calibrated 0.6 s [progress: 38087/38087 (100%) - 5043 spectra/s] 7.6s 007. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.mzBIN_calibrated 0.7 s [progress: 39586/39586 (100%) - 4715 spectra/s] 8.4s 008. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.mzBIN_calibrated 0.5 s [progress: 34934/34934 (100%) - 8891 spectra/s] 3.9s 009. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.mzBIN_calibrated 0.9 s [progress: 37762/37762 (100%) - 6713 spectra/s] 5.6s 010. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.mzBIN_calibrated 0.9 s [progress: 39884/39884 (100%) - 4556 spectra/s] 8.8s 011. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.mzBIN_calibrated 0.6 s [progress: 38014/38014 (100%) - 3539 spectra/s] 10.7s 012. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.mzBIN_calibrated 1.0 s [progress: 39590/39590 (100%) - 3853 spectra/s] 10.3s 013. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.mzBIN_calibrated 0.7 s [progress: 35781/35781 (100%) - 6060 spectra/s] 5.9s 014. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.mzBIN_calibrated 0.5 s [progress: 38309/38309 (100%) - 3146 spectra/s] 12.2s 015. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.mzBIN_calibrated 0.6 s [progress: 40218/40218 (100%) - 2938 spectra/s] 13.7s 016. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.mzBIN_calibrated 1.2 s [progress: 37400/37400 (100%) - 3367 spectra/s] 11.1s 017. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.mzBIN_calibrated 1.1 s [progress: 38969/38969 (100%) - 3346 spectra/s] 11.6s 018. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.mzBIN_calibrated 0.8 s [progress: 34666/34666 (100%) - 5100 spectra/s] 6.8s 019. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.mzBIN_calibrated 1.1 s [progress: 37618/37618 (100%) - 4331 spectra/s] 8.7s 020. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.mzBIN_calibrated 1.2 s [progress: 38981/38981 (100%) - 2957 spectra/s] 13.2s Operating on slice 3 of 9: Fragment index slice generated in 50.80 s 001. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.mzBIN_calibrated 0.5 s [progress: 38967/38967 (100%) - 10779 spectra/s] 3.6s 002. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.mzBIN_calibrated 0.5 s [progress: 40508/40508 (100%) - 5902 spectra/s] 6.9s 003. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.mzBIN_calibrated 0.9 s [progress: 36256/36256 (100%) - 15587 spectra/s] 2.3s 004. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.mzBIN_calibrated 0.8 s [progress: 39294/39294 (100%) - 14362 spectra/s] 2.7s 005. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.mzBIN_calibrated 0.5 s [progress: 40522/40522 (100%) - 2786 spectra/s] 14.5s 006. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.mzBIN_calibrated 0.5 s [progress: 38087/38087 (100%) - 4770 spectra/s] 8.0s 007. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.mzBIN_calibrated 1.7 s [progress: 39586/39586 (100%) - 5453 spectra/s] 7.3s 008. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.mzBIN_calibrated 0.5 s [progress: 34934/34934 (100%) - 10444 spectra/s] 3.3s 009. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.mzBIN_calibrated 0.7 s [progress: 37762/37762 (100%) - 6454 spectra/s] 5.9s 010. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.mzBIN_calibrated 0.7 s [progress: 39884/39884 (100%) - 4840 spectra/s] 8.2s 011. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.mzBIN_calibrated 0.5 s [progress: 38014/38014 (100%) - 6126 spectra/s] 6.2s 012. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.mzBIN_calibrated 0.5 s [progress: 39590/39590 (100%) - 5958 spectra/s] 6.6s 013. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.mzBIN_calibrated 0.6 s [progress: 35781/35781 (100%) - 8407 spectra/s] 4.3s 014. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.mzBIN_calibrated 0.5 s [progress: 38309/38309 (100%) - 8986 spectra/s] 4.3s 015. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.mzBIN_calibrated 0.5 s [progress: 40218/40218 (100%) - 4342 spectra/s] 9.3s 016. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.mzBIN_calibrated 0.5 s [progress: 37400/37400 (100%) - 5875 spectra/s] 6.4s 017. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.mzBIN_calibrated 0.5 s [progress: 38969/38969 (100%) - 5181 spectra/s] 7.5s 018. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.mzBIN_calibrated 0.6 s [progress: 34666/34666 (100%) - 7955 spectra/s] 4.4s 019. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.mzBIN_calibrated 0.4 s [progress: 37618/37618 (100%) - 5886 spectra/s] 6.4s 020. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.mzBIN_calibrated 0.6 s [progress: 38981/38981 (100%) - 3815 spectra/s] 10.2s Operating on slice 4 of 9: Fragment index slice generated in 63.83 s 001. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.mzBIN_calibrated 0.5 s [progress: 38967/38967 (100%) - 6328 spectra/s] 6.2s 002. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.mzBIN_calibrated 0.6 s [progress: 40508/40508 (100%) - 7657 spectra/s] 5.3s 003. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.mzBIN_calibrated 0.8 s [progress: 36256/36256 (100%) - 12650 spectra/s] 2.9s 004. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.mzBIN_calibrated 1.4 s [progress: 39294/39294 (100%) - 9824 spectra/s] 4.0s 005. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.mzBIN_calibrated 0.8 s [progress: 40522/40522 (100%) - 6550 spectra/s] 6.2s 006. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.mzBIN_calibrated 1.4 s [progress: 38087/38087 (100%) - 6236 spectra/s] 6.1s 007. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.mzBIN_calibrated 1.5 s [progress: 39586/39586 (100%) - 6320 spectra/s] 6.3s 008. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.mzBIN_calibrated 0.3 s [progress: 34934/34934 (100%) - 10475 spectra/s] 3.3s 009. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.mzBIN_calibrated 0.5 s [progress: 37762/37762 (100%) - 7989 spectra/s] 4.7s 010. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.mzBIN_calibrated 1.5 s [progress: 39884/39884 (100%) - 5975 spectra/s] 6.7s 011. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.mzBIN_calibrated 0.8 s [progress: 38014/38014 (100%) - 5569 spectra/s] 6.8s 012. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.mzBIN_calibrated 0.6 s [progress: 39590/39590 (100%) - 7286 spectra/s] 5.4s 013. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.mzBIN_calibrated 0.9 s [progress: 35781/35781 (100%) - 9516 spectra/s] 3.8s 014. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.mzBIN_calibrated 0.5 s [progress: 38309/38309 (100%) - 10116 spectra/s] 3.8s 015. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.mzBIN_calibrated 0.6 s [progress: 40218/40218 (100%) - 6651 spectra/s] 6.0s 016. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.mzBIN_calibrated 1.0 s [progress: 37400/37400 (100%) - 5409 spectra/s] 6.9s 017. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.mzBIN_calibrated 0.6 s [progress: 38969/38969 (100%) - 6716 spectra/s] 5.8s 018. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.mzBIN_calibrated 0.3 s [progress: 34666/34666 (100%) - 6328 spectra/s] 5.5s 019. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.mzBIN_calibrated 0.5 s [progress: 37618/37618 (100%) - 7880 spectra/s] 4.8s 020. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.mzBIN_calibrated 0.5 s [progress: 38981/38981 (100%) - 4523 spectra/s] 8.6s Operating on slice 5 of 9: Fragment index slice generated in 68.35 s 001. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.mzBIN_calibrated 0.6 s [progress: 38967/38967 (100%) - 7939 spectra/s] 4.9s 002. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.mzBIN_calibrated 0.6 s [progress: 40508/40508 (100%) - 4396 spectra/s] 9.2s 003. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.mzBIN_calibrated 0.4 s [progress: 36256/36256 (100%) - 15454 spectra/s] 2.3s 004. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.mzBIN_calibrated 0.6 s [progress: 39294/39294 (100%) - 10091 spectra/s] 3.9s 005. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.mzBIN_calibrated 0.6 s [progress: 40522/40522 (100%) - 7258 spectra/s] 5.6s 006. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.mzBIN_calibrated 0.5 s [progress: 38087/38087 (100%) - 4308 spectra/s] 8.8s 007. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.mzBIN_calibrated 0.5 s [progress: 39586/39586 (100%) - 4920 spectra/s] 8.0s 008. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.mzBIN_calibrated 0.3 s [progress: 34934/34934 (100%) - 11786 spectra/s] 3.0s 009. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.mzBIN_calibrated 0.5 s [progress: 37762/37762 (100%) - 7910 spectra/s] 4.8s 010. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.mzBIN_calibrated 1.6 s [progress: 39884/39884 (100%) - 6585 spectra/s] 6.1s 011. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.mzBIN_calibrated 1.5 s [progress: 38014/38014 (100%) - 7317 spectra/s] 5.2s 012. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.mzBIN_calibrated 0.5 s [progress: 39590/39590 (100%) - 5649 spectra/s] 7.0s 013. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.mzBIN_calibrated 0.6 s [progress: 35781/35781 (100%) - 11023 spectra/s] 3.2s 014. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.mzBIN_calibrated 0.5 s [progress: 38309/38309 (100%) - 10880 spectra/s] 3.5s 015. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.mzBIN_calibrated 0.6 s [progress: 40218/40218 (100%) - 5266 spectra/s] 7.6s 016. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.mzBIN_calibrated 0.5 s [progress: 37400/37400 (100%) - 6652 spectra/s] 5.6s 017. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.mzBIN_calibrated 0.6 s [progress: 38969/38969 (100%) - 4891 spectra/s] 8.0s 018. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.mzBIN_calibrated 0.3 s [progress: 34666/34666 (100%) - 11281 spectra/s] 3.1s 019. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.mzBIN_calibrated 0.6 s [progress: 37618/37618 (100%) - 7896 spectra/s] 4.8s 020. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.mzBIN_calibrated 0.5 s [progress: 38981/38981 (100%) - 5769 spectra/s] 6.8s Operating on slice 6 of 9: Fragment index slice generated in 68.28 s 001. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.mzBIN_calibrated 0.5 s [progress: 38967/38967 (100%) - 9180 spectra/s] 4.2s 002. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.mzBIN_calibrated 0.7 s [progress: 40508/40508 (100%) - 8071 spectra/s] 5.0s 003. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.mzBIN_calibrated 1.3 s [progress: 36256/36256 (100%) - 18517 spectra/s] 2.0s 004. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.mzBIN_calibrated 0.4 s [progress: 39294/39294 (100%) - 10075 spectra/s] 3.9s 005. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.mzBIN_calibrated 1.5 s [progress: 40522/40522 (100%) - 6707 spectra/s] 6.0s 006. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.mzBIN_calibrated 0.5 s [progress: 38087/38087 (100%) - 5452 spectra/s] 7.0s 007. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.mzBIN_calibrated 1.5 s [progress: 39586/39586 (100%) - 5287 spectra/s] 7.5s 008. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.mzBIN_calibrated 0.6 s [progress: 34934/34934 (100%) - 10314 spectra/s] 3.4s 009. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.mzBIN_calibrated 0.5 s [progress: 37762/37762 (100%) - 8927 spectra/s] 4.2s 010. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.mzBIN_calibrated 0.6 s [progress: 39884/39884 (100%) - 6433 spectra/s] 6.2s 011. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.mzBIN_calibrated 0.7 s [progress: 38014/38014 (100%) - 7007 spectra/s] 5.4s 012. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.mzBIN_calibrated 1.1 s [progress: 39590/39590 (100%) - 7931 spectra/s] 5.0s 013. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.mzBIN_calibrated 0.4 s [progress: 35781/35781 (100%) - 12666 spectra/s] 2.8s 014. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.mzBIN_calibrated 0.5 s [progress: 38309/38309 (100%) - 10510 spectra/s] 3.6s 015. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.mzBIN_calibrated 0.8 s [progress: 40218/40218 (100%) - 5946 spectra/s] 6.8s 016. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.mzBIN_calibrated 0.5 s [progress: 37400/37400 (100%) - 8376 spectra/s] 4.5s 017. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.mzBIN_calibrated 0.5 s [progress: 38969/38969 (100%) - 6444 spectra/s] 6.0s 018. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.mzBIN_calibrated 0.3 s [progress: 34666/34666 (100%) - 16650 spectra/s] 2.1s 019. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.mzBIN_calibrated 1.0 s [progress: 37618/37618 (100%) - 5192 spectra/s] 7.2s 020. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.mzBIN_calibrated 0.6 s [progress: 38981/38981 (100%) - 7702 spectra/s] 5.1s Operating on slice 7 of 9: Fragment index slice generated in 68.94 s 001. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.mzBIN_calibrated 0.5 s [progress: 38967/38967 (100%) - 9128 spectra/s] 4.3s 002. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.mzBIN_calibrated 1.5 s [progress: 40508/40508 (100%) - 7348 spectra/s] 5.5s 003. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.mzBIN_calibrated 1.3 s [progress: 36256/36256 (100%) - 19492 spectra/s] 1.9s 004. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.mzBIN_calibrated 0.5 s [progress: 39294/39294 (100%) - 10034 spectra/s] 3.9s 005. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.mzBIN_calibrated 1.6 s [progress: 40522/40522 (100%) - 7005 spectra/s] 5.8s 006. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.mzBIN_calibrated 0.5 s [progress: 38087/38087 (100%) - 6117 spectra/s] 6.2s 007. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.mzBIN_calibrated 0.6 s [progress: 39586/39586 (100%) - 7240 spectra/s] 5.5s 008. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.mzBIN_calibrated 0.4 s [progress: 34934/34934 (100%) - 11838 spectra/s] 3.0s 009. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.mzBIN_calibrated 0.7 s [progress: 37762/37762 (100%) - 12146 spectra/s] 3.1s 010. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.mzBIN_calibrated 0.6 s [progress: 39884/39884 (100%) - 8513 spectra/s] 4.7s 011. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.mzBIN_calibrated 0.5 s [progress: 38014/38014 (100%) - 10455 spectra/s] 3.6s 012. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.mzBIN_calibrated 1.5 s [progress: 39590/39590 (100%) - 10345 spectra/s] 3.8s 013. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.mzBIN_calibrated 1.2 s [progress: 35781/35781 (100%) - 12023 spectra/s] 3.0s 014. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.mzBIN_calibrated 0.5 s [progress: 38309/38309 (100%) - 15929 spectra/s] 2.4s 015. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.mzBIN_calibrated 1.2 s [progress: 40218/40218 (100%) - 6835 spectra/s] 5.9s 016. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.mzBIN_calibrated 0.7 s [progress: 37400/37400 (100%) - 9383 spectra/s] 4.0s 017. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.mzBIN_calibrated 0.5 s [progress: 38969/38969 (100%) - 10828 spectra/s] 3.6s 018. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.mzBIN_calibrated 0.3 s [progress: 34666/34666 (100%) - 13933 spectra/s] 2.5s 019. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.mzBIN_calibrated 0.4 s [progress: 37618/37618 (100%) - 13774 spectra/s] 2.7s 020. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.mzBIN_calibrated 0.5 s [progress: 38981/38981 (100%) - 8303 spectra/s] 4.7s Operating on slice 8 of 9: Fragment index slice generated in 59.70 s 001. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.mzBIN_calibrated 0.8 s [progress: 38967/38967 (100%) - 10444 spectra/s] 3.7s 002. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.mzBIN_calibrated 0.6 s [progress: 40508/40508 (100%) - 8131 spectra/s] 5.0s 003. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.mzBIN_calibrated 0.5 s [progress: 36256/36256 (100%) - 20437 spectra/s] 1.8s 004. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.mzBIN_calibrated 1.0 s [progress: 39294/39294 (100%) - 16692 spectra/s] 2.4s 005. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.mzBIN_calibrated 0.8 s [progress: 40522/40522 (100%) - 8798 spectra/s] 4.6s 006. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.mzBIN_calibrated 0.5 s [progress: 38087/38087 (100%) - 8519 spectra/s] 4.5s 007. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.mzBIN_calibrated 1.0 s [progress: 39586/39586 (100%) - 7597 spectra/s] 5.2s 008. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.mzBIN_calibrated 0.4 s [progress: 34934/34934 (100%) - 13519 spectra/s] 2.6s 009. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.mzBIN_calibrated 0.5 s [progress: 37762/37762 (100%) - 10569 spectra/s] 3.6s 010. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.mzBIN_calibrated 1.0 s [progress: 39884/39884 (100%) - 7267 spectra/s] 5.5s 011. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.mzBIN_calibrated 0.9 s [progress: 38014/38014 (100%) - 7755 spectra/s] 4.9s 012. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.mzBIN_calibrated 0.8 s [progress: 39590/39590 (100%) - 9922 spectra/s] 4.0s 013. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.mzBIN_calibrated 0.4 s [progress: 35781/35781 (100%) - 14903 spectra/s] 2.4s 014. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.mzBIN_calibrated 0.6 s [progress: 38309/38309 (100%) - 12282 spectra/s] 3.1s 015. 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4.9s | remapping alternative proteins and postprocessing 18.2 s 002. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.mzBIN_calibrated 0.5 s [progress: 40508/40508 (100%) - 5805 spectra/s] 7.0s | remapping alternative proteins and postprocessing 13.9 s 003. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.mzBIN_calibrated 0.8 s [progress: 36256/36256 (100%) - 12593 spectra/s] 2.9s | remapping alternative proteins and postprocessing 10.4 s 004. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.mzBIN_calibrated 1.0 s [progress: 39294/39294 (100%) - 9480 spectra/s] 4.1s | remapping alternative proteins and postprocessing 12.3 s 005. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.mzBIN_calibrated 1.2 s [progress: 40522/40522 (100%) - 5692 spectra/s] 7.1s | remapping alternative proteins and postprocessing 8.4 s 006. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.mzBIN_calibrated 0.5 s [progress: 38087/38087 (100%) - 12545 spectra/s] 3.0s | remapping alternative proteins and postprocessing 6.3 s 007. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.mzBIN_calibrated 0.5 s [progress: 39586/39586 (100%) - 10987 spectra/s] 3.6s | remapping alternative proteins and postprocessing 6.5 s 008. