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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Process 'IonQuant' finished, exit code: 1 #197

Closed cesarrivera closed 4 years ago

cesarrivera commented 4 years ago

Hello. I was analyzing 12 TIMS TOF samples and this error appeared: Process 'IonQuant' finished, exit code: 1.

Log file:

System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 13.0 MSFragger version 3.0 Philosopher version 3.2.7 (build 1591393649)

LCMS files: Experiment/Group: Control_1

140 commands to execute: WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck MsFragger [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx28G D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\MSFragger-3.0\MSFragger-3.0.jar D:\ProteomicaAftas\2020_06_15_FragPipe13\fragger.params D:\ProteomicaAftas\Experimentar\Saliva_C1_ControlSano_Slot2-49_1_3551.d D:\ProteomicaAftas\Experimentar\Saliva_C2_ControlSano_Slot2-50_1_3553.d D:\ProteomicaAftas\Experimentar\Saliva_C3_ControlSano_Slot2-51_1_3555.d D:\ProteomicaAftas\Experimentar\Saliva_R1_recurrencia_Slot2-1_1_3563.d D:\ProteomicaAftas\Experimentar\Saliva_R2_recurrencia_Slot2-2_1_3565.d D:\ProteomicaAftas\Experimentar\Saliva_R3_recurrencia_Slot2-3_1_3567.d D:\ProteomicaAftas\Experimentar\Saliva_D1_desaparicion_Slot2-52_1_3557.d D:\ProteomicaAftas\Experimentar\Saliva_D2_desaparicion_Slot2-53_1_3559.d D:\ProteomicaAftas\Experimentar\Saliva_D3_desaparicion_Slot2-54_1_3561.d D:\ProteomicaAftas\Experimentar\Saliva_A1_AFTA_Slot2-46_1_3547.d D:\ProteomicaAftas\Experimentar\Saliva_A2_AFTA_Slot2-47_1_3545.d D:\ProteomicaAftas\Experimentar\Saliva_A3_AFTA_Slot2-48_1_3549.d MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_A1_AFTA_Slot2-46_1_3547.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\Saliva_A1_AFTA_Slot2-46_1_3547.pepXML MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_A2_AFTA_Slot2-47_1_3545.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\Saliva_A2_AFTA_Slot2-47_1_3545.pepXML MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_A3_AFTA_Slot2-48_1_3549.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\Saliva_A3_AFTA_Slot2-48_1_3549.pepXML PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\fragpipe-Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\fragpipe-Saliva_A1_AFTA_Slot2-46_1_3547.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\fragpipe-Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\fragpipe-Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\fragpipe-Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\fragpipe-Saliva_A2_AFTA_Slot2-47_1_3545.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\fragpipe-Saliva_A3_AFTA_Slot2-48_1_3549.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\fragpipe-Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\fragpipe-Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\fragpipe-Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\fragpipe-Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\fragpipe-Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\fragpipe-Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\fragpipe-Saliva_A1_AFTA_Slot2-46_1_3547.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_A1_AFTA_Slot2-46_1_3547.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\fragpipe-Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\fragpipe-Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\fragpipe-Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\fragpipe-Saliva_A2_AFTA_Slot2-47_1_3545.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_A2_AFTA_Slot2-47_1_3545.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\fragpipe-Saliva_A3_AFTA_Slot2-48_1_3549.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_A3_AFTA_Slot2-48_1_3549.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\fragpipe-Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\fragpipe-Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\fragpipe-Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\fragpipe-Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\fragpipe-Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\fragpipe-Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML-temp PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\fragpipe-Saliva_A1_AFTA_Slot2-46_1_3547.pepXML-temp PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\fragpipe-Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML-temp PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\fragpipe-Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML-temp PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\fragpipe-Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML-temp PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\fragpipe-Saliva_A2_AFTA_Slot2-47_1_3545.pepXML-temp PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\fragpipe-Saliva_A3_AFTA_Slot2-48_1_3549.pepXML-temp PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\fragpipe-Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML-temp PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\fragpipe-Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML-temp PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\fragpipe-Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML-temp PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\fragpipe-Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML-temp PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\fragpipe-Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML-temp ProteinProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\interact-Saliva_C3_ControlSano_Slot2-51_1_3555.