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.mzBIN_calibrated 0.9 s [progress: 34934/34934 (100%) - 22758 spectra/s] 1.5s | remapping alternative proteins and postprocessing 5.7 s 009. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.mzBIN_calibrated 0.6 s [progress: 37762/37762 (100%) - 8200 spectra/s] 4.6s | remapping alternative proteins and postprocessing 6.4 s 010. 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.mzBIN_calibrated 0.6 s [progress: 39884/39884 (100%) - 11386 spectra/s] 3.5s | remapping alternative proteins and postprocessing 6.9 s 011. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.mzBIN_calibrated 0.5 s [progress: 38014/38014 (100%) - 8755 spectra/s] 4.3s | remapping alternative proteins and postprocessing 12.0 s 012. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.mzBIN_calibrated 0.6 s [progress: 39590/39590 (100%) - 7344 spectra/s] 5.4s | remapping alternative proteins and postprocessing 19.1 s 013. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.mzBIN_calibrated 0.4 s [progress: 35781/35781 (100%) - 18724 spectra/s] 1.9s | remapping alternative proteins and postprocessing 8.6 s 014. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.mzBIN_calibrated 0.5 s [progress: 38309/38309 (100%) - 9914 spectra/s] 3.9s | remapping alternative proteins and postprocessing 9.3 s 015. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.mzBIN_calibrated 0.5 s [progress: 40218/40218 (100%) - 8601 spectra/s] 4.7s | remapping alternative proteins and postprocessing 10.5 s 016. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.mzBIN_calibrated 1.7 s [progress: 37400/37400 (100%) - 7190 spectra/s] 5.2s | remapping alternative proteins and postprocessing 9.1 s 017. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.mzBIN_calibrated 0.5 s [progress: 38969/38969 (100%) - 7950 spectra/s] 4.9s | remapping alternative proteins and postprocessing 9.3 s 018. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.mzBIN_calibrated 0.3 s [progress: 34666/34666 (100%) - 9222 spectra/s] 3.8s | remapping alternative proteins and postprocessing 8.2 s 019. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.mzBIN_calibrated 0.5 s [progress: 37618/37618 (100%) - 9944 spectra/s] 3.8s | remapping alternative proteins and postprocessing 8.5 s 020. 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.mzBIN_calibrated 0.6 s [progress: 38981/38981 (100%) - 7453 spectra/s] 5.2s | remapping alternative proteins and postprocessing 11.9 s ***************************MAIN SEARCH DONE IN 36.763 MIN*************************** *******************************TOTAL TIME 76.147 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.pepXML G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.pin G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.pepXML G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/E:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.pin G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx181G -cp E:\FragPipe-jre-21.1\fragpipe\tools\msbooster-1.1.28.jar;E:\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar Features.MainClass --paramsList G:\Juanjuan_2\WDR33i\msbooster_params.txt MSBooster v1.1.28 Using 20 threads 319163 unique peptides from 603567 PSMs createFull input file generation took 8209 milliseconds Input file at G:\Juanjuan_2\WDR33i\2\spectraRT_full.tsv Generating input file for DIA-NN 276289 unique peptides from 603567 PSMs Writing DIA-NN input file Diann input file generation took 7486 milliseconds Input file at G:\Juanjuan_2\WDR33i\2\spectraRT.tsv Generating DIA-NN predictions "C:\Users\KBH Universitet\Downloads\FragPipe-jre-21.1\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe" --lib G:\Juanjuan_2\WDR33i\2\spectraRT.tsv --predict --threads 20 --strip-unknown-mods --predict-n-frag 100 DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks) Compiled on Sep 15 2022 18:28:57 Current date and time: Thu Apr 11 14:17:43 2024 CPU: AuthenticAMD AMD Ryzen Threadripper 3990X 64-Core Processor SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 SSE4a Logical CPU cores: 64 Predicted spectra will be saved in a binary format Thread number set to 20 DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option Deep learning predictor will predict 100 fragments 0 files will be processed [0:00] Loading spectral library G:\Juanjuan_2\WDR33i\2\spectraRT.tsv [0:01] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) [0:01] Spectral library loaded: 0 protein isoforms, 0 protein groups and 276289 precursors in 265276 elution groups. [0:02] Encoding peptides for spectra and RTs prediction [0:03] Predicting spectra and IMs [2:35] Predicting RTs [3:27] Decoding predicted spectra and IMs [3:35] Decoding RTs [3:35] Saving the list of predictions to G:\Juanjuan_2\WDR33i\2\spectraRT.predicted.bin Finished Done generating DIA-NN predictions Model running took 217426 milliseconds Generating edited pin with following features: [unweightedSpectralEntropy, deltaRTLOESS] Loading predicted spectra Processing K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_edited.pin Processing K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_edited.pin Processing K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_edited.pin Processing K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_edited.pin Processing K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_edited.pin Processing K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_edited.pin Processing K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_edited.pin Processing K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 4793 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_edited.pin Processing K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_edited.pin Processing K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_edited.pin Processing K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_edited.pin Processing K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_edited.pin Processing K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_edited.pin Processing K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_edited.pin Processing K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_edited.pin Processing K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_edited.pin Processing K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_edited.pin Processing K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_edited.pin Processing K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_edited.pin Processing K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_edited.pin Feature calculation and edited pin writing done in 120806 ms Process 'MSBooster' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_edited.pin Started Thu Apr 11 14:23:22 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 32080 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 23651 positives and 8429 negatives, size ratio=2.80591 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 10020 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 9949 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 9923 training set positives with q<0.01 in that direction. Found 14933 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 1.6510 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 15573 PSMs with q<0.01 Iteration 2: Estimated 15680 PSMs with q<0.01 Iteration 3: Estimated 15705 PSMs with q<0.01 Iteration 4: Estimated 15718 PSMs with q<0.01 Iteration 5: Estimated 15717 PSMs with q<0.01 Iteration 6: Estimated 15713 PSMs with q<0.01 Iteration 7: Estimated 15714 PSMs with q<0.01 Iteration 8: Estimated 15716 PSMs with q<0.01 Iteration 9: Estimated 15714 PSMs with q<0.01 Iteration 10: Estimated 15712 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 0.2881 0.0816 0.1174 abs_ppm -0.1329 -0.0161 -0.0543 isotope_errors -0.3565 -1.6729 -1.6885 log10_evalue -0.7038 -1.5064 -0.5086 hyperscore 1.8258 1.3660 1.3403 delta_hyperscore 2.9995 2.4343 2.1702 matched_ion_num -0.9977 -1.0040 -1.3170 complementary_ions -0.0234 -0.0406 0.0393 ion_series -1.1760 -1.0751 -1.1708 weighted_average_abs_fragment_ppm -0.0633 -0.0711 -0.0866 length_7 -0.1021 -0.0581 -0.0800 length_8 -0.0499 -0.0563 -0.0283 length_9_30 0.0958 0.0916 0.0728 length_31 0.0000 0.0000 0.0000 ntt -0.1105 -0.0194 0.0142 nmc 0.0000 0.0000 0.0000 charge_1 0.0944 0.0610 0.0803 charge_2 0.0547 -0.0314 -0.0249 charge_3 -0.1298 0.0093 -0.0343 charge_4 -0.0925 -0.1075 0.0031 charge_5 0.0555 0.0979 -0.0996 charge_6 -0.0347 -0.0280 -0.0394 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 -0.1903 -0.0832 -0.2142 10.008269R -0.0097 -0.0658 -0.0129 15.9949M -0.0397 -0.0336 -0.1673 4.025107K -0.0691 0.0349 0.0164 6.020129R 0.2747 0.3216 0.2786 79.96633STY 0.0653 -0.0100 -0.0058 8.014199K 1.5961 1.2614 1.4311 unweighted_spectral_entropy -0.7291 -0.9758 -0.9736 delta_RT_loess 0.8456 0.6828 0.9607 m0 Found 15664 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 23651 target PSMs and 8429 decoy PSMs. Calculating q values. Final list yields 15667 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 8.8350 cpu seconds or 9 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_edited.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_edited.pin Started Thu Apr 11 14:23:33 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 24897 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 18255 positives and 6642 negatives, size ratio=2.74842 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 7318 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 7236 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 7247 training set positives with q<0.01 in that direction. Found 10904 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.3730 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 11638 PSMs with q<0.01 Iteration 2: Estimated 11762 PSMs with q<0.01 Iteration 3: Estimated 11813 PSMs with q<0.01 Iteration 4: Estimated 11837 PSMs with q<0.01 Iteration 5: Estimated 11850 PSMs with q<0.01 Iteration 6: Estimated 11854 PSMs with q<0.01 Iteration 7: Estimated 11854 PSMs with q<0.01 Iteration 8: Estimated 11852 PSMs with q<0.01 Iteration 9: Estimated 11854 PSMs with q<0.01 Iteration 10: Estimated 11854 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 -0.2098 -0.1787 -0.2304 abs_ppm 0.0299 0.0509 0.0723 isotope_errors -0.7379 -0.7445 -0.7698 log10_evalue 0.2544 -0.0029 -0.0559 hyperscore 0.8540 0.8831 0.9693 delta_hyperscore 1.1506 0.9735 0.9748 matched_ion_num -0.6641 -0.6298 -0.4830 complementary_ions 0.0004 -0.1622 -0.0724 ion_series -1.1307 -0.8100 -0.9387 weighted_average_abs_fragment_ppm -0.0814 -0.0558 -0.0775 length_7 -0.1908 -0.1481 -0.1241 length_8 0.0090 0.0150 0.0218 length_9_30 0.1456 0.1000 0.0871 length_31 0.0000 0.0000 0.0000 ntt -0.3422 -0.3092 -0.1313 nmc 0.0000 0.0000 0.0000 charge_1 -0.0337 -0.0332 -0.0590 charge_2 0.0154 0.0032 -0.0127 charge_3 0.0372 0.0399 0.1139 charge_4 0.0088 0.0852 0.1311 charge_5 0.0030 0.0026 0.0058 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.1172 -0.0681 -0.1467 10.008269R 0.0636 0.0806 0.0498 15.9949M -0.1179 0.0186 -0.1294 4.025107K -0.0063 -0.0819 -0.1017 6.020129R 0.3892 0.3228 0.3204 79.96633STY 0.0112 0.0545 -0.0264 8.014199K 1.3285 1.2387 1.2705 unweighted_spectral_entropy -1.4220 -1.1815 -1.1219 delta_RT_loess -0.1373 -0.1199 -0.2638 m0 Found 11818 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 18255 target PSMs and 6642 decoy PSMs. Calculating q values. Final list yields 11822 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 3.3330 cpu seconds or 3 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_edited.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_edited.pin Started Thu Apr 11 14:23:37 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 30201 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 22399 positives and 7802 negatives, size ratio=2.87093 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 9641 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 9435 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 9525 training set positives with q<0.01 in that direction. Found 14275 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.4630 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 14977 PSMs with q<0.01 Iteration 2: Estimated 15075 PSMs with q<0.01 Iteration 3: Estimated 15107 PSMs with q<0.01 Iteration 4: Estimated 15121 PSMs with q<0.01 Iteration 5: Estimated 15136 PSMs with q<0.01 Iteration 6: Estimated 15134 PSMs with q<0.01 Iteration 7: Estimated 15137 PSMs with q<0.01 Iteration 8: Estimated 15138 PSMs with q<0.01 Iteration 9: Estimated 15136 PSMs with q<0.01 Iteration 10: Estimated 15139 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 -0.1500 -0.3496 -0.2594 abs_ppm -0.0836 0.0565 0.0156 isotope_errors -0.6438 -0.7146 -0.5803 log10_evalue -0.4963 0.3867 0.2925 hyperscore 1.7604 1.0905 0.9527 delta_hyperscore 2.4312 0.8535 1.1048 matched_ion_num -1.2332 -0.8149 -0.8369 complementary_ions -0.1309 -0.2249 -0.2032 ion_series -0.7131 -0.7990 -0.8367 weighted_average_abs_fragment_ppm -0.0305 -0.0711 -0.0667 length_7 -0.0033 -0.0509 -0.0441 length_8 -0.0215 -0.0530 -0.0419 length_9_30 0.0328 0.0956 0.0800 length_31 0.0000 0.0000 0.0000 ntt -0.0563 -0.0624 -0.1364 nmc 0.0000 0.0000 0.0000 charge_1 0.0007 0.0899 0.0232 charge_2 0.0259 -0.0628 -0.0366 charge_3 -0.0240 -0.0418 0.0357 charge_4 -0.0846 -0.0420 -0.0366 charge_5 -0.0285 -0.0141 -0.0123 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.1183 -0.1387 -0.1853 10.008269R 0.2118 0.0143 0.0591 15.9949M 0.0848 -0.0105 0.0186 4.025107K -0.0668 -0.1280 -0.0722 6.020129R 0.2867 0.2547 0.2717 79.96633STY 0.0587 -0.0532 0.0017 8.014199K 1.5808 1.1914 1.1733 unweighted_spectral_entropy -0.4879 -0.6029 -0.4444 delta_RT_loess 1.1669 0.5789 0.5052 m0 Found 15091 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 22399 target PSMs and 7802 decoy PSMs. Calculating q values. Final list yields 15094 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 3.6330 cpu seconds or 4 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_edited.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_edited.pin Started Thu Apr 11 14:23:42 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 30323 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 22986 positives and 7337 negatives, size ratio=3.13289 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 10253 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 10133 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 10077 training set positives with q<0.01 in that direction. Found 15238 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.5360 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 15966 PSMs with q<0.01 Iteration 2: Estimated 16096 PSMs with q<0.01 Iteration 3: Estimated 16144 PSMs with q<0.01 Iteration 4: Estimated 16166 PSMs with q<0.01 Iteration 5: Estimated 16168 PSMs with q<0.01 Iteration 6: Estimated 16172 PSMs with q<0.01 Iteration 7: Estimated 16174 PSMs with q<0.01 Iteration 8: Estimated 16174 PSMs with q<0.01 Iteration 9: Estimated 16174 PSMs with q<0.01 Iteration 10: Estimated 16174 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 -0.0857 -0.1625 -0.1172 abs_ppm -0.0402 -0.0415 -0.0916 isotope_errors -1.6492 -1.0313 -0.8044 log10_evalue -0.6630 -0.7527 -0.9461 hyperscore 0.8304 0.9698 1.0080 delta_hyperscore 1.4417 1.6754 1.7339 matched_ion_num -0.9953 -0.8160 -0.8555 complementary_ions 0.1094 0.2125 0.3459 ion_series -0.7725 -0.6234 -0.5792 weighted_average_abs_fragment_ppm -0.0564 -0.0761 -0.0831 length_7 -0.0379 -0.0706 -0.0794 length_8 0.0201 0.0406 0.0029 length_9_30 0.0233 0.0266 0.0781 length_31 0.0000 0.0000 0.0000 ntt -0.0256 -0.1874 -0.0910 nmc 0.0000 0.0000 0.0000 charge_1 -0.0049 -0.1102 -0.0039 charge_2 0.0497 0.0700 0.0722 charge_3 -0.0323 0.0753 -0.1027 charge_4 -0.0906 0.0012 -0.0093 charge_5 -0.0255 -0.0236 -0.0155 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.0685 -0.0637 -0.1285 10.008269R -0.0786 -0.1311 -0.0786 15.9949M 0.0553 -0.0666 -0.0390 4.025107K -0.1011 -0.0046 -0.0613 6.020129R 0.2892 0.3376 0.2723 79.96633STY -0.0120 -0.0225 -0.0171 8.014199K 1.3028 1.3418 1.3145 unweighted_spectral_entropy -1.2388 -1.2884 -1.4009 delta_RT_loess 0.7609 0.7044 0.4620 m0 Found 16154 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 22986 target PSMs and 7337 decoy PSMs. Calculating q values. Final list yields 16154 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 3.9790 cpu seconds or 4 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_edited.pin Started Thu Apr 11 14:23:48 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 34774 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 25789 positives and 8985 negatives, size ratio=2.87023 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 11030 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 11052 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 11056 training set positives with q<0.01 in that direction. Found 16554 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.6210 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 17095 PSMs with q<0.01 Iteration 2: Estimated 17239 PSMs with q<0.01 Iteration 3: Estimated 17285 PSMs with q<0.01 Iteration 4: Estimated 17307 PSMs with q<0.01 Iteration 5: Estimated 17317 PSMs with q<0.01 Iteration 6: Estimated 17320 PSMs with q<0.01 Iteration 7: Estimated 17323 PSMs with q<0.01 Iteration 8: Estimated 17327 PSMs with q<0.01 Iteration 9: Estimated 17325 PSMs with q<0.01 Iteration 10: Estimated 17328 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 -0.0091 0.0902 -0.1269 abs_ppm -0.0082 -0.0987 -0.0331 isotope_errors -0.8195 -1.7016 -1.6548 log10_evalue 0.1782 -0.6682 -0.9018 hyperscore 0.7105 0.4779 0.8709 delta_hyperscore 1.2142 2.0754 2.1973 matched_ion_num -0.5848 -0.8488 -0.9913 complementary_ions 0.1549 0.2205 0.1595 ion_series -1.0162 -1.1199 -1.4278 weighted_average_abs_fragment_ppm -0.0571 -0.0827 -0.1255 length_7 -0.0857 -0.0790 -0.1308 length_8 -0.0322 -0.0601 -0.0848 length_9_30 0.0775 0.1118 0.1664 length_31 0.0000 0.0000 0.0000 ntt -0.1318 -0.2435 -0.3021 nmc 0.0000 0.0000 0.0000 charge_1 -0.0028 -0.0930 -0.0881 charge_2 0.0656 0.1325 0.1286 charge_3 -0.0293 -0.0199 -0.0246 charge_4 -0.0981 -0.1017 -0.1021 charge_5 -0.0423 0.0459 0.0623 charge_6 0.0114 -0.0138 0.0133 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 -0.1344 -0.1204 -0.1125 10.008269R -0.1678 -0.2050 -0.1842 15.9949M -0.0924 -0.1177 -0.1247 4.025107K -0.0034 -0.0415 0.0151 6.020129R 0.1830 0.2224 0.1501 79.96633STY -0.0752 -0.1296 -0.0417 8.014199K 0.8922 1.1325 1.1280 unweighted_spectral_entropy -0.6868 -0.9001 -0.7301 delta_RT_loess 0.6487 0.8582 0.7900 m0 Found 17302 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 25789 target PSMs and 8985 decoy PSMs. Calculating q values. Final list yields 17303 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 5.5570 cpu seconds or 6 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_edited.pin Started Thu Apr 11 14:23:55 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 29083 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 21839 positives and 7244 negatives, size ratio=3.01477 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 9340 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 9313 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 9376 training set positives with q<0.01 in that direction. Found 13986 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.4760 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 14935 PSMs with q<0.01 Iteration 2: Estimated 15123 PSMs with q<0.01 Iteration 3: Estimated 15158 PSMs with q<0.01 Iteration 4: Estimated 15171 PSMs with q<0.01 Iteration 5: Estimated 15177 PSMs with q<0.01 Iteration 6: Estimated 15177 PSMs with q<0.01 Iteration 7: Estimated 15178 PSMs with q<0.01 Iteration 8: Estimated 15179 PSMs with q<0.01 Iteration 9: Estimated 15178 PSMs with q<0.01 Iteration 10: Estimated 15174 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 -0.0785 -0.0639 -0.1797 abs_ppm -0.0116 0.0987 0.0785 isotope_errors -0.2964 -0.4902 -0.7910 log10_evalue -0.0314 -0.1121 -0.7170 hyperscore 0.8979 1.0142 1.5285 delta_hyperscore 1.4929 1.0037 2.4552 matched_ion_num -0.8012 -0.6229 -1.1338 complementary_ions 0.0693 0.2691 -0.1298 ion_series -0.9724 -0.9192 -1.2319 weighted_average_abs_fragment_ppm -0.0579 -0.0725 -0.0963 length_7 -0.0486 -0.0805 -0.0686 length_8 0.0002 0.0192 -0.0665 length_9_30 0.0434 0.0427 0.1402 length_31 0.0000 0.0000 0.0000 ntt 0.0241 0.0316 0.0677 nmc 0.0000 0.0000 0.0000 charge_1 0.0692 0.1056 0.1098 charge_2 -0.0455 0.0039 0.0875 charge_3 -0.0624 -0.0941 -0.1590 charge_4 0.0204 -0.1374 -0.2416 charge_5 0.0988 0.0805 0.0872 charge_6 -0.0028 -0.0028 -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 -0.1266 -0.1218 -0.1366 10.008269R 0.0855 -0.0093 -0.0494 15.9949M -0.0786 -0.0339 -0.0958 4.025107K 0.0598 -0.0501 0.0635 6.020129R 0.3356 0.3151 0.2677 79.96633STY -0.0261 -0.0676 -0.0869 8.014199K 1.0404 1.0209 1.1832 unweighted_spectral_entropy -1.3101 -1.2895 -1.2439 delta_RT_loess 0.2101 0.2118 0.8064 m0 Found 15134 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 21839 target PSMs and 7244 decoy PSMs. Calculating q values. Final list yields 15136 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 4.9710 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_edited.