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\interact-Saliva_A1_AFTA_Slot2-46_1_3547.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\interact-Saliva_C1_ControlSano_Slot2-49_1_3551.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\interact-Saliva_R2_recurrencia_Slot2-2_1_3565.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\interact-Saliva_D3_desaparicion_Slot2-54_1_3561.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\interact-Saliva_A2_AFTA_Slot2-47_1_3545.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\interact-Saliva_A3_AFTA_Slot2-48_1_3549.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\interact-Saliva_D2_desaparicion_Slot2-53_1_3559.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\interact-Saliva_R1_recurrencia_Slot2-1_1_3563.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\interact-Saliva_C2_ControlSano_Slot2-50_1_3553.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\interact-Saliva_R3_recurrencia_Slot2-3_1_3567.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\interact-Saliva_D1_desaparicion_Slot2-52_1_3557.pep.xml PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report PhilosopherAbacus [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe abacus --razor --reprint --tag rev --protein Ulcer_3 Remission_3 Ulcer_2 Remission_1 Recurrence_3 Ulcer_1 Recurrence_2 Recurrence_1 Control_1 Remission_2 Control_2 Control_3 IonQuant [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Xmx28G -Dlibs.bruker.dir="D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\MSFragger-3.0\ext\bruker" -Dlibs.thermo.dir="D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\MSFragger-3.0\ext\thermo" -cp "D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\tools\ionquant-1.3.0.jar;D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar" ionquant.IonQuant --threads 12 --ionmobility 1 --mbr 1 --proteinquant 2 --requantify 0 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0.5 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 3 --ionfdr 0.01 --proteinfdr 0.01 --peptidefdr 0.01 --normalization 1 --minisotopes 2 --tp 3 --minfreq 0.5 --minions 2 --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\psm.tsv --multidir D:\ProteomicaAftas\2020_06_15_FragPipe13 D:\ProteomicaAftas\Experimentar\Saliva_C3_ControlSano_Slot2-51_1_3555.d Control_3\Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML D:\ProteomicaAftas\Experimentar\Saliva_A1_AFTA_Slot2-46_1_3547.d Ulcer_1\Saliva_A1_AFTA_Slot2-46_1_3547.pepXML D:\ProteomicaAftas\Experimentar\Saliva_C1_ControlSano_Slot2-49_1_3551.d Control_1\Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML D:\ProteomicaAftas\Experimentar\Saliva_R2_recurrencia_Slot2-2_1_3565.d Recurrence_2\Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML D:\ProteomicaAftas\Experimentar\Saliva_D3_desaparicion_Slot2-54_1_3561.d Remission_3\Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML D:\ProteomicaAftas\Experimentar\Saliva_A2_AFTA_Slot2-47_1_3545.d Ulcer_2\Saliva_A2_AFTA_Slot2-47_1_3545.pepXML D:\ProteomicaAftas\Experimentar\Saliva_A3_AFTA_Slot2-48_1_3549.d Ulcer_3\Saliva_A3_AFTA_Slot2-48_1_3549.pepXML D:\ProteomicaAftas\Experimentar\Saliva_D2_desaparicion_Slot2-53_1_3559.d Remission_2\Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML D:\ProteomicaAftas\Experimentar\Saliva_C2_ControlSano_Slot2-50_1_3553.d Control_2\Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML D:\ProteomicaAftas\Experimentar\Saliva_R1_recurrencia_Slot2-1_1_3563.d Recurrence_1\Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML D:\ProteomicaAftas\Experimentar\Saliva_R3_recurrencia_Slot2-3_1_3567.d Recurrence_3\Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML D:\ProteomicaAftas\Experimentar\Saliva_D1_desaparicion_Slot2-52_1_3557.d Remission_1\Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck SpecLibGen [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3] C:\ProgramData\Anaconda3\python -u D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3 D:\ProteomicaAftas\Experimentar\Saliva_A3_AFTA_Slot2-48_1_3549_calibrated.mgf;D:\ProteomicaAftas\Experimentar\Saliva_A3_AFTA_Slot2-48_1_3549_uncalibrated.mgf D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3 True unused