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_edited.pin Started Thu Apr 11 14:24:00 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 29964 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 22248 positives and 7716 negatives, size ratio=2.88336 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 9254 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 9311 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 9282 training set positives with q<0.01 in that direction. Found 13904 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.4810 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 14605 PSMs with q<0.01 Iteration 2: Estimated 14718 PSMs with q<0.01 Iteration 3: Estimated 14761 PSMs with q<0.01 Iteration 4: Estimated 14796 PSMs with q<0.01 Iteration 5: Estimated 14821 PSMs with q<0.01 Iteration 6: Estimated 14829 PSMs with q<0.01 Iteration 7: Estimated 14833 PSMs with q<0.01 Iteration 8: Estimated 14837 PSMs with q<0.01 Iteration 9: Estimated 14840 PSMs with q<0.01 Iteration 10: Estimated 14841 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 -0.3270 -0.2073 -0.2633 abs_ppm -0.0252 0.0114 0.0244 isotope_errors -0.8953 -1.3829 -0.9273 log10_evalue -0.4766 -0.0843 0.1260 hyperscore 1.2607 0.7021 0.7738 delta_hyperscore 2.4189 1.4459 1.0410 matched_ion_num -1.2565 -1.0042 -0.7513 complementary_ions -0.0475 0.0309 0.1074 ion_series -0.9784 -0.9360 -0.7829 weighted_average_abs_fragment_ppm -0.0470 -0.0435 -0.0628 length_7 -0.0690 -0.0507 -0.0408 length_8 -0.0027 -0.0264 -0.0527 length_9_30 0.0481 0.0651 0.0959 length_31 0.0000 0.0000 0.0000 ntt 0.0450 -0.0944 -0.0531 nmc 0.0000 0.0000 0.0000 charge_1 0.1068 0.0279 0.0247 charge_2 -0.0962 -0.0188 -0.0168 charge_3 -0.0163 -0.0040 0.0015 charge_4 -0.0350 -0.0533 -0.0653 charge_5 -0.0114 -0.0118 -0.0096 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.1716 -0.1669 -0.1186 10.008269R 0.0944 0.0452 0.0526 15.9949M -0.1380 -0.1421 -0.0718 4.025107K -0.1062 -0.0355 -0.0774 6.020129R 0.2432 0.2630 0.1957 79.96633STY -0.1664 -0.0402 -0.0560 8.014199K 1.0883 1.2194 1.1260 unweighted_spectral_entropy -1.4468 -0.9864 -0.8948 delta_RT_loess 0.5279 0.5458 0.4432 m0 Found 14809 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 22248 target PSMs and 7716 decoy PSMs. Calculating q values. Final list yields 14813 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 5.4800 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_edited.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_edited.pin Started Thu Apr 11 14:24:07 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 24357 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 17788 positives and 6569 negatives, size ratio=2.70787 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 7005 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 6983 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 7043 training set positives with q<0.01 in that direction. Found 10454 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 1.4750 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 11242 PSMs with q<0.01 Iteration 2: Estimated 11358 PSMs with q<0.01 Iteration 3: Estimated 11384 PSMs with q<0.01 Iteration 4: Estimated 11406 PSMs with q<0.01 Iteration 5: Estimated 11418 PSMs with q<0.01 Iteration 6: Estimated 11418 PSMs with q<0.01 Iteration 7: Estimated 11418 PSMs with q<0.01 Iteration 8: Estimated 11417 PSMs with q<0.01 Iteration 9: Estimated 11419 PSMs with q<0.01 Iteration 10: Estimated 11419 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 -0.1253 -0.3412 -0.3145 abs_ppm -0.0364 0.0006 -0.0315 isotope_errors -0.4919 -1.0146 -0.8864 log10_evalue 0.1538 -0.5946 -0.2455 hyperscore 1.0244 1.1651 1.2010 delta_hyperscore 1.0750 2.0884 1.8401 matched_ion_num -0.7831 -0.8518 -0.8213 complementary_ions -0.1315 -0.1570 -0.2915 ion_series -0.9181 -1.3114 -1.0383 weighted_average_abs_fragment_ppm -0.0796 -0.1391 -0.0681 length_7 -0.1619 -0.1385 -0.1502 length_8 -0.0620 -0.0448 0.0324 length_9_30 0.2282 0.2227 0.0968 length_31 0.0000 0.0000 0.0000 ntt -0.1293 -0.2040 -0.1288 nmc 0.0000 0.0000 0.0000 charge_1 0.0317 0.0365 -0.0468 charge_2 0.0027 -0.0048 0.0179 charge_3 -0.0897 -0.0794 0.0773 charge_4 0.0068 -0.0039 -0.0082 charge_5 0.0025 -0.0015 -0.0031 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.1245 -0.0878 -0.0805 10.008269R 0.0489 0.1237 0.1279 15.9949M -0.1414 -0.1911 -0.0460 4.025107K -0.0324 -0.0642 -0.0242 6.020129R 0.2677 0.2393 0.2262 79.96633STY -0.0498 -0.1126 -0.0336 8.014199K 1.3037 1.2717 1.4268 unweighted_spectral_entropy -1.0039 -1.3632 -1.3436 delta_RT_loess -0.1257 0.0730 0.1513 m0 Found 11375 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 17788 target PSMs and 6569 decoy PSMs. Calculating q values. Final list yields 11378 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 4.7980 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_edited.pin Started Thu Apr 11 14:24:14 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 25521 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 19207 positives and 6314 negatives, size ratio=3.04197 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 8352 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 8154 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 8102 training set positives with q<0.01 in that direction. Found 12191 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.4560 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 12999 PSMs with q<0.01 Iteration 2: Estimated 13102 PSMs with q<0.01 Iteration 3: Estimated 13133 PSMs with q<0.01 Iteration 4: Estimated 13138 PSMs with q<0.01 Iteration 5: Estimated 13141 PSMs with q<0.01 Iteration 6: Estimated 13141 PSMs with q<0.01 Iteration 7: Estimated 13143 PSMs with q<0.01 Iteration 8: Estimated 13143 PSMs with q<0.01 Iteration 9: Estimated 13142 PSMs with q<0.01 Iteration 10: Estimated 13143 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 -0.2344 -0.1487 -0.3317 abs_ppm -0.0178 -0.0250 -0.0056 isotope_errors -0.3186 -0.9536 -0.7476 log10_evalue -0.3182 -0.4942 0.2522 hyperscore 1.0463 0.7830 0.7927 delta_hyperscore 1.9921 1.3853 0.9349 matched_ion_num -0.8357 -0.5028 -0.4612 complementary_ions -0.1799 -0.0535 0.0038 ion_series -0.9406 -0.8910 -0.9876 weighted_average_abs_fragment_ppm -0.1097 -0.1191 -0.1492 length_7 -0.1064 -0.1443 -0.1575 length_8 -0.0742 -0.0478 -0.0499 length_9_30 0.2149 0.2117 0.2381 length_31 0.0000 0.0000 0.0000 ntt -0.0109 -0.0304 -0.0315 nmc 0.0000 0.0000 0.0000 charge_1 0.1160 0.0263 0.0820 charge_2 -0.0044 -0.0372 -0.0124 charge_3 -0.2687 0.0246 -0.1649 charge_4 -0.0149 -0.0050 -0.0228 charge_5 -0.0044 -0.0015 -0.0067 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.0055 -0.0680 -0.1347 10.008269R 0.0711 0.0874 0.1096 15.9949M -0.0310 -0.0307 -0.0894 4.025107K 0.0087 -0.0114 -0.0315 6.020129R 0.2750 0.3197 0.3863 79.96633STY -0.0645 -0.0238 -0.0723 8.014199K 1.2980 1.2332 1.1923 unweighted_spectral_entropy -1.0391 -0.9962 -0.8176 delta_RT_loess 0.3140 0.1057 0.4819 m0 Found 13093 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 19207 target PSMs and 6314 decoy PSMs. Calculating q values. Final list yields 13094 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 5.2970 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_edited.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_edited.pin Started Thu Apr 11 14:24:20 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 31205 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 22733 positives and 8472 negatives, size ratio=2.68331 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 9414 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 9438 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 9407 training set positives with q<0.01 in that direction. Found 14125 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 1.6810 cpu seconds or 2 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 14666 PSMs with q<0.01 Iteration 2: Estimated 14766 PSMs with q<0.01 Iteration 3: Estimated 14784 PSMs with q<0.01 Iteration 4: Estimated 14802 PSMs with q<0.01 Iteration 5: Estimated 14810 PSMs with q<0.01 Iteration 6: Estimated 14811 PSMs with q<0.01 Iteration 7: Estimated 14816 PSMs with q<0.01 Iteration 8: Estimated 14815 PSMs with q<0.01 Iteration 9: Estimated 14815 PSMs with q<0.01 Iteration 10: Estimated 14816 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 0.0909 0.0528 -0.0241 abs_ppm 0.0341 0.0820 0.0473 isotope_errors -2.3065 -1.7363 -1.7909 log10_evalue -0.9861 -0.7309 -0.4563 hyperscore 0.2400 0.5617 0.2435 delta_hyperscore 1.7254 1.1404 1.2087 matched_ion_num -1.0265 -0.9053 -0.9132 complementary_ions -0.3228 0.0519 -0.1416 ion_series -1.0370 -1.0164 -1.1037 weighted_average_abs_fragment_ppm -0.1091 -0.1594 -0.1043 length_7 -0.1263 -0.1388 -0.0875 length_8 -0.0589 -0.0679 -0.0724 length_9_30 0.1160 0.1387 0.1185 length_31 0.0000 0.0000 0.0000 ntt -0.1343 -0.1281 -0.0378 nmc 0.0000 0.0000 0.0000 charge_1 0.0302 0.0403 0.0079 charge_2 0.0308 0.0984 0.0806 charge_3 -0.0959 -0.1648 -0.1002 charge_4 0.0265 0.0245 0.0138 charge_5 0.0515 -0.0553 -0.0629 charge_6 -0.0060 -0.0092 0.0001 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 -0.1268 -0.1453 -0.1854 10.008269R -0.0833 -0.0293 -0.0355 15.9949M 0.0408 -0.0683 0.0013 4.025107K -0.0291 -0.0455 -0.0243 6.020129R 0.3077 0.2564 0.2931 79.96633STY -0.1754 -0.1503 -0.0348 8.014199K 1.7341 1.8465 1.6444 unweighted_spectral_entropy -1.1722 -0.7549 -0.5314 delta_RT_loess 0.1983 0.3059 -0.0046 m0 Found 14775 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 22733 target PSMs and 8472 decoy PSMs. Calculating q values. Final list yields 14776 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 5.4600 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_edited.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_edited.pin Started Thu Apr 11 14:24:28 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 32850 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 24525 positives and 8325 negatives, size ratio=2.94595 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 10553 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 10646 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 10711 training set positives with q<0.01 in that direction. Found 15932 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.5270 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 16531 PSMs with q<0.01 Iteration 2: Estimated 16660 PSMs with q<0.01 Iteration 3: Estimated 16710 PSMs with q<0.01 Iteration 4: Estimated 16723 PSMs with q<0.01 Iteration 5: Estimated 16726 PSMs with q<0.01 Iteration 6: Estimated 16728 PSMs with q<0.01 Iteration 7: Estimated 16732 PSMs with q<0.01 Iteration 8: Estimated 16734 PSMs with q<0.01 Iteration 9: Estimated 16737 PSMs with q<0.01 Iteration 10: Estimated 16737 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 -0.0790 0.0132 -0.0550 abs_ppm 0.0063 0.0409 0.0526 isotope_errors -1.1325 -2.4247 -1.9101 log10_evalue 0.1433 -0.3870 0.5578 hyperscore 0.3788 0.5049 0.4002 delta_hyperscore 0.9640 1.1114 0.7210 matched_ion_num -0.6813 -0.6664 -0.7977 complementary_ions 0.0100 0.1126 0.1947 ion_series -1.0604 -1.1689 -1.0676 weighted_average_abs_fragment_ppm -0.0788 -0.1039 -0.0962 length_7 -0.1034 -0.1136 -0.1009 length_8 -0.0397 -0.0416 -0.0312 length_9_30 0.0937 0.1052 0.0884 length_31 0.0000 0.0000 0.0000 ntt -0.0684 -0.1097 -0.1349 nmc 0.0000 0.0000 0.0000 charge_1 0.0082 -0.0751 0.0304 charge_2 0.0499 0.0821 0.0287 charge_3 -0.0650 0.0195 -0.0315 charge_4 0.0069 -0.0254 -0.0320 charge_5 -0.0376 -0.0946 -0.0913 charge_6 -0.0111 -0.0280 -0.0270 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 -0.0950 -0.1246 -0.0755 10.008269R -0.0866 -0.0875 -0.1616 15.9949M -0.0740 -0.2059 -0.1598 4.025107K -0.0995 -0.0633 0.0010 6.020129R 0.1702 0.1916 0.2334 79.96633STY -0.1290 -0.1044 -0.2291 8.014199K 1.0465 1.3100 1.1174 unweighted_spectral_entropy -0.7992 -0.9906 -0.9720 delta_RT_loess 0.4299 1.0819 1.0447 m0 Found 16714 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 24525 target PSMs and 8325 decoy PSMs. Calculating q values. Final list yields 16717 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 5.9050 cpu seconds or 6 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_edited.pin Started Thu Apr 11 14:24:35 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 30375 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 23092 positives and 7283 negatives, size ratio=3.17067 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 10335 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 10174 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 10243 training set positives with q<0.01 in that direction. Found 15380 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 1.0840 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 16052 PSMs with q<0.01 Iteration 2: Estimated 16132 PSMs with q<0.01 Iteration 3: Estimated 16166 PSMs with q<0.01 Iteration 4: Estimated 16177 PSMs with q<0.01 Iteration 5: Estimated 16185 PSMs with q<0.01 Iteration 6: Estimated 16188 PSMs with q<0.01 Iteration 7: Estimated 16187 PSMs with q<0.01 Iteration 8: Estimated 16190 PSMs with q<0.01 Iteration 9: Estimated 16193 PSMs with q<0.01 Iteration 10: Estimated 16192 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 -0.0787 -0.0061 -0.0816 abs_ppm -0.0051 -0.0422 -0.0341 isotope_errors -0.5628 -0.9582 -1.4054 log10_evalue 0.1844 -0.4172 0.2364 hyperscore 0.8603 0.8567 0.9174 delta_hyperscore 0.5857 1.5617 0.6869 matched_ion_num -0.5657 -0.7904 -0.8066 complementary_ions 0.1374 0.1310 0.0541 ion_series -0.8379 -0.9669 -0.7964 weighted_average_abs_fragment_ppm -0.0585 -0.1066 -0.0697 length_7 0.0087 -0.0809 -0.0260 length_8 0.0731 -0.0167 0.0340 length_9_30 -0.0628 0.1007 0.0024 length_31 0.0000 0.0000 0.0000 ntt -0.0913 -0.0473 -0.0470 nmc 0.0000 0.0000 0.0000 charge_1 -0.0156 0.0149 0.0487 charge_2 -0.0050 -0.0023 -0.0141 charge_3 0.0048 -0.0349 -0.0884 charge_4 0.0732 0.0447 0.0901 charge_5 -0.0129 -0.0267 -0.0343 charge_6 -0.0019 -0.0039 -0.0050 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 -0.0623 -0.1250 -0.0710 10.008269R -0.0014 -0.0125 0.0816 15.9949M -0.0935 -0.1296 -0.0024 4.025107K -0.0681 -0.0381 -0.0141 6.020129R 0.2648 0.3907 0.3352 79.96633STY -0.0795 -0.0397 -0.0506 8.014199K 1.0337 1.3195 1.2801 unweighted_spectral_entropy -1.1977 -1.1245 -1.1892 delta_RT_loess 0.3286 0.6789 0.8724 m0 Found 16136 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 23092 target PSMs and 7283 decoy PSMs. Calculating q values. Final list yields 16137 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 4.8250 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_edited.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_edited.pin Started Thu Apr 11 14:24:42 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 29295 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 22199 positives and 7096 negatives, size ratio=3.12838 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 9746 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 9757 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 9774 training set positives with q<0.01 in that direction. Found 14586 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.4640 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 15283 PSMs with q<0.01 Iteration 2: Estimated 15391 PSMs with q<0.01 Iteration 3: Estimated 15440 PSMs with q<0.01 Iteration 4: Estimated 15456 PSMs with q<0.01 Iteration 5: Estimated 15460 PSMs with q<0.01 Iteration 6: Estimated 15462 PSMs with q<0.01 Iteration 7: Estimated 15462 PSMs with q<0.01 Iteration 8: Estimated 15462 PSMs with q<0.01 Iteration 9: Estimated 15462 PSMs with q<0.01 Iteration 10: Estimated 15461 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 -0.1217 -0.1259 -0.0783 abs_ppm 0.0206 0.1086 -0.0210 isotope_errors -0.8755 -0.7973 -0.7610 log10_evalue 0.2414 0.1094 0.2745 hyperscore 1.1439 1.1382 1.6296 delta_hyperscore 1.6393 0.7894 1.3111 matched_ion_num -1.0605 -0.7627 -1.0640 complementary_ions -0.0686 0.0854 -0.0583 ion_series -0.7976 -0.8402 -0.9067 weighted_average_abs_fragment_ppm -0.0353 -0.0645 -0.0419 length_7 -0.0574 -0.0664 -0.0146 length_8 -0.0245 -0.0385 0.0214 length_9_30 0.0565 0.0822 -0.0064 length_31 0.0000 0.0000 0.0000 ntt -0.0374 -0.0450 0.0410 nmc 0.0000 0.0000 0.0000 charge_1 0.0645 0.0206 -0.0049 charge_2 -0.0318 -0.0012 -0.0097 charge_3 0.0016 0.0160 0.0731 charge_4 -0.1354 -0.1211 -0.1280 charge_5 -0.0371 -0.0249 -0.0423 charge_6 -0.0114 -0.0077 -0.0131 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 -0.1825 -0.0523 -0.1803 10.008269R 0.1048 0.0383 0.1036 15.9949M -0.1449 -0.1171 -0.2081 4.025107K -0.0876 -0.0477 0.0383 6.020129R 0.3442 0.2587 0.3422 79.96633STY -0.0706 -0.0462 -0.0215 8.014199K 1.3735 1.3472 1.5885 unweighted_spectral_entropy -1.2188 -0.8134 -0.4787 delta_RT_loess 0.9797 0.6563 1.1169 m0 Found 15435 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 22199 target PSMs and 7096 decoy PSMs. Calculating q values. Final list yields 15435 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 7.8590 cpu seconds or 8 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_edited.