use_easypqp noiRT 12 "--rt_lowess_fraction 0.04" SpecLibGen [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3] C:\ProgramData\Anaconda3\python -u D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3 D:\ProteomicaAftas\Experimentar\Saliva_D3_desaparicion_Slot2-54_1_3561_calibrated.mgf;D:\ProteomicaAftas\Experimentar\Saliva_D3_desaparicion_Slot2-54_1_3561_uncalibrated.mgf D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3 True unused use_easypqp noiRT 12 "--rt_lowess_fraction 0.04" SpecLibGen [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2] C:\ProgramData\Anaconda3\python -u D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2 D:\ProteomicaAftas\Experimentar\Saliva_A2_AFTA_Slot2-47_1_3545_calibrated.mgf;D:\ProteomicaAftas\Experimentar\Saliva_A2_AFTA_Slot2-47_1_3545_uncalibrated.mgf D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2 True unused use_easypqp noiRT 12 "--rt_lowess_fraction 0.04" SpecLibGen [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1] C:\ProgramData\Anaconda3\python -u D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1 D:\ProteomicaAftas\Experimentar\Saliva_D1_desaparicion_Slot2-52_1_3557_calibrated.mgf;D:\ProteomicaAftas\Experimentar\Saliva_D1_desaparicion_Slot2-52_1_3557_uncalibrated.mgf D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1 True unused use_easypqp noiRT 12 "--rt_lowess_fraction 0.04" SpecLibGen [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3] C:\ProgramData\Anaconda3\python -u D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3 D:\ProteomicaAftas\Experimentar\Saliva_R3_recurrencia_Slot2-3_1_3567_calibrated.mgf;D:\ProteomicaAftas\Experimentar\Saliva_R3_recurrencia_Slot2-3_1_3567_uncalibrated.mgf D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3 True unused use_easypqp noiRT 12 "--rt_lowess_fraction 0.04" SpecLibGen [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1] C:\ProgramData\Anaconda3\python -u D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1 D:\ProteomicaAftas\Experimentar\Saliva_A1_AFTA_Slot2-46_1_3547_calibrated.mgf;D:\ProteomicaAftas\Experimentar\Saliva_A1_AFTA_Slot2-46_1_3547_uncalibrated.mgf D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1 True unused use_easypqp noiRT 12 "--rt_lowess_fraction 0.04" SpecLibGen [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2] C:\ProgramData\Anaconda3\python -u D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2 D:\ProteomicaAftas\Experimentar\Saliva_R2_recurrencia_Slot2-2_1_3565_calibrated.mgf;D:\ProteomicaAftas\Experimentar\Saliva_R2_recurrencia_Slot2-2_1_3565_uncalibrated.mgf D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2 True unused use_easypqp noiRT 12 "--rt_lowess_fraction 0.04" SpecLibGen [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1] C:\ProgramData\Anaconda3\python -u D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1 D:\ProteomicaAftas\Experimentar\Saliva_R1_recurrencia_Slot2-1_1_3563_calibrated.mgf;D:\ProteomicaAftas\Experimentar\Saliva_R1_recurrencia_Slot2-1_1_3563_uncalibrated.mgf D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1 True unused use_easypqp noiRT 12 "--rt_lowess_fraction 0.04" SpecLibGen [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1] C:\ProgramData\Anaconda3\python -u D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1 D:\ProteomicaAftas\Experimentar\Saliva_C1_ControlSano_Slot2-49_1_3551_calibrated.mgf;D:\ProteomicaAftas\Experimentar\Saliva_C1_ControlSano_Slot2-49_1_3551_uncalibrated.mgf D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1 True unused use_easypqp noiRT 12 "--rt_lowess_fraction 0.04" SpecLibGen [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2] C:\ProgramData\Anaconda3\python -u D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2 D:\ProteomicaAftas\Experimentar\Saliva_D2_desaparicion_Slot2-53_1_3559_calibrated.mgf;D:\ProteomicaAftas\Experimentar\Saliva_D2_desaparicion_Slot2-53_1_3559_uncalibrated.mgf D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2 True unused use_easypqp noiRT 12 "--rt_lowess_fraction 0.04" SpecLibGen [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2] C:\ProgramData\Anaconda3\python -u D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2 D:\ProteomicaAftas\Experimentar\Saliva_C2_ControlSano_Slot2-50_1_3553_calibrated.mgf;D:\ProteomicaAftas\Experimentar\Saliva_C2_ControlSano_Slot2-50_1_3553_uncalibrated.mgf D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2 True unused use_easypqp noiRT 12 "--rt_lowess_fraction 0.04" SpecLibGen [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] C:\ProgramData\Anaconda3\python -u D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3 D:\ProteomicaAftas\Experimentar\Saliva_C3_ControlSano_Slot2-51_1_3555_calibrated.mgf;D:\ProteomicaAftas\Experimentar\Saliva_C3_ControlSano_Slot2-51_1_3555_uncalibrated.mgf D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3 True unused use_easypqp noiRT 12 "--rt_lowess_fraction 0.04"


Execution order:

    Cmd: [START], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2]
    Cmd: [MsFragger], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13]
    Cmd: [PeptideProphet], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13]
    Cmd: [ProteinProphet], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13]
    Cmd: [PhilosopherFilter], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13]
    Cmd: [PhilosopherReport], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13]
    Cmd: [PhilosopherAbacus], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13]
    Cmd: [IonQuant], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1]
    Cmd: [WorkspaceClean], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2]
    Cmd: [SpecLibGen], Work dir: [D:\ProteomicaAftas\2020_06_15_FragPipe13]

# FragPipe v13.0ui state cache

crystalc.correct_isotope_error=false
crystalc.isotope_number=3
crystalc.max-charge=6
crystalc.precursor_isolation_window=0.7
crystalc.precursor_mass=20
crystalc.run-crystalc=false
database.db-path=D\:\\Programas\\Programas espectrometr\u00EDa de masas\\Transformar archivos d a mzxl\\Fasta philosopher\\2020-06-15-decoys-reviewed-contam-UP000005640.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=D\:\\Programas\\Programas espectrometr\u00EDa de masas\\Transformar archivos d a mzxl\\MSFragger-3.0\\MSFragger-3.0.jar
fragpipe-config.bin-philosopher=D\:\\Programas\\Programas espectrometr\u00EDa de masas\\Transformar archivos d a mzxl\\philosopher_v3.2.7_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.label=
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0.5
ionquant.mbrrttol=1
ionquant.mbrtoprun=3
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=0.01
ionquant.proteinfdr=0.01
ionquant.proteinquant=2
ionquant.requantify=0
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
msfragger.Y_type_masses=0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=1
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deltamass_allowed_residues=ST
msfragger.diagnostic_fragments=204.086646 186.076086 168.065526 366.139466 144.0656 138.055 126.055 163.060096 512.197375 292.1026925 274.0921325 657.2349 243.026426 405.079246 485.045576 308.09761
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.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.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown=trypsin
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=1
msfragger.output_format=pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-50
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=50
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=P
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=trypsin
msfragger.table.fix-mods=0.00000,C-Term Peptide,false,-1; 0.00000,N-Term Peptide,false,-1; 0.00000,C-Term Protein,false,-1; 0.00000,N-Term Protein,false,-1; 0.00000,G (glycine),false,-1; 0.00000,A (alanine),false,-1; 0.00000,S (serine),false,-1; 0.00000,P (proline),false,-1; 0.00000,V (valine),false,-1; 0.00000,T (threonine),false,-1; 57.02146,C (cysteine),true,-1; 0.00000,L (leucine),false,-1; 0.00000,I (isoleucine),false,-1; 0.00000,N (asparagine),false,-1; 0.00000,D (aspartic acid),false,-1; 0.00000,Q (glutamine),false,-1; 0.00000,K (lysine),false,-1; 0.00000,E (glutamic acid),false,-1; 0.00000,M (methionine),false,-1; 0.00000,H (histidine),false,-1; 0.00000,F (phenylalanine),false,-1; 0.00000,R (arginine),false,-1; 0.00000,Y (tyrosine),false,-1; 0.00000,W (tryptophan),false,-1; 0.00000,B ,false,-1; 0.00000,J,false,-1; 0.00000,O,false,-1; 0.00000,U,false,-1; 0.00000,X,false,-1; 0.00000,Z,false,-1
msfragger.table.var-mods=15.99490,M,true,3; 42.01060,[^,true,1; 79.96633,STY,false,3; -17.02650,nQnC,false,1; -18.01060,nE,false,1; 0.00000,site_06,false,1; 0.00000,site_07,false,1; 0.00000,site_08,false,1; 0.00000,site_09,false,1; 0.00000,site_10,false,1; 0.00000,site_11,false,1; 0.00000,site_12,false,1; 0.00000,site_13,false,1; 0.00000,site_14,false,1; 0.00000,site_15,false,1; 0.00000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=true
msfragger.zero_bin_accept_expect=0.00
msfragger.zero_bin_mult_expect=1.00
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01
phi-report.pep-level-summary=false
phi-report.print-decoys=false
phi-report.run-report=true
phi-report.write-mzid=false
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmshepherd.annotation_tol=0.01
ptmshepherd.histo_smoothbins=2
ptmshepherd.localization_background=4
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.run-shepherd=false
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
speclibgen.easypqp.extras.rt_lowess_fraction=0.04
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=true
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
tmtintegrator.add_Ref=-1
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=0
tmtintegrator.labelquant=--tol 20 --level 2
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.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\ProteomicaAftas\\2020_06_15_FragPipe13
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=12

WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:06:11] Executing Workspace v3.2.7
INFO[16:06:11] Removing workspace
WARN[16:06:11] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:11] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[16:06:12] Executing Workspace v3.2.7
INFO[16:06:12] Creating workspace
INFO[16:06:12] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:06:12] Executing Workspace v3.2.7
INFO[16:06:12] Removing workspace
WARN[16:06:12] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:12] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[16:06:12] Executing Workspace v3.2.7
INFO[16:06:12] Creating workspace
INFO[16:06:12] Done
WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[16:06:12] Executing Workspace v3.2.7
INFO[16:06:12] Removing workspace
WARN[16:06:12] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:12] Done
WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[16:06:12] Executing Workspace v3.2.7
INFO[16:06:12] Creating workspace
INFO[16:06:13] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:06:13] Executing Workspace v3.2.7
INFO[16:06:13] Removing workspace
WARN[16:06:13] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:13] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[16:06:13] Executing Workspace v3.2.7
INFO[16:06:13] Creating workspace
INFO[16:06:13] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:06:13] Executing Workspace v3.2.7
INFO[16:06:13] Removing workspace
WARN[16:06:13] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:13] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[16:06:13] Executing Workspace v3.2.7
INFO[16:06:13] Creating workspace
INFO[16:06:13] Done
WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[16:06:14] Executing Workspace v3.2.7
INFO[16:06:14] Removing workspace
WARN[16:06:14] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:14] Done
WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[16:06:14] Executing Workspace v3.2.7
INFO[16:06:14] Creating workspace
INFO[16:06:14] Done
WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:06:14] Executing Workspace v3.2.7
INFO[16:06:14] Removing workspace
WARN[16:06:14] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:14] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[16:06:14] Executing Workspace v3.2.7
INFO[16:06:14] Creating workspace
INFO[16:06:14] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[16:06:14] Executing Workspace v3.2.7
INFO[16:06:14] Removing workspace
WARN[16:06:14] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:14] Done
WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:06:15] Executing Workspace v3.2.7
INFO[16:06:15] Creating workspace
INFO[16:06:15] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[16:06:15] Executing Workspace v3.2.7
INFO[16:06:15] Removing workspace
WARN[16:06:15] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:15] Done
WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[16:06:15] Executing Workspace v3.2.7
INFO[16:06:15] Creating workspace
INFO[16:06:15] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:06:15] Executing Workspace v3.2.7
INFO[16:06:15] Removing workspace
WARN[16:06:15] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:15] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[16:06:15] Executing Workspace v3.2.7
INFO[16:06:15] Creating workspace
INFO[16:06:15] Done
WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:06:16] Executing Workspace v3.2.7
INFO[16:06:16] Removing workspace
WARN[16:06:16] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:16] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[16:06:16] Executing Workspace v3.2.7
INFO[16:06:16] Creating workspace
INFO[16:06:16] Done
WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:06:16] Executing Workspace v3.2.7
INFO[16:06:16] Removing workspace
WARN[16:06:16] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:16] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[16:06:16] Executing Workspace v3.2.7
INFO[16:06:16] Creating workspace
INFO[16:06:16] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:06:18] Executing Workspace v3.2.7
INFO[16:06:18] Removing workspace
WARN[16:06:18] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:06:18] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[16:06:18] Executing Workspace v3.2.7
INFO[16:06:18] Creating workspace
INFO[16:06:18] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MsFragger [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx28G D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\MSFragger-3.0\MSFragger-3.0.jar D:\ProteomicaAftas\2020_06_15_FragPipe13\fragger.params D:\ProteomicaAftas\Experimentar\Saliva_C1_ControlSano_Slot2-49_1_3551.d D:\ProteomicaAftas\Experimentar\Saliva_C2_ControlSano_Slot2-50_1_3553.d D:\ProteomicaAftas\Experimentar\Saliva_C3_ControlSano_Slot2-51_1_3555.d D:\ProteomicaAftas\Experimentar\Saliva_R1_recurrencia_Slot2-1_1_3563.d D:\ProteomicaAftas\Experimentar\Saliva_R2_recurrencia_Slot2-2_1_3565.d D:\ProteomicaAftas\Experimentar\Saliva_R3_recurrencia_Slot2-3_1_3567.d D:\ProteomicaAftas\Experimentar\Saliva_D1_desaparicion_Slot2-52_1_3557.d D:\ProteomicaAftas\Experimentar\Saliva_D2_desaparicion_Slot2-53_1_3559.d D:\ProteomicaAftas\Experimentar\Saliva_D3_desaparicion_Slot2-54_1_3561.d D:\ProteomicaAftas\Experimentar\Saliva_A1_AFTA_Slot2-46_1_3547.d D:\ProteomicaAftas\Experimentar\Saliva_A2_AFTA_Slot2-47_1_3545.d D:\ProteomicaAftas\Experimentar\Saliva_A3_AFTA_Slot2-48_1_3549.d MSFragger version MSFragger-3.0 Batmass-IO version 1.17.4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, JVM started with 24 GB memory Checking database... Checking D:\ProteomicaAftas\Experimentar\Saliva_C1_ControlSano_Slot2-49_1_3551.d... Checking D:\ProteomicaAftas\Experimentar\Saliva_C2_ControlSano_Slot2-50_1_3553.d... Checking D:\ProteomicaAftas\Experimentar\Saliva_C3_ControlSano_Slot2-51_1_3555.d... Checking D:\ProteomicaAftas\Experimentar\Saliva_R1_recurrencia_Slot2-1_1_3563.d... Checking D:\ProteomicaAftas\Experimentar\Saliva_R2_recurrencia_Slot2-2_1_3565.d... Checking D:\ProteomicaAftas\Experimentar\Saliva_R3_recurrencia_Slot2-3_1_3567.d... Checking D:\ProteomicaAftas\Experimentar\Saliva_D1_desaparicion_Slot2-52_1_3557.d... Checking D:\ProteomicaAftas\Experimentar\Saliva_D2_desaparicion_Slot2-53_1_3559.d... Checking D:\ProteomicaAftas\Experimentar\Saliva_D3_desaparicion_Slot2-54_1_3561.d... Checking D:\ProteomicaAftas\Experimentar\Saliva_A1_AFTA_Slot2-46_1_3547.d... Checking D:\ProteomicaAftas\Experimentar\Saliva_A2_AFTA_Slot2-47_1_3545.d... Checking D:\ProteomicaAftas\Experimentar\Saliva_A3_AFTA_Slot2-48_1_3549.d... ***FIRST SEARCH**** Parameters: num_threads = 12 database_name = D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = true isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y diagnostic_intensity_filter = 0.0 Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279 diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.0656/138.055/126.055/163.060096/512.197375/292.1026925/274.0921325/657.2349/243.026426/405.079246/485.045576/308.09761 search_enzyme_name = trypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = P num_enzyme_termini = 2 allowed_missed_cleavage = 1 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.50,1.50 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.99490 M 3 variable_mod_02 = 42.01060 [^ 1 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 Selected fragment tolerance 0.10 Da. 159782084 fragments to be searched in 1 slices (2.38 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.69 s