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_edited.pin Started Thu Apr 11 14:24:51 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 29344 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 22439 positives and 6905 negatives, size ratio=3.24967 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 10207 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 9971 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 10022 training set positives with q<0.01 in that direction. Found 15106 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.8420 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 15752 PSMs with q<0.01 Iteration 2: Estimated 15859 PSMs with q<0.01 Iteration 3: Estimated 15929 PSMs with q<0.01 Iteration 4: Estimated 15952 PSMs with q<0.01 Iteration 5: Estimated 15951 PSMs with q<0.01 Iteration 6: Estimated 15958 PSMs with q<0.01 Iteration 7: Estimated 15958 PSMs with q<0.01 Iteration 8: Estimated 15961 PSMs with q<0.01 Iteration 9: Estimated 15962 PSMs with q<0.01 Iteration 10: Estimated 15964 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 -0.2295 -0.1319 -0.1049 abs_ppm 0.0656 0.0280 0.0043 isotope_errors -0.1654 -0.5994 -0.4074 log10_evalue -0.2365 0.3901 0.1268 hyperscore 1.6566 1.1050 1.2466 delta_hyperscore 2.2099 1.1461 1.1904 matched_ion_num -1.2445 -0.9201 -0.8682 complementary_ions -0.1987 -0.0366 0.0148 ion_series -0.9844 -0.7783 -0.7784 weighted_average_abs_fragment_ppm -0.0603 -0.0494 -0.0612 length_7 -0.0631 -0.0704 -0.0560 length_8 -0.0582 -0.0578 0.0043 length_9_30 0.1003 0.0997 0.0317 length_31 0.0000 0.0000 0.0000 ntt -0.0157 -0.0101 0.0175 nmc 0.0000 0.0000 0.0000 charge_1 0.0193 0.0381 0.0481 charge_2 0.0002 0.0373 0.0235 charge_3 -0.0706 -0.0589 -0.0736 charge_4 0.1222 -0.1531 -0.1021 charge_5 -0.0371 0.0055 0.0188 charge_6 -0.0080 -0.0077 -0.0073 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 -0.1721 -0.0983 -0.1530 10.008269R -0.1004 -0.0424 -0.0815 15.9949M -0.0892 -0.0685 -0.0586 4.025107K -0.0962 -0.0535 -0.0572 6.020129R 0.1853 0.2052 0.2175 79.96633STY 0.0004 -0.0439 -0.1079 8.014199K 1.2851 1.1904 1.1731 unweighted_spectral_entropy -0.9548 -0.6236 -0.5167 delta_RT_loess 0.9692 0.9379 0.8848 m0 Found 15920 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 22439 target PSMs and 6905 decoy PSMs. Calculating q values. Final list yields 15922 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 14.0320 cpu seconds or 14 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_edited.pin Started Thu Apr 11 14:25:06 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 32958 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 24467 positives and 8491 negatives, size ratio=2.88152 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 10696 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 10649 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 10783 training set positives with q<0.01 in that direction. Found 16061 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 1.1250 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 16675 PSMs with q<0.01 Iteration 2: Estimated 16779 PSMs with q<0.01 Iteration 3: Estimated 16818 PSMs with q<0.01 Iteration 4: Estimated 16830 PSMs with q<0.01 Iteration 5: Estimated 16836 PSMs with q<0.01 Iteration 6: Estimated 16837 PSMs with q<0.01 Iteration 7: Estimated 16841 PSMs with q<0.01 Iteration 8: Estimated 16838 PSMs with q<0.01 Iteration 9: Estimated 16838 PSMs with q<0.01 Iteration 10: Estimated 16837 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 0.0282 -0.0777 -0.0628 abs_ppm 0.0364 0.0165 0.1131 isotope_errors -0.7909 -1.1586 -1.2216 log10_evalue 0.1050 0.3352 0.0472 hyperscore 0.4057 0.1347 0.5178 delta_hyperscore 1.0236 1.4477 0.7728 matched_ion_num -0.6040 -0.7371 -0.5084 complementary_ions 0.2417 0.0605 0.4018 ion_series -0.8466 -0.8520 -0.9070 weighted_average_abs_fragment_ppm -0.0409 -0.0671 -0.0581 length_7 -0.1095 -0.1240 -0.1355 length_8 -0.0353 -0.0252 -0.0378 length_9_30 0.0798 0.0802 0.0944 length_31 0.0000 0.0000 0.0000 ntt -0.1453 -0.2480 -0.0497 nmc 0.0000 0.0000 0.0000 charge_1 0.0534 0.0107 -0.0197 charge_2 0.0555 0.0840 0.0692 charge_3 -0.1139 -0.1017 -0.0491 charge_4 0.0044 -0.0144 -0.0213 charge_5 -0.0461 0.0028 0.0089 charge_6 -0.0158 -0.0280 -0.0207 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 -0.1455 -0.1205 -0.1290 10.008269R 0.0001 -0.0035 -0.0331 15.9949M -0.0755 -0.0884 -0.0798 4.025107K -0.0626 -0.1291 -0.1328 6.020129R 0.2050 0.2697 0.1972 79.96633STY -0.1011 -0.1546 -0.1655 8.014199K 1.1878 1.2664 1.2637 unweighted_spectral_entropy -0.7922 -1.0226 -0.5767 delta_RT_loess 0.4283 0.7575 0.5604 m0 Found 16830 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 24467 target PSMs and 8491 decoy PSMs. Calculating q values. Final list yields 16831 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 7.0670 cpu seconds or 7 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_edited.pin Started Thu Apr 11 14:25:15 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 34486 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 26102 positives and 8384 negatives, size ratio=3.11331 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 11687 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 11566 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 11667 training set positives with q<0.01 in that direction. Found 17433 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.5660 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 18172 PSMs with q<0.01 Iteration 2: Estimated 18266 PSMs with q<0.01 Iteration 3: Estimated 18299 PSMs with q<0.01 Iteration 4: Estimated 18318 PSMs with q<0.01 Iteration 5: Estimated 18331 PSMs with q<0.01 Iteration 6: Estimated 18331 PSMs with q<0.01 Iteration 7: Estimated 18334 PSMs with q<0.01 Iteration 8: Estimated 18336 PSMs with q<0.01 Iteration 9: Estimated 18332 PSMs with q<0.01 Iteration 10: Estimated 18333 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 0.0544 0.0121 0.0105 abs_ppm 0.0092 -0.0100 0.0676 isotope_errors -0.8518 -1.0214 -0.7878 log10_evalue -0.4132 -0.8955 0.0196 hyperscore 0.7841 1.1831 0.6032 delta_hyperscore 2.3306 2.3328 1.0051 matched_ion_num -0.9923 -1.0879 -0.7189 complementary_ions 0.0112 0.0716 0.1473 ion_series -0.9582 -0.9769 -0.7676 weighted_average_abs_fragment_ppm -0.0753 -0.1006 -0.0939 length_7 -0.0865 -0.0930 -0.0773 length_8 -0.1504 -0.1131 -0.0755 length_9_30 0.2105 0.1805 0.1334 length_31 0.0000 0.0000 0.0000 ntt 0.0578 -0.0868 -0.0317 nmc 0.0000 0.0000 0.0000 charge_1 0.0525 -0.0093 0.0819 charge_2 0.0798 0.0959 0.0339 charge_3 -0.0814 -0.0893 -0.0908 charge_4 -0.2141 -0.0544 -0.1441 charge_5 -0.0506 -0.0564 -0.0382 charge_6 -0.0152 -0.0170 -0.0115 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 -0.0590 -0.0764 -0.0685 10.008269R -0.1135 -0.0190 -0.0663 15.9949M -0.0459 -0.0464 -0.0206 4.025107K 0.0058 -0.0481 -0.0116 6.020129R 0.2369 0.2491 0.2594 79.96633STY -0.1709 -0.1072 -0.1442 8.014199K 1.3750 1.4006 1.1464 unweighted_spectral_entropy -1.0554 -1.0558 -0.8025 delta_RT_loess 0.8163 0.9104 0.6162 m0 Found 18299 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 26102 target PSMs and 8384 decoy PSMs. Calculating q values. Final list yields 18303 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 5.4790 cpu seconds or 6 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_edited.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_edited.pin Started Thu Apr 11 14:25:22 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 35567 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 26531 positives and 9036 negatives, size ratio=2.93614 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 11589 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 11547 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 11609 training set positives with q<0.01 in that direction. Found 17362 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.6650 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 17796 PSMs with q<0.01 Iteration 2: Estimated 17864 PSMs with q<0.01 Iteration 3: Estimated 17919 PSMs with q<0.01 Iteration 4: Estimated 17931 PSMs with q<0.01 Iteration 5: Estimated 17949 PSMs with q<0.01 Iteration 6: Estimated 17965 PSMs with q<0.01 Iteration 7: Estimated 17975 PSMs with q<0.01 Iteration 8: Estimated 17980 PSMs with q<0.01 Iteration 9: Estimated 17980 PSMs with q<0.01 Iteration 10: Estimated 17983 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 -0.0120 -0.0702 -0.1284 abs_ppm -0.1164 -0.0318 0.0594 isotope_errors -0.4845 -0.5036 -0.6027 log10_evalue 0.3545 0.1578 0.1671 hyperscore 0.4837 0.6420 0.6020 delta_hyperscore 1.5348 1.2396 0.9833 matched_ion_num -0.7673 -0.7068 -0.5110 complementary_ions 0.0533 0.1402 0.1877 ion_series -0.6884 -0.8187 -0.7904 weighted_average_abs_fragment_ppm -0.0307 -0.0668 -0.0784 length_7 -0.0823 -0.0691 -0.0235 length_8 -0.0342 -0.0412 -0.0079 length_9_30 0.0728 0.0856 0.0380 length_31 0.0000 0.0000 0.0000 ntt -0.1308 -0.1143 -0.1657 nmc 0.0000 0.0000 0.0000 charge_1 0.0745 0.0322 -0.0124 charge_2 0.0856 0.1201 0.0770 charge_3 -0.1381 -0.1583 -0.0851 charge_4 -0.1550 -0.1344 -0.0380 charge_5 -0.0290 0.0894 0.0891 charge_6 -0.0058 -0.0044 -0.0067 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 -0.1050 -0.1388 -0.2047 10.008269R -0.1835 -0.1920 -0.0741 15.9949M 0.0435 -0.0468 -0.0809 4.025107K -0.1005 -0.0046 -0.0650 6.020129R 0.2999 0.1855 0.1291 79.96633STY -0.1002 -0.0613 -0.0565 8.014199K 1.1128 1.1127 1.1280 unweighted_spectral_entropy -0.7599 -0.7440 -0.6825 delta_RT_loess 0.4882 0.3698 0.5636 m0 Found 17935 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 26531 target PSMs and 9036 decoy PSMs. Calculating q values. Final list yields 17935 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 6.0520 cpu seconds or 6 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_edited.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_target_psms.tsv --decoy-results-psms 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_edited.pin Started Thu Apr 11 14:25:30 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 23756 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 17321 positives and 6435 negatives, size ratio=2.69169 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 6845 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 6896 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 6948 training set positives with q<0.01 in that direction. Found 10307 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.3930 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 11089 PSMs with q<0.01 Iteration 2: Estimated 11221 PSMs with q<0.01 Iteration 3: Estimated 11272 PSMs with q<0.01 Iteration 4: Estimated 11283 PSMs with q<0.01 Iteration 5: Estimated 11291 PSMs with q<0.01 Iteration 6: Estimated 11295 PSMs with q<0.01 Iteration 7: Estimated 11295 PSMs with q<0.01 Iteration 8: Estimated 11297 PSMs with q<0.01 Iteration 9: Estimated 11297 PSMs with q<0.01 Iteration 10: Estimated 11295 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 -0.2234 -0.3684 -0.3003 abs_ppm -0.0709 -0.0409 -0.0523 isotope_errors -0.8277 -0.4079 -0.5790 log10_evalue 0.4328 0.7562 0.5563 hyperscore 0.5125 1.2818 0.7030 delta_hyperscore 1.2306 1.6492 1.3579 matched_ion_num -0.6267 -1.1138 -0.8907 complementary_ions -0.0821 0.0529 -0.1737 ion_series -0.8736 -1.1214 -0.6658 weighted_average_abs_fragment_ppm -0.0984 -0.1425 -0.0785 length_7 -0.0834 -0.2019 -0.0862 length_8 -0.0469 -0.1222 -0.0333 length_9_30 0.1944 0.4205 0.1653 length_31 0.0000 0.0000 0.0000 ntt -0.0710 -0.1416 -0.1062 nmc 0.0000 0.0000 0.0000 charge_1 0.0235 0.1819 0.0870 charge_2 0.0084 0.0303 0.0297 charge_3 -0.1388 -0.4003 -0.2682 charge_4 0.0666 -0.1862 -0.0377 charge_5 0.0633 -0.0027 0.0272 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.0538 -0.0730 -0.0554 10.008269R 0.0464 0.2183 0.0411 15.9949M -0.0258 0.0472 0.0283 4.025107K -0.0400 -0.0619 -0.0026 6.020129R 0.2464 0.2675 0.1964 79.96633STY -0.0157 -0.0338 -0.0795 8.014199K 1.1187 1.5968 1.2240 unweighted_spectral_entropy -0.8935 -1.0060 -0.8231 delta_RT_loess 0.0972 0.1529 0.1387 m0 Found 11245 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 17321 target PSMs and 6435 decoy PSMs. Calculating q values. Final list yields 11246 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 4.5450 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_edited.pin Started Thu Apr 11 14:25:35 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 34442 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 25935 positives and 8507 negatives, size ratio=3.04867 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 11700 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 11573 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 11527 training set positives with q<0.01 in that direction. Found 17386 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.5650 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 18038 PSMs with q<0.01 Iteration 2: Estimated 18126 PSMs with q<0.01 Iteration 3: Estimated 18148 PSMs with q<0.01 Iteration 4: Estimated 18152 PSMs with q<0.01 Iteration 5: Estimated 18155 PSMs with q<0.01 Iteration 6: Estimated 18158 PSMs with q<0.01 Iteration 7: Estimated 18161 PSMs with q<0.01 Iteration 8: Estimated 18159 PSMs with q<0.01 Iteration 9: Estimated 18162 PSMs with q<0.01 Iteration 10: Estimated 18163 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 -0.0435 0.0203 -0.0946 abs_ppm 0.0263 -0.0435 -0.0893 isotope_errors -0.7876 -1.0060 -1.4968 log10_evalue -0.0339 -0.4426 -0.3377 hyperscore 1.2896 1.5337 1.0946 delta_hyperscore 0.7629 1.4289 1.5869 matched_ion_num -0.6307 -0.9635 -1.2894 complementary_ions 0.1841 0.0449 0.0129 ion_series -0.6988 -1.1108 -1.0260 weighted_average_abs_fragment_ppm -0.0782 -0.1293 -0.1494 length_7 -0.0716 -0.1143 -0.1341 length_8 -0.0829 -0.1716 -0.1802 length_9_30 0.1331 0.2550 0.2762 length_31 0.0000 0.0000 0.0000 ntt -0.0442 -0.0927 -0.1160 nmc 0.0000 0.0000 0.0000 charge_1 -0.0227 0.0265 0.1380 charge_2 0.0481 0.0787 0.0526 charge_3 -0.0704 -0.1340 -0.1890 charge_4 0.0426 -0.0180 -0.1685 charge_5 0.0889 -0.0590 -0.0650 charge_6 -0.0168 -0.0189 -0.0209 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 -0.0915 -0.0835 -0.0398 10.008269R -0.1072 -0.0823 0.0173 15.9949M -0.0094 0.0013 0.0969 4.025107K -0.0723 0.0329 -0.0892 6.020129R 0.3054 0.2463 0.2917 79.96633STY -0.0643 -0.0865 -0.0905 8.014199K 1.1875 1.3851 1.4459 unweighted_spectral_entropy -0.8119 -0.7387 -0.6102 delta_RT_loess 0.8993 1.0144 1.1175 m0 Found 18104 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 25935 target PSMs and 8507 decoy PSMs. Calculating q values. Final list yields 18110 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 8.1000 cpu seconds or 8 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_edited.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\FragPipe-jre-21.1\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 20 --results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_target_psms.tsv --decoy-results-psms 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_edited.pin Started Thu Apr 11 14:25:44 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 10.008269R 15.9949M 4.025107K 6.020129R 79.96633STY 8.014199K unweighted_spectral_entropy delta_RT_loess Found 28089 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 20908 positives and 7181 negatives, size ratio=2.91157 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 34 as initial direction. Could separate 8923 training set positives with q<0.01 in that direction. Split 2: Selected feature 34 as initial direction. Could separate 8898 training set positives with q<0.01 in that direction. Split 3: Selected feature 34 as initial direction. Could separate 8860 training set positives with q<0.01 in that direction. Found 13339 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.4180 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 14136 PSMs with q<0.01 Iteration 2: Estimated 14265 PSMs with q<0.01 Iteration 3: Estimated 14322 PSMs with q<0.01 Iteration 4: Estimated 14341 PSMs with q<0.01 Iteration 5: Estimated 14352 PSMs with q<0.01 Iteration 6: Estimated 14348 PSMs with q<0.01 Iteration 7: Estimated 14345 PSMs with q<0.01 Iteration 8: Estimated 14345 PSMs with q<0.01 Iteration 9: Estimated 14345 PSMs with q<0.01 Iteration 10: Estimated 14349 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 0.0038 0.0205 -0.0614 abs_ppm -0.0151 0.0923 -0.0802 isotope_errors -0.9398 -0.9997 -1.8223 log10_evalue 0.1943 -0.0374 -1.0587 hyperscore 0.8224 0.7042 0.8064 delta_hyperscore 0.9121 0.9299 1.8385 matched_ion_num -0.7522 -0.8839 -0.7966 complementary_ions -0.0819 0.1420 -0.1007 ion_series -0.9229 -0.9746 -1.0536 weighted_average_abs_fragment_ppm -0.0683 -0.0868 -0.1154 length_7 -0.0196 -0.0386 -0.0826 length_8 0.0274 0.0458 0.0672 length_9_30 0.0029 -0.0021 0.0043 length_31 0.0000 0.0000 0.0000 ntt 0.0664 -0.1205 -0.1196 nmc 0.0000 0.0000 0.0000 charge_1 0.0549 0.0070 0.0146 charge_2 -0.0524 -0.0431 -0.1018 charge_3 0.0195 0.0269 0.0504 charge_4 -0.0483 0.0149 0.1550 charge_5 -0.0179 0.1035 -0.0274 charge_6 -0.0029 -0.0031 -0.0045 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 -0.1692 -0.1485 -0.1221 10.008269R -0.0230 -0.0413 0.0456 15.9949M -0.0688 -0.0840 0.0197 4.025107K -0.0856 -0.1074 -0.0522 6.020129R 0.2992 0.2572 0.3639 79.96633STY -0.0257 -0.0433 0.0160 8.014199K 1.0835 1.0901 1.2427 unweighted_spectral_entropy -1.1791 -0.9966 -1.5471 delta_RT_loess 0.3461 0.3646 0.5293 m0 Found 14324 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 20908 target PSMs and 7181 decoy PSMs. Calculating q values. Final list yields 14324 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 5.2810 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.pin 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_target_psms.tsv 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_decoy_psms.tsv interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35 DDA 0.5 K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\1\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.pin 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_target_psms.tsv 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_decoy_psms.tsv interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03 DDA 0.5 K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp E:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete G:\Juanjuan_2\WDR33i\2\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined G:\Juanjuan_2\WDR33i\filelist_proteinprophet.txt INFO[14:26:44] Executing ProteinProphet v5.1.0 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 G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.pep.xml... ...read in 0 1+, 9683 2+, 5587 3+, 903 4+, 65 5+, 6 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.pep.xml... ...read in 0 1+, 8229 2+, 8835 3+, 1295 4+, 81 5+, 7 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.pep.xml... ...read in 0 1+, 8979 2+, 2444 3+, 101 4+, 7 5+, 4 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.pep.xml... ...read in 0 1+, 8807 2+, 5594 3+, 599 4+, 22 5+, 1 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.pep.xml... ...read in 0 1+, 6446 2+, 8757 3+, 2085 4+, 169 5+, 9 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.pep.xml... ...read in 0 1+, 7774 2+, 6106 3+, 1340 4+, 137 5+, 10 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.pep.xml... ...read in 0 1+, 6179 2+, 7454 3+, 1834 4+, 198 5+, 18 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.pep.xml... ...read in 0 1+, 8026 2+, 3416 3+, 221 4+, 5 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.pep.xml... ...read in 0 1+, 7134 2+, 7727 3+, 1051 4+, 45 5+, 5 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.pep.xml... ...read in 0 1+, 5731 2+, 8331 3+, 2483 4+, 323 5+, 20 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.pep.xml... ...read in 0 1+, 9186 2+, 6018 3+, 1021 4+, 97 5+, 6 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.pep.xml... ...read in 0 1+, 8519 2+, 8435 3+, 1138 4+, 74 5+, 5 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.pep.xml... ...read in 0 1+, 9670 2+, 3508 3+, 233 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.pep.xml... ...read in 0 1+, 8718 2+, 5927 3+, 667 4+, 17 5+, 1 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.pep.xml... ...read in 0 1+, 7124 2+, 8929 3+, 1909 4+, 111 5+, 13 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.pep.xml... ...read in 0 1+, 7544 2+, 5676 3+, 1162 4+, 93 5+, 4 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.pep.xml... ...read in 0 1+, 5847 2+, 7343 3+, 1572 4+, 145 5+, 11 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.pep.xml... ...read in 0 1+, 8067 2+, 3700 3+, 334 4+, 8 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.pep.xml... ...read in 0 1+, 7131 2+, 7293 3+, 997 4+, 30 5+, 4 6+, 0 7+ spectra with min prob 0.05 Reading in G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.pep.xml... ...read in 0 1+, 5936 2+, 8412 3+, 2218 4+, 250 5+, 17 6+, 0 7+ spectra with min prob 0.05 Initializing 75623 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database K:\20190404-wjj-phospho-KD-WDR33-Federico\2024-04-10-decoys-contam-HUMAN_2018_06.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........43000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........44000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........45000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........46000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........47000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........48000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........49000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........50000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........51000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........52000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........53000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........54000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........55000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........56000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........57000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........58000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........59000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........60000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........61000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........62000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........63000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........64000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........65000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........66000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........67000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........68000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........78000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........82000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........85000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........86000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........87000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........88000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........89000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........90000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........91000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........92000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........93000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........94000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........95000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........96000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........97000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........98000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........99000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........100000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........101000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........102000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........103000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........104000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........105000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........106000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........107000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........108000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........109000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........110000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........111000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........112000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........113000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........114000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........115000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........116000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........117000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........118000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........119000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........120000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........121000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........122000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........123000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........124000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........125000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........126000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........127000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........128000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........129000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........130000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........131000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........132000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........133000 .........:.........:.........:.........:.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q9NZV5-2|SELN_HUMAN : U MGRARPGQRGPPSPGPAAQPPAPPRRRARSLALLGALLAAAAAAAVRVCARHAEAQAAARQELALKTLGTDGLFLFSSLDTDGDMYISPEEFKPIAEKLTGSTPAASCEEEELPPDPSEETLTIEARFQPLLPETMTKSKDGFLGVSRLALSGLRNWTAAASPSAVFATRHFQPFLPPPGQELGEPWWIIPSELSMFTGYLSNNRFYPPPPKGKEVIIHRLLSMFHPRPFVKTRFAPQGAVACLTAISDFYYTVMFRIHAEFQLSEPPDFPFWFSPAQFTGHIILSKDATHVRDFRLFVPNHRSLNVDMEWLYGASESSNMEVDIGYIPQMELEATGPSVPSVILDEDGSMIDSHLPSGEPLQFVFEEIKWQQELSWEEAARRLEVAMYPFKKVSYLPFTEAFDRAKAENKLVHSILLWGALDDQSCUGSGRTLRETVLESSPILTLLNESFISTWSLVKELEELQNNQENSSHQKLAGLHLEKYSFPVEMMICLPNGTVVHHINANYFLDITSVKPEEIESNLFSFSSTFEDPSTATYMQFLKEGLRRGLPLLQP WARNING: Found the following zero-mass residues in protein entry sp|Q9NZV5|SELN_HUMAN : UU MGRARPGQRGPPSPGPAAQPPAPPRRRARSLALLGALLAAAAAAAVRVCARHAEAQAAARQELALKTLGTDGLFLFSSLDTDGDMYISPEEFKPIAEKLTGSCSVTQTGVQWCSHSSLQPQLPWLNUSSCLSLLRSTPAASCEEEELPPDPSEETLTIEARFQPLLPETMTKSKDGFLGVSRLALSGLRNWTAAASPSAVFATRHFQPFLPPPGQELGEPWWIIPSELSMFTGYLSNNRFYPPPPKGKEVIIHRLLSMFHPRPFVKTRFAPQGAVACLTAISDFYYTVMFRIHAEFQLSEPPDFPFWFSPAQFTGHIILSKDATHVRDFRLFVPNHRSLNVDMEWLYGASESSNMEVDIGYIPQMELEATGPSVPSVILDEDGSMIDSHLPSGEPLQFVFEEIKWQQELSWEEAARRLEVAMYPFKKVSYLPFTEAFDRAKAENKLVHSILLWGALDDQSCUGSGRTLRETVLESSPILTLLNESFISTWSLVKELEELQNNQENSSHQKLAGLHLEKYSFPVEMMICLPNGTVVHHINANYFLDITSVKPEEIESNLFSFSSTFEDPSTATYMQFLKEGLRRGLPLLQP .....:.........:.........134000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........135000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........136000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........137000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........138000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........139000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........140000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........141000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........142000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........143000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........144000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........145000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........146000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........147000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........148000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........149000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........150000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........151000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........152000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........153000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........154000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........155000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........156000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........157000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........158000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........159000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........160000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........161000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........162000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........163000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........164000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........165000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........166000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........167000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........168000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........169000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........170000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........171000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........172000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........173000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........174000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........175000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........176000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........177000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........178000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........179000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........180000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........181000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........182000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........183000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........184000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........185000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........186000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........187000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........188000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........189000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........190000 .........:... Total: 190136 Computing degenerate peptides for 26552 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 32474 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 32474 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 32474 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 32474 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 32474 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 32474 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 32474 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=1.56499e-05, db_size=150738113 Computing MU for 32474 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO[14:27:59] Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate K:\20190404-wjj-phospho-KD-WDR33-Federico\2024-04-10-decoys-contam-HUMAN_2018_06.fasta.fas --prefix rev_ INFO[14:27:59] Executing Database v5.1.0 INFO[14:27:59] Annotating the database INFO[14:28:00] Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml G:\Juanjuan_2\WDR33i\1 --protxml G:\Juanjuan_2\WDR33i\combined.prot.xml --razor INFO[14:28:00] Executing Filter v5.1.0 INFO[14:28:00] Processing peptide identification files INFO[14:28:00] Parsing G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.pep.xml INFO[14:28:00] Parsing G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.pep.xml INFO[14:28:00] Parsing G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.pep.xml INFO[14:28:00] Parsing G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.pep.xml INFO[14:28:00] Parsing G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.pep.xml INFO[14:28:00] Parsing G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.pep.xml INFO[14:28:00] Parsing G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.pep.xml INFO[14:28:00] Parsing G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.pep.xml INFO[14:28:00] Parsing G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.pep.xml INFO[14:28:00] Parsing G:\Juanjuan_2\WDR33i\1\interact-20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.pep.xml INFO[14:28:08] 1+ Charge profile decoy=0 target=0 INFO[14:28:08] 2+ Charge profile decoy=886 target=76102 INFO[14:28:08] 3+ Charge profile decoy=529 target=63722 INFO[14:28:08] 4+ Charge profile decoy=85 target=11827 INFO[14:28:08] 5+ Charge profile decoy=19 target=1033 INFO[14:28:08] 6+ Charge profile decoy=2 target=78 INFO[14:28:09] Database search results ions=52085 peptides=17085 psms=154283 INFO[14:28:09] Converged to 1.00 % FDR with 152762 PSMs decoy=1521 threshold=0.500032 total=154283 INFO[14:28:09] Converged to 1.00 % FDR with 14870 Peptides decoy=148 threshold=0.899552 total=15018 INFO[14:28:09] Converged to 1.00 % FDR with 49923 Ions decoy=499 threshold=0.755216 total=50422 INFO[14:28:09] Protein inference results decoy=1972 target=9547 INFO[14:28:09] Converged to 0.99 % FDR with 4455 Proteins decoy=44 threshold=0.9778 total=4499 INFO[14:28:10] Applying sequential FDR estimation ions=50157 peptides=15279 psms=152056 INFO[14:28:11] Converged to 0.13 % FDR with 151861 PSMs decoy=195 threshold=0.500046 total=152056 INFO[14:28:11] Converged to 0.27 % FDR with 15238 Peptides decoy=41 threshold=0.500046 total=15279 INFO[14:28:12] Converged to 0.15 % FDR with 50084 Ions decoy=73 threshold=0.500046 total=50157 INFO[14:28:12] Post processing identifications INFO[14:28:14] Assigning protein identifications to layers INFO[14:28:53] Processing protein inference INFO[14:28:53] Synchronizing PSMs and proteins INFO[14:28:54] Final report numbers after FDR filtering, and post-processing ions=50082 peptides=15237 proteins=4227 psms=151858 INFO[14:28:54] Saving INFO[14:28:56] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml G:\Juanjuan_2\WDR33i\2 --dbbin G:\Juanjuan_2\WDR33i\1 --protxml G:\Juanjuan_2\WDR33i\combined.prot.xml --probin G:\Juanjuan_2\WDR33i\1 --razor INFO[14:28:57] Executing Filter v5.1.0 INFO[14:28:57] Fetching protein inference from G:\Juanjuan_2\WDR33i\1 INFO[14:28:57] Processing peptide identification files INFO[14:28:57] Parsing G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.pep.xml INFO[14:28:57] Parsing G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.pep.xml INFO[14:28:57] Parsing G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.pep.xml INFO[14:28:57] Parsing G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.pep.xml INFO[14:28:57] Parsing G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.pep.xml INFO[14:28:57] Parsing G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.pep.xml INFO[14:28:57] Parsing G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.pep.xml INFO[14:28:57] Parsing G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.pep.xml INFO[14:28:57] Parsing G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.pep.xml INFO[14:28:57] Parsing G:\Juanjuan_2\WDR33i\2\interact-20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.pep.xml INFO[14:29:03] 1+ Charge profile decoy=0 target=0 INFO[14:29:03] 2+ Charge profile decoy=910 target=76832 INFO[14:29:03] 3+ Charge profile decoy=563 target=64678 INFO[14:29:03] 4+ Charge profile decoy=103 target=11148 INFO[14:29:03] 5+ Charge profile decoy=18 target=807 INFO[14:29:03] 6+ Charge profile decoy=1 target=60 INFO[14:29:03] Database search results ions=49114 peptides=16295 psms=155120 INFO[14:29:03] Converged to 1.00 % FDR with 153446 PSMs decoy=1534 threshold=0.513246 total=154980 INFO[14:29:03] Converged to 1.00 % FDR with 13901 Peptides decoy=139 threshold=0.918142 total=14040 INFO[14:29:03] Converged to 1.00 % FDR with 46843 Ions decoy=468 threshold=0.755095 total=47311 INFO[14:29:03] Protein inference results decoy=1972 target=9547 INFO[14:29:04] Converged to 0.99 % FDR with 4455 Proteins decoy=44 threshold=0.9778 total=4499 INFO[14:29:05] Applying sequential FDR estimation ions=47080 peptides=14396 psms=152758 INFO[14:29:05] Converged to 0.13 % FDR with 152562 PSMs decoy=196 threshold=0.513246 total=152758 INFO[14:29:05] Converged to 0.29 % FDR with 14355 Peptides decoy=41 threshold=0.513246 total=14396 INFO[14:29:05] Converged to 0.16 % FDR with 47005 Ions decoy=75 threshold=0.513246 total=47080 INFO[14:29:05] Post processing identifications INFO[14:29:07] Assigning protein identifications to layers INFO[14:29:34] Processing protein inference INFO[14:29:35] Synchronizing PSMs and proteins INFO[14:29:36] Final report numbers after FDR filtering, and post-processing ions=47005 peptides=14355 proteins=4116 psms=152562 INFO[14:29:36] Saving INFO[14:29:37] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[14:29:37] Executing Report v5.1.0 INFO[14:29:37] Creating reports INFO[14:29:41] Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[14:29:41] Executing Report v5.1.0 INFO[14:29:41] Creating reports INFO[14:29:44] Done Process 'PhilosopherReport' finished, exit code: 0 PTMShepherd [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx181G -Dlibs.thermo.dir=E:\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp E:\FragPipe-jre-21.1\fragpipe\tools\ptmshepherd-2.0.6.jar;E:\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar;E:\FragPipe-jre-21.1\fragpipe\tools\commons-math3-3.6.1.jar;E:\FragPipe-jre-21.1\fragpipe\tools\hipparchus-1.8\hipparchus-core-1.8.jar;E:\FragPipe-jre-21.1\fragpipe\tools\hipparchus-1.8\hipparchus-stat-1.8.jar edu.umich.andykong.ptmshepherd.PTMShepherd "G:\Juanjuan_2\WDR33i\shepherd.config" PTM-Shepherd version 2.0.6 (c) 2022 University of Michigan Using Java 11.0.9.1 on 185344MB memory Finding spectral data Indexing data from 1 Indexing data from 2 Done finding spectral data Caching spectral data Caching data from 1 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06 - 15546 (2768 ms, 2458 ms) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03 - 16039 (2003 ms, 2012 ms) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35 - 11234 (1349 ms, 729 ms) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45 - 14752 (1343 ms, 1651 ms) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85 - 17180 (1511 ms, 2523 ms) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85 - 16682 (1935 ms, 2629 ms) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45 - 15776 (1694 ms, 1677 ms) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35 - 11380 (1552 ms, 639 ms) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03 - 15070 (1197 ms, 1869 ms) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06 - 18199 (1580 ms, 2733 ms) Done caching data from 1 Caching data from 2 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45 - 15298 (1290 ms, 1671 ms) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85 - 17801 (1615 ms, 2390 ms) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35 - 13096 (1193 ms, 996 ms) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45 - 15057 (1161 ms, 1575 ms) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03 - 14236 (1459 ms, 1691 ms) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03 - 16040 (1154 ms, 2069 ms) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35 - 11808 (958 ms, 716 ms) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06 - 17973 (1488 ms, 2233 ms) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06 - 14667 (1551 ms, 1919 ms) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85 - 16586 (1553 ms, 2327 ms) Done caching data from 2 Done caching spectral data Counting MS2 scans for dataset 1 151858 MS2 scans present in dataset 1 Done counting MS2 scans for dataset 1 Counting MS2 scans for dataset 2 152562 MS2 scans present in dataset 2 Done counting MS2 scans for dataset 2 Creating combined histogram Generated histogram file for dataset 1 [-5 - 7] Generated histogram file for dataset 2 [-5 - 7] Done creating combined histogram Running peak picking Picked top 20 peaks Removed 4 peaks with insufficient PSMs Created summary table Done running peak picking Annotated summary table Mapping modifications back into PSM lists Created modification summary Begin localization annotation 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06 - 15546 lines (264 ms reading, 1881 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03 - 16039 lines (169 ms reading, 1637 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35 - 11234 lines (105 ms reading, 1041 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45 - 14752 lines (141 ms reading, 1534 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85 - 17180 lines (175 ms reading, 1914 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85 - 16682 lines (159 ms reading, 1863 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45 - 15776 lines (148 ms reading, 1711 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35 - 11380 lines (121 ms reading, 1092 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03 - 15070 lines (131 ms reading, 1593 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06 - 18199 lines (173 ms reading, 1983 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45 - 15298 lines (140 ms reading, 1654 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85 - 17801 lines (144 ms reading, 2104 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35 - 13096 lines (184 ms reading, 1312 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45 - 15057 lines (141 ms reading, 1633 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03 - 14236 lines (367 ms reading, 1607 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03 - 16040 lines (221 ms reading, 1731 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35 - 11808 lines (115 ms reading, 1191 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06 - 17973 lines (149 ms reading, 2012 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06 - 14667 lines (150 ms reading, 1675 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85 - 16586 lines (165 ms reading, 2038 ms processing) Done Created localization reports Begin similarity and retention time annotation Spectral data read into memory (1739 ms reading) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06 - 15546 lines (419 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03 - 16039 lines (377 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35 - 11234 lines (275 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45 - 14752 lines (333 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85 - 17180 lines (310 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85 - 16682 lines (300 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45 - 15776 lines (343 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35 - 11380 lines (249 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03 - 15070 lines (289 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06 - 18199 lines (348 ms processing) Spectral data read into memory (1319 ms reading) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45 - 15298 lines (286 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85 - 17801 lines (315 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35 - 13096 lines (268 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45 - 15057 lines (317 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03 - 14236 lines (251 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03 - 16040 lines (275 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35 - 11808 lines (243 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06 - 17973 lines (311 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06 - 14667 lines (267 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85 - 16586 lines (305 ms processing) Done Created similarity/RT reports Beginning diagnostic ion mining Preprocessing dataset 1 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06 - 15546 lines (124 ms reading, 6950 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03 - 16039 lines (131 ms reading, 9030 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35 - 11234 lines (99 ms reading, 7869 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45 - 14752 lines (137 ms reading, 10432 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85 - 17180 lines (176 ms reading, 13087 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85 - 16682 lines (150 ms reading, 12975 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45 - 15776 lines (299 ms reading, 11846 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35 - 11380 lines (102 ms reading, 6226 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03 - 15070 lines (151 ms reading, 12023 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06 - 18199 lines (152 ms reading, 14281 ms processing) Done preprocessing dataset 1 - 106619 ms total Preprocessing dataset 2 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45 - 15298 lines (133 ms reading, 10631 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85 - 17801 lines (143 ms reading, 14383 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35 - 13096 lines (123 ms reading, 9700 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45 - 15057 lines (146 ms reading, 9897 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03 - 14236 lines (118 ms reading, 10033 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03 - 16040 lines (284 ms reading, 11118 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35 - 11808 lines (103 ms reading, 6927 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06 - 17973 lines (181 ms reading, 13114 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06 - 14667 lines (144 ms reading, 10633 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85 - 16586 lines (288 ms reading, 11166 ms processing) Done preprocessing dataset 2 - 216288 ms total Identifying candidate ions Building feature histograms Testing histogram peaks for significance Done identifying candidate ions Extracting ions from spectra 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06 - 15546 lines (210 ms reading, 31 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03 - 16039 lines (217 ms reading, 14 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35 - 11234 lines (149 ms reading, 8 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45 - 14752 lines (199 ms reading, 17 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85 - 17180 lines (229 ms reading, 19 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85 - 16682 lines (229 ms reading, 9 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45 - 15776 lines (209 ms reading, 7 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35 - 11380 lines (149 ms reading, 4 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03 - 15070 lines (194 ms reading, 8 ms processing) 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06 - 18199 lines (240 ms reading, 9 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45 - 15298 lines (200 ms reading, 6 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85 - 17801 lines (215 ms reading, 6 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35 - 13096 lines (105 ms reading, 4 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45 - 15057 lines (133 ms reading, 5 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03 - 14236 lines (161 ms reading, 5 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03 - 16040 lines (126 ms reading, 13 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35 - 11808 lines (128 ms reading, 6 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06 - 17973 lines (231 ms reading, 11 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06 - 14667 lines (294 ms reading, 9 ms processing) 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85 - 16586 lines (222 ms reading, 9 ms processing) Done mining diagnostic ions Combining and cleaning reports Writing combined table for dataset 1 Writing combined table for dataset 2 Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\peaks.tsv Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\peaksummary.annotated.tsv Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\peaksummary.tsv Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\combined.tsv Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\combined.histo Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\global.locprofile.txt Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\global.simrtprofile.txt Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\1.locprofile.txt Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\1.simrtprofile.txt Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\1.profile.tsv Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\1.histo Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\1.ms2counts Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\2.locprofile.txt Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\2.simrtprofile.txt Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\2.profile.tsv Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\2.histo Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\2.ms2counts Deleted file: 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G:\Juanjuan_2\WDR33i\ptm-shepherd-output\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.mzBIN_cache Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.mzBIN_cache Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.mzBIN_cache Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\2.rawlocalize Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\2.rawsimrt Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.mzBIN_cache Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.mzBIN_cache Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.mzBIN_cache Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.mzBIN_cache Deleted file: 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G:\Juanjuan_2\WDR33i\ptm-shepherd-output\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.diagBIN Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.diagBIN Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\cache-17599ba85739483.txt Deleted file: G:\Juanjuan_2\WDR33i\ptm-shepherd-output\cache-a01a1a2957c06b0.txt Process 'PTMShepherd' finished, exit code: 0 WorkspaceClean [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[14:37:58] Executing Workspace v5.1.0 INFO[14:37:58] Removing workspace INFO[14:37:58] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: G:\Juanjuan_2\WDR33i\1] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[14:37:59] Executing Workspace v5.1.0 INFO[14:37:59] Removing workspace INFO[14:37:59] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: G:\Juanjuan_2\WDR33i\2] E:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[14:38:00] Executing Workspace v5.1.0 INFO[14:38:00] Removing workspace INFO[14:38:00] Done Process 'WorkspaceClean' finished, exit code: 0 IonQuant [Work dir: G:\Juanjuan_2\WDR33i] E:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx181G -Dlibs.bruker.dir=E:\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=E:\FragPipe-jre-21.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp E:\FragPipe-jre-21.1\fragpipe\tools\jfreechart-1.5.3.jar;E:\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar;E:\FragPipe-jre-21.1\fragpipe\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 20 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --light K0;R0 --medium K4.025107;R6.020129 --heavy K8.014199;R10.008269 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist G:\Juanjuan_2\WDR33i\filelist_ionquant.txt --modlist G:\Juanjuan_2\WDR33i\modmasses_ionquant.txt IonQuant version IonQuant-1.10.12 Batmass-IO version 1.30.0 timsdata library version timsdata-2-21-0-4 (c) University of Michigan System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 181 GB memory 2024-04-11 14:38:01 [WARNING] - There are only 2 experiments. Will not calculate MaxLFQ intensity. 2024-04-11 14:38:02 [INFO] - Collecting variable modifications from all psm.tsv files... 2024-04-11 14:38:04 [INFO] - Loading and indexing all psm.tsv files... 2024-04-11 14:38:06 [INFO] - Collecting all compensation voltages if applicable... 2024-04-11 14:38:34 [INFO] - Parameters: 2024-04-11 14:38:34 [INFO] - perform-ms1quant = 1 2024-04-11 14:38:34 [INFO] - perform-isoquant = 0 2024-04-11 14:38:34 [INFO] - isotol = 20.0 2024-04-11 14:38:34 [INFO] - isolevel = 2 2024-04-11 14:38:34 [INFO] - isotype = tmt10 2024-04-11 14:38:34 [INFO] - site-reports = 1 2024-04-11 14:38:34 [INFO] - threads = 20 2024-04-11 14:38:34 [INFO] - mztol = 10.0 2024-04-11 14:38:34 [INFO] - rttol = 0.4 2024-04-11 14:38:34 [INFO] - imtol = 0.05 2024-04-11 14:38:34 [INFO] - minisotopes = 2 2024-04-11 14:38:34 [INFO] - minscans = 3 2024-04-11 14:38:34 [INFO] - psm = G:\Juanjuan_2\WDR33i\1\psm.tsv 2024-04-11 14:38:34 [INFO] - psm = G:\Juanjuan_2\WDR33i\2\psm.tsv 2024-04-11 14:38:34 [INFO] - multidir = G:\Juanjuan_2\WDR33i\.\ 2024-04-11 14:38:34 [INFO] - excludemods = 2024-04-11 14:38:34 [INFO] - minions = 2 2024-04-11 14:38:34 [INFO] - maxlfq = 0 2024-04-11 14:38:34 [INFO] - ibaq = 0 2024-04-11 14:38:34 [INFO] - normalization = 1 2024-04-11 14:38:34 [INFO] - minexps = 1 2024-04-11 14:38:34 [INFO] - minfreq = 0.0 2024-04-11 14:38:34 [INFO] - tp = 0 2024-04-11 14:38:34 [INFO] - mbr = 1 2024-04-11 14:38:34 [INFO] - mbrrttol = 1.0 2024-04-11 14:38:34 [INFO] - mbrimtol = 0.05 2024-04-11 14:38:34 [INFO] - mbrtoprun = 10 2024-04-11 14:38:34 [INFO] - mbrmincorr = 0.0 2024-04-11 14:38:34 [INFO] - ionmobility = 0 2024-04-11 14:38:34 [INFO] - ionfdr = 0.01 2024-04-11 14:38:34 [INFO] - peptidefdr = 1.0 2024-04-11 14:38:34 [INFO] - proteinfdr = 1.0 2024-04-11 14:38:34 [INFO] - light = K0;R0 2024-04-11 14:38:34 [INFO] - medium = K4.025107;R6.020129 2024-04-11 14:38:34 [INFO] - heavy = K8.014199;R10.008269 2024-04-11 14:38:34 [INFO] - requantify = 1 2024-04-11 14:38:34 [INFO] - writeindex = 0 2024-04-11 14:38:34 [INFO] - locprob = 0.75 2024-04-11 14:38:34 [INFO] - uniqueness = 0 2024-04-11 14:38:34 [INFO] - filelist = G:\Juanjuan_2\WDR33i\filelist_ionquant.txt 2024-04-11 14:38:34 [INFO] - specdir = K:\20190404-WDR33_PRIDE 2024-04-11 14:38:34 [INFO] - Light labelling: R 0.0 2024-04-11 14:38:34 [INFO] - Light labelling: K 0.0 2024-04-11 14:38:34 [INFO] - Medium labelling: R 6.020129 2024-04-11 14:38:34 [INFO] - Medium labelling: K 4.025107 2024-04-11 14:38:34 [INFO] - Heavy labelling: R 10.008269 2024-04-11 14:38:34 [INFO] - Heavy labelling: K 8.014199 2024-04-11 14:38:34 [INFO] - modlist = G:\Juanjuan_2\WDR33i\modmasses_ionquant.txt 2024-04-11 14:38:34 [INFO] - mod masses: 2024-04-11 14:38:34 [INFO] - 4.025107 2024-04-11 14:38:34 [INFO] - 6.020129 2024-04-11 14:38:34 [INFO] - 8.014199 2024-04-11 14:38:34 [INFO] - 10.008269 2024-04-11 14:38:34 [INFO] - 15.9949 2024-04-11 14:38:34 [INFO] - 42.0106 2024-04-11 14:38:34 [INFO] - 57.02146 2024-04-11 14:38:34 [INFO] - 79.96633 2024-04-11 14:38:34 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2024-04-11 14:38:34 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.raw... 2024-04-11 14:38:57 [INFO] - Building index... 2024-04-11 14:38:57 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.quantindex 2024-04-11 14:38:58 [INFO] - Quantifying... 2024-04-11 14:38:59 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.raw... 2024-04-11 14:39:32 [INFO] - Building index... 2024-04-11 14:39:32 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.quantindex 2024-04-11 14:39:32 [INFO] - Quantifying... 2024-04-11 14:39:33 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.raw... 2024-04-11 14:39:56 [INFO] - Building index... 2024-04-11 14:39:56 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.quantindex 2024-04-11 14:39:57 [INFO] - Quantifying... 2024-04-11 14:39:57 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.raw... 2024-04-11 14:40:20 [INFO] - Building index... 2024-04-11 14:40:21 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.quantindex 2024-04-11 14:40:21 [INFO] - Quantifying... 2024-04-11 14:40:21 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.raw... 2024-04-11 14:40:46 [INFO] - Building index... 2024-04-11 14:40:47 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.quantindex 2024-04-11 14:40:47 [INFO] - Quantifying... 2024-04-11 14:40:47 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.raw... 2024-04-11 14:41:28 [INFO] - Building index... 2024-04-11 14:41:28 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.quantindex 2024-04-11 14:41:28 [INFO] - Quantifying... 2024-04-11 14:41:28 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.raw... 2024-04-11 14:42:03 [INFO] - Building index... 2024-04-11 14:42:03 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.quantindex 2024-04-11 14:42:04 [INFO] - Quantifying... 2024-04-11 14:42:04 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.raw... 2024-04-11 14:42:19 [INFO] - Building index... 2024-04-11 14:42:20 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.quantindex 2024-04-11 14:42:20 [INFO] - Quantifying... 2024-04-11 14:42:20 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.raw... 2024-04-11 14:42:41 [INFO] - Building index... 2024-04-11 14:42:41 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.quantindex 2024-04-11 14:42:41 [INFO] - Quantifying... 2024-04-11 14:42:41 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.raw... 2024-04-11 14:43:14 [INFO] - Building index... 2024-04-11 14:43:14 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.quantindex 2024-04-11 14:43:14 [INFO] - Quantifying... 2024-04-11 14:43:15 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.raw... 2024-04-11 14:43:38 [INFO] - Building index... 2024-04-11 14:43:39 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.quantindex 2024-04-11 14:43:39 [INFO] - Quantifying... 2024-04-11 14:43:39 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.raw... 2024-04-11 14:44:02 [INFO] - Building index... 2024-04-11 14:44:03 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.quantindex 2024-04-11 14:44:03 [INFO] - Quantifying... 2024-04-11 14:44:03 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.raw... 2024-04-11 14:44:26 [INFO] - Building index... 2024-04-11 14:44:26 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.quantindex 2024-04-11 14:44:27 [INFO] - Quantifying... 2024-04-11 14:44:27 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.raw... 2024-04-11 14:44:54 [INFO] - Building index... 2024-04-11 14:44:54 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.quantindex 2024-04-11 14:44:55 [INFO] - Quantifying... 2024-04-11 14:44:55 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.raw... 2024-04-11 14:45:28 [INFO] - Building index... 2024-04-11 14:45:29 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.quantindex 2024-04-11 14:45:29 [INFO] - Quantifying... 2024-04-11 14:45:29 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.raw... 2024-04-11 14:45:59 [INFO] - Building index... 2024-04-11 14:45:59 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.quantindex 2024-04-11 14:45:59 [INFO] - Quantifying... 2024-04-11 14:45:59 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.raw... 2024-04-11 14:46:30 [INFO] - Building index... 2024-04-11 14:46:30 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.quantindex 2024-04-11 14:46:30 [INFO] - Quantifying... 2024-04-11 14:46:30 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.raw... 2024-04-11 14:46:55 [INFO] - Building index... 2024-04-11 14:46:55 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.quantindex 2024-04-11 14:46:55 [INFO] - Quantifying... 2024-04-11 14:46:55 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.raw... 2024-04-11 14:47:23 [INFO] - Building index... 2024-04-11 14:47:23 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.quantindex 2024-04-11 14:47:24 [INFO] - Quantifying... 2024-04-11 14:47:24 [INFO] - Loading K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.raw... 2024-04-11 14:47:54 [INFO] - Building index... 2024-04-11 14:47:55 [INFO] - Writing index to K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.quantindex 2024-04-11 14:47:55 [INFO] - Quantifying... 2024-04-11 14:47:55 [INFO] - Updating Philosopher's tables... 2024-04-11 14:48:03 [INFO] - Matching-between-runs: 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:03 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:04 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03.quantindex 2024-04-11 14:48:04 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35... 2024-04-11 14:48:05 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:05 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35... 2024-04-11 14:48:05 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45... 2024-04-11 14:48:05 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:06 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35... 2024-04-11 14:48:06 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85... 2024-04-11 14:48:06 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:06 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35... 2024-04-11 14:48:06 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45... 2024-04-11 14:48:06 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:06 [INFO] - #{+1} = 11767, #{-1} = 2423, #{+2} = 9257, #{-2} = 1811 2024-04-11 14:48:06 [INFO] - Standardized coefficients: 2024-04-11 14:48:06 [INFO] - log10(intensity): 0.7813265077437201 2024-04-11 14:48:06 [INFO] - log10(KL): -0.34884026732044154 2024-04-11 14:48:06 [INFO] - abs(ppm): -0.5369848092782443 2024-04-11 14:48:06 [INFO] - RT diff: -0.1391877798601334 2024-04-11 14:48:06 [INFO] - Fitting a mixture model... 2024-04-11 14:48:11 [INFO] - Matching-between-runs: 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06... 2024-04-11 14:48:11 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:11 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06.quantindex 2024-04-11 14:48:11 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:12 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45... 2024-04-11 14:48:12 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:12 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06... 2024-04-11 14:48:12 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:12 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06... 2024-04-11 14:48:13 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45... 2024-04-11 14:48:13 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85... 2024-04-11 14:48:13 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06... 2024-04-11 14:48:14 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85... 2024-04-11 14:48:14 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:14 [INFO] - #{+1} = 10031, #{-1} = 1922, #{+2} = 8656, #{-2} = 1687 2024-04-11 14:48:14 [INFO] - Standardized coefficients: 2024-04-11 14:48:14 [INFO] - log10(intensity): 0.9297780932522548 2024-04-11 14:48:14 [INFO] - log10(KL): -0.2872204761706517 2024-04-11 14:48:14 [INFO] - abs(ppm): -0.1838794331089704 2024-04-11 14:48:14 [INFO] - RT diff: -0.1385837272410776 2024-04-11 14:48:14 [INFO] - Fitting a mixture model... 2024-04-11 14:48:14 [INFO] - Matching-between-runs: 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35... 2024-04-11 14:48:14 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:15 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35.quantindex 2024-04-11 14:48:15 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:15 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45... 2024-04-11 14:48:15 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:15 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35... 2024-04-11 14:48:15 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:15 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06... 2024-04-11 14:48:16 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35... 2024-04-11 14:48:16 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45... 2024-04-11 14:48:16 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:16 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35... 2024-04-11 14:48:16 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:16 [INFO] - #{+1} = 5713, #{-1} = 988, #{+2} = 4703, #{-2} = 680 2024-04-11 14:48:16 [INFO] - Standardized coefficients: 2024-04-11 14:48:16 [INFO] - log10(intensity): 0.7048527441538988 2024-04-11 14:48:16 [INFO] - log10(KL): -0.24625224073072793 2024-04-11 14:48:16 [INFO] - abs(ppm): -0.6828980825716187 2024-04-11 14:48:16 [INFO] - RT diff: -0.0665530028988885 2024-04-11 14:48:16 [INFO] - Fitting a mixture model... 2024-04-11 14:48:16 [INFO] - Matching-between-runs: 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45... 2024-04-11 14:48:16 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:17 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45.quantindex 2024-04-11 14:48:17 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:17 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35... 2024-04-11 14:48:17 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:17 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45... 2024-04-11 14:48:17 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:17 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06... 2024-04-11 14:48:17 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35... 2024-04-11 14:48:18 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45... 2024-04-11 14:48:18 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06... 2024-04-11 14:48:18 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45... 2024-04-11 14:48:18 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:18 [INFO] - #{+1} = 7909, #{-1} = 1286, #{+2} = 6147, #{-2} = 1005 2024-04-11 14:48:18 [INFO] - Standardized coefficients: 2024-04-11 14:48:18 [INFO] - log10(intensity): 0.7360792014131909 2024-04-11 14:48:18 [INFO] - log10(KL): -0.2520071294088633 2024-04-11 14:48:18 [INFO] - abs(ppm): -0.612359299541929 2024-04-11 14:48:18 [INFO] - RT diff: -0.14034209717166687 2024-04-11 14:48:18 [INFO] - Fitting a mixture model... 2024-04-11 14:48:18 [INFO] - Matching-between-runs: 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85... 2024-04-11 14:48:18 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:18 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85.quantindex 2024-04-11 14:48:19 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:19 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06... 2024-04-11 14:48:19 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:19 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06... 2024-04-11 14:48:19 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85... 2024-04-11 14:48:20 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:20 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06... 2024-04-11 14:48:20 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85... 2024-04-11 14:48:20 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:20 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85... 2024-04-11 14:48:21 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:21 [INFO] - #{+1} = 12347, #{-1} = 2636, #{+2} = 9137, #{-2} = 1871 2024-04-11 14:48:21 [INFO] - Standardized coefficients: 2024-04-11 14:48:21 [INFO] - log10(intensity): 0.9456552632304869 2024-04-11 14:48:21 [INFO] - log10(KL): -0.28673815712871076 2024-04-11 14:48:21 [INFO] - abs(ppm): -0.13178100203430465 2024-04-11 14:48:21 [INFO] - RT diff: -0.07842907543599051 2024-04-11 14:48:21 [INFO] - Fitting a mixture model... 2024-04-11 14:48:21 [INFO] - Matching-between-runs: 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:21 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:21 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03.quantindex 2024-04-11 14:48:22 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:22 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35... 2024-04-11 14:48:22 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45... 2024-04-11 14:48:22 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85... 2024-04-11 14:48:22 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:22 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35... 2024-04-11 14:48:22 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:22 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35... 2024-04-11 14:48:23 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45... 2024-04-11 14:48:23 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85... 2024-04-11 14:48:23 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:23 [INFO] - #{+1} = 10914, #{-1} = 2530, #{+2} = 8613, #{-2} = 1631 2024-04-11 14:48:23 [INFO] - Standardized coefficients: 2024-04-11 14:48:23 [INFO] - log10(intensity): 0.8557911651977872 2024-04-11 14:48:23 [INFO] - log10(KL): -0.32209798644494253 2024-04-11 14:48:23 [INFO] - abs(ppm): -0.33344488986143694 2024-04-11 14:48:23 [INFO] - RT diff: -0.22954057184476506 2024-04-11 14:48:23 [INFO] - Fitting a mixture model... 2024-04-11 14:48:23 [INFO] - Matching-between-runs: 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06... 2024-04-11 14:48:23 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:24 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06.quantindex 2024-04-11 14:48:24 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06... 2024-04-11 14:48:24 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:24 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45... 2024-04-11 14:48:24 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85... 2024-04-11 14:48:24 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:24 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06... 2024-04-11 14:48:24 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:25 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06... 2024-04-11 14:48:25 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45... 2024-04-11 14:48:25 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85... 2024-04-11 14:48:25 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:25 [INFO] - #{+1} = 9747, #{-1} = 2018, #{+2} = 7964, #{-2} = 1555 2024-04-11 14:48:25 [INFO] - Standardized coefficients: 2024-04-11 14:48:25 [INFO] - log10(intensity): 0.9380456380081439 2024-04-11 14:48:25 [INFO] - log10(KL): -0.28670460405524933 2024-04-11 14:48:25 [INFO] - abs(ppm): -0.1294967785289233 2024-04-11 14:48:25 [INFO] - RT diff: -0.14526333115431447 2024-04-11 14:48:25 [INFO] - Fitting a mixture model... 2024-04-11 14:48:26 [INFO] - Matching-between-runs: 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35... 2024-04-11 14:48:26 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:26 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35.quantindex 2024-04-11 14:48:27 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:27 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35... 2024-04-11 14:48:27 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45... 2024-04-11 14:48:27 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:27 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45... 2024-04-11 14:48:27 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:27 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35... 2024-04-11 14:48:27 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:27 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35... 2024-04-11 14:48:28 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45... 2024-04-11 14:48:28 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:28 [INFO] - #{+1} = 6015, #{-1} = 1005, #{+2} = 5621, #{-2} = 859 2024-04-11 14:48:28 [INFO] - Standardized coefficients: 2024-04-11 14:48:28 [INFO] - log10(intensity): 0.6808095439473352 2024-04-11 14:48:28 [INFO] - log10(KL): -0.195834913445044 2024-04-11 14:48:28 [INFO] - abs(ppm): -0.7007112324909475 2024-04-11 14:48:28 [INFO] - RT diff: -0.1838466828927951 2024-04-11 14:48:28 [INFO] - Fitting a mixture model... 2024-04-11 14:48:28 [INFO] - Matching-between-runs: 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45... 2024-04-11 14:48:28 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:28 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45.quantindex 2024-04-11 14:48:28 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:29 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45... 2024-04-11 14:48:29 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:29 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06... 2024-04-11 14:48:29 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:29 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45... 2024-04-11 14:48:29 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:29 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06... 2024-04-11 14:48:29 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35... 2024-04-11 14:48:29 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45... 2024-04-11 14:48:30 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:30 [INFO] - #{+1} = 8442, #{-1} = 1575, #{+2} = 8051, #{-2} = 1366 2024-04-11 14:48:30 [INFO] - Standardized coefficients: 2024-04-11 14:48:30 [INFO] - log10(intensity): 0.7833274340390877 2024-04-11 14:48:30 [INFO] - log10(KL): -0.30405139360603634 2024-04-11 14:48:30 [INFO] - abs(ppm): -0.523878957401814 2024-04-11 14:48:30 [INFO] - RT diff: -0.13964855573744514 2024-04-11 14:48:30 [INFO] - Fitting a mixture model... 2024-04-11 14:48:30 [INFO] - Matching-between-runs: 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85... 2024-04-11 14:48:30 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:31 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85.quantindex 2024-04-11 14:48:31 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:31 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85... 2024-04-11 14:48:31 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:31 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06... 2024-04-11 14:48:32 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:32 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06... 2024-04-11 14:48:32 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85... 2024-04-11 14:48:32 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:32 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06... 2024-04-11 14:48:32 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85... 2024-04-11 14:48:33 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:33 [INFO] - #{+1} = 10898, #{-1} = 2449, #{+2} = 8802, #{-2} = 1834 2024-04-11 14:48:33 [INFO] - Standardized coefficients: 2024-04-11 14:48:33 [INFO] - log10(intensity): 0.9430511654486835 2024-04-11 14:48:33 [INFO] - log10(KL): -0.29617913845293253 2024-04-11 14:48:33 [INFO] - abs(ppm): -0.06779409364207065 2024-04-11 14:48:33 [INFO] - RT diff: -0.1354118833722083 2024-04-11 14:48:33 [INFO] - Fitting a mixture model... 2024-04-11 14:48:33 [INFO] - Matching-between-runs: 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:33 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:34 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03.quantindex 2024-04-11 14:48:34 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:34 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35... 2024-04-11 14:48:34 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:34 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35... 2024-04-11 14:48:34 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45... 2024-04-11 14:48:34 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35... 2024-04-11 14:48:34 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85... 2024-04-11 14:48:35 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:35 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35... 2024-04-11 14:48:35 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45... 2024-04-11 14:48:35 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:35 [INFO] - #{+1} = 11561, #{-1} = 2471, #{+2} = 9168, #{-2} = 1797 2024-04-11 14:48:35 [INFO] - Standardized coefficients: 2024-04-11 14:48:35 [INFO] - log10(intensity): 0.8430662953969601 2024-04-11 14:48:35 [INFO] - log10(KL): -0.29788356036681557 2024-04-11 14:48:35 [INFO] - abs(ppm): -0.4116716076340133 2024-04-11 14:48:35 [INFO] - RT diff: -0.1761564460837647 2024-04-11 14:48:35 [INFO] - Fitting a mixture model... 2024-04-11 14:48:35 [INFO] - Matching-between-runs: 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06... 2024-04-11 14:48:35 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:36 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06.quantindex 2024-04-11 14:48:36 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:36 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06... 2024-04-11 14:48:36 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:36 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06... 2024-04-11 14:48:36 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:36 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45... 2024-04-11 14:48:37 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85... 2024-04-11 14:48:37 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:37 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06... 2024-04-11 14:48:37 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85... 2024-04-11 14:48:37 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:37 [INFO] - #{+1} = 10305, #{-1} = 1947, #{+2} = 8941, #{-2} = 1726 2024-04-11 14:48:37 [INFO] - Standardized coefficients: 2024-04-11 14:48:37 [INFO] - log10(intensity): 0.9044157054960325 2024-04-11 14:48:37 [INFO] - log10(KL): -0.28413972988482583 2024-04-11 14:48:37 [INFO] - abs(ppm): -0.2681897416177563 2024-04-11 14:48:37 [INFO] - RT diff: -0.17138001063161737 2024-04-11 14:48:37 [INFO] - Fitting a mixture model... 2024-04-11 14:48:37 [INFO] - Matching-between-runs: 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35... 2024-04-11 14:48:38 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:38 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35.quantindex 2024-04-11 14:48:38 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:39 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35... 2024-04-11 14:48:39 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45... 2024-04-11 14:48:39 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:39 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35... 2024-04-11 14:48:39 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:39 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06... 2024-04-11 14:48:40 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45... 2024-04-11 14:48:40 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:40 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35... 2024-04-11 14:48:40 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:40 [INFO] - #{+1} = 8280, #{-1} = 1362, #{+2} = 6387, #{-2} = 1031 2024-04-11 14:48:40 [INFO] - Standardized coefficients: 2024-04-11 14:48:40 [INFO] - log10(intensity): 0.725560258076319 2024-04-11 14:48:40 [INFO] - log10(KL): -0.2053160966242917 2024-04-11 14:48:40 [INFO] - abs(ppm): -0.6618406196676315 2024-04-11 14:48:40 [INFO] - RT diff: -0.15221606758327155 2024-04-11 14:48:40 [INFO] - Fitting a mixture model... 2024-04-11 14:48:40 [INFO] - Matching-between-runs: 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45... 2024-04-11 14:48:40 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:41 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45.quantindex 2024-04-11 14:48:41 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:41 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35... 2024-04-11 14:48:41 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45... 2024-04-11 14:48:41 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:41 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45... 2024-04-11 14:48:41 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:41 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06... 2024-04-11 14:48:42 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35... 2024-04-11 14:48:42 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06... 2024-04-11 14:48:42 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45... 2024-04-11 14:48:42 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:42 [INFO] - #{+1} = 7584, #{-1} = 1242, #{+2} = 5831, #{-2} = 967 2024-04-11 14:48:42 [INFO] - Standardized coefficients: 2024-04-11 14:48:42 [INFO] - log10(intensity): 0.8508685273957627 2024-04-11 14:48:42 [INFO] - log10(KL): -0.18241703735008188 2024-04-11 14:48:42 [INFO] - abs(ppm): -0.4585483748392201 2024-04-11 14:48:42 [INFO] - RT diff: -0.1802225332861991 2024-04-11 14:48:42 [INFO] - Fitting a mixture model... 2024-04-11 14:48:42 [INFO] - Matching-between-runs: 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85... 2024-04-11 14:48:42 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:42 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85.quantindex 2024-04-11 14:48:43 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:43 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06... 2024-04-11 14:48:43 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85... 2024-04-11 14:48:43 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:43 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06... 2024-04-11 14:48:43 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85... 2024-04-11 14:48:43 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:44 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06... 2024-04-11 14:48:44 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:44 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85... 2024-04-11 14:48:45 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:45 [INFO] - #{+1} = 13598, #{-1} = 2776, #{+2} = 9631, #{-2} = 1984 2024-04-11 14:48:45 [INFO] - Standardized coefficients: 2024-04-11 14:48:45 [INFO] - log10(intensity): 0.9523356542493879 2024-04-11 14:48:45 [INFO] - log10(KL): -0.262266004716933 2024-04-11 14:48:45 [INFO] - abs(ppm): -0.12758426036955386 2024-04-11 14:48:45 [INFO] - RT diff: -0.08941812412012393 2024-04-11 14:48:45 [INFO] - Fitting a mixture model... 2024-04-11 14:48:45 [INFO] - Matching-between-runs: 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:45 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:46 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03.quantindex 2024-04-11 14:48:46 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:46 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:46 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35... 2024-04-11 14:48:46 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45... 2024-04-11 14:48:46 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85... 2024-04-11 14:48:46 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:46 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35... 2024-04-11 14:48:47 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35... 2024-04-11 14:48:47 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45... 2024-04-11 14:48:47 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85... 2024-04-11 14:48:47 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:47 [INFO] - #{+1} = 10579, #{-1} = 2358, #{+2} = 8085, #{-2} = 1538 2024-04-11 14:48:47 [INFO] - Standardized coefficients: 2024-04-11 14:48:47 [INFO] - log10(intensity): 0.8569275839467994 2024-04-11 14:48:47 [INFO] - log10(KL): -0.3480820527950434 2024-04-11 14:48:47 [INFO] - abs(ppm): -0.31791029199958165 2024-04-11 14:48:47 [INFO] - RT diff: -0.20843955151033788 2024-04-11 14:48:47 [INFO] - Fitting a mixture model... 2024-04-11 14:48:47 [INFO] - Matching-between-runs: 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06... 2024-04-11 14:48:47 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:48 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06.quantindex 2024-04-11 14:48:48 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:48 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06... 2024-04-11 14:48:48 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:48 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06... 2024-04-11 14:48:48 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45... 2024-04-11 14:48:48 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:48 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06... 2024-04-11 14:48:49 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:49 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45... 2024-04-11 14:48:49 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85... 2024-04-11 14:48:49 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:49 [INFO] - #{+1} = 9639, #{-1} = 1849, #{+2} = 7562, #{-2} = 1405 2024-04-11 14:48:49 [INFO] - Standardized coefficients: 2024-04-11 14:48:49 [INFO] - log10(intensity): 0.9427468073717041 2024-04-11 14:48:49 [INFO] - log10(KL): -0.282096159596389 2024-04-11 14:48:49 [INFO] - abs(ppm): -0.1269875657592105 2024-04-11 14:48:49 [INFO] - RT diff: -0.1245968381379636 2024-04-11 14:48:49 [INFO] - Fitting a mixture model... 2024-04-11 14:48:49 [INFO] - Matching-between-runs: 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35... 2024-04-11 14:48:49 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:50 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35.quantindex 2024-04-11 14:48:50 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:50 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35... 2024-04-11 14:48:50 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:51 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35... 2024-04-11 14:48:51 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45... 2024-04-11 14:48:51 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:51 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35... 2024-04-11 14:48:51 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45... 2024-04-11 14:48:51 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:52 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45... 2024-04-11 14:48:52 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:52 [INFO] - #{+1} = 7499, #{-1} = 1359, #{+2} = 5980, #{-2} = 974 2024-04-11 14:48:52 [INFO] - Standardized coefficients: 2024-04-11 14:48:52 [INFO] - log10(intensity): 0.7812247239322195 2024-04-11 14:48:52 [INFO] - log10(KL): -0.23234113972797119 2024-04-11 14:48:52 [INFO] - abs(ppm): -0.5636458500266683 2024-04-11 14:48:52 [INFO] - RT diff: -0.22805849094312972 2024-04-11 14:48:52 [INFO] - Fitting a mixture model... 2024-04-11 14:48:52 [INFO] - Matching-between-runs: 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45... 2024-04-11 14:48:52 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:52 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45.quantindex 2024-04-11 14:48:52 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:52 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45... 2024-04-11 14:48:53 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:53 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06... 2024-04-11 14:48:53 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45... 2024-04-11 14:48:53 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:53 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45... 2024-04-11 14:48:53 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:53 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06... 2024-04-11 14:48:53 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35... 2024-04-11 14:48:53 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:54 [INFO] - #{+1} = 8843, #{-1} = 1650, #{+2} = 7824, #{-2} = 1333 2024-04-11 14:48:54 [INFO] - Standardized coefficients: 2024-04-11 14:48:54 [INFO] - log10(intensity): 0.8276748623565613 2024-04-11 14:48:54 [INFO] - log10(KL): -0.2517110357342148 2024-04-11 14:48:54 [INFO] - abs(ppm): -0.45719359221050826 2024-04-11 14:48:54 [INFO] - RT diff: -0.2063247342281285 2024-04-11 14:48:54 [INFO] - Fitting a mixture model... 2024-04-11 14:48:54 [INFO] - Matching-between-runs: 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85... 2024-04-11 14:48:54 [INFO] - Calculating correlations between all other runs... 2024-04-11 14:48:54 [INFO] - Reading index from K:\20190404-WDR33_PRIDE\20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85.quantindex 2024-04-11 14:48:54 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03... 2024-04-11 14:48:54 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85... 2024-04-11 14:48:54 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03... 2024-04-11 14:48:54 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06... 2024-04-11 14:48:55 [INFO] - Transferring 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85... 2024-04-11 14:48:55 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03... 2024-04-11 14:48:55 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06... 2024-04-11 14:48:55 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85... 2024-04-11 14:48:55 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03... 2024-04-11 14:48:55 [INFO] - Transferring 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06... 2024-04-11 14:48:55 [INFO] - Training LDA models for all matched features. 2024-04-11 14:48:56 [INFO] - #{+1} = 11595, #{-1} = 2498, #{+2} = 8999, #{-2} = 1809 2024-04-11 14:48:56 [INFO] - Standardized coefficients: 2024-04-11 14:48:56 [INFO] - log10(intensity): 0.930075682337411 2024-04-11 14:48:56 [INFO] - log10(KL): -0.3031333450848408 2024-04-11 14:48:56 [INFO] - abs(ppm): -0.15639989175073368 2024-04-11 14:48:56 [INFO] - RT diff: -0.13641288092637374 2024-04-11 14:48:56 [INFO] - Fitting a mixture model... 2024-04-11 14:48:56 [INFO] - Estimating match-between-runs FDR... 2024-04-11 14:48:59 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.974200 2024-04-11 14:48:59 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100 2024-04-11 14:48:59 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100 2024-04-11 14:48:59 [INFO] - Updating Philosopher's tables... 2024-04-11 14:49:02 [INFO] - Performing label quant... 2024-04-11 14:49:02 [INFO] - Re-quantifying 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_06 ... 2024-04-11 14:49:02 [INFO] - Re-quantifying 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_03 ... 2024-04-11 14:49:02 [INFO] - Re-quantifying 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_35 ... 2024-04-11 14:49:02 [INFO] - Re-quantifying 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_45 ... 2024-04-11 14:49:03 [INFO] - Re-quantifying 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_85 ... 2024-04-11 14:49:03 [INFO] - Re-quantifying 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_85 ... 2024-04-11 14:49:03 [INFO] - Re-quantifying 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_45 ... 2024-04-11 14:49:03 [INFO] - Re-quantifying 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_35 ... 2024-04-11 14:49:03 [INFO] - Re-quantifying 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_2_SCX_03 ... 2024-04-11 14:49:03 [INFO] - Re-quantifying 20190404_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp1_1_SCX_06 ... 2024-04-11 14:49:09 [INFO] - Re-quantifying 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_45 ... 2024-04-11 14:49:09 [INFO] - Re-quantifying 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_85 ... 2024-04-11 14:49:09 [INFO] - Re-quantifying 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_35 ... 2024-04-11 14:49:09 [INFO] - Re-quantifying 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_45 ... 2024-04-11 14:49:09 [INFO] - Re-quantifying 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_03 ... 2024-04-11 14:49:09 [INFO] - Re-quantifying 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_35 ... 2024-04-11 14:49:10 [INFO] - Re-quantifying 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_03 ... 2024-04-11 14:49:10 [INFO] - Re-quantifying 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_1_SCX_06 ... 2024-04-11 14:49:10 [INFO] - Re-quantifying 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_06 ... 2024-04-11 14:49:10 [INFO] - Re-quantifying 20190405_QEP1_SILAC_U2OS_KD_WDR33_TiO2_exp2_2_SCX_85 ... 2024-04-11 14:49:15 [INFO] - Combining experiments and estimating protein intensity... java.lang.ArrayIndexOutOfBoundsException: Index -6 out of bounds for length 58464 at r.a(Unknown Source) at r.(Unknown Source) at ionquant.IonQuant.main(Unknown Source) 2024-04-11 14:49:19 [ERROR] - Index -6 out of bounds for length 58464 Process 'IonQuant' finished, exit code: 1 Process returned non-zero exit code, stopping ~~~~~~~~~~~~~~~~~~~~ Cancelling 1 remaining tasks