  1. Saliva_A1_AFTA_Slot2-46_1_3547.d loading 99%1098.5 s | deisotoping 6.8 s [progress: 170277/170277 (100%) - 20037 spectra/s] 8.5s | postprocessing 0.3 s
  2. Saliva_A2_AFTA_Slot2-47_1_3545.d loading 99%1163.4 s | deisotoping 6.6 s [progress: 180627/180627 (100%) - 24396 spectra/s] 7.4s | postprocessing 0.4 s
  3. Saliva_A3_AFTA_Slot2-48_1_3549.d loading 99%1172.9 s | deisotoping 6.8 s [progress: 180483/180483 (100%) - 24321 spectra/s] 7.4s | postprocessing 0.2 s
  4. Saliva_C1_ControlSano_Slot2-49_1_3551.d loading 99%1190.7 s | deisotoping 7.1 s [progress: 180649/180649 (100%) - 24605 spectra/s] 7.3s | postprocessing 0.3 s
  5. Saliva_C2_ControlSano_Slot2-50_1_3553.d loading 99%1094.4 s | deisotoping 6.0 s [progress: 167589/167589 (100%) - 24441 spectra/s] 6.9s | postprocessing 0.2 s
  6. Saliva_C3_ControlSano_Slot2-51_1_3555.d loading 99%1153.4 s | deisotoping 6.0 s [progress: 175556/175556 (100%) - 24325 spectra/s] 7.2s | postprocessing 0.3 s
  7. Saliva_D1_desaparicion_Slot2-52_1_3557.d loading 99%1194.0 s | deisotoping 7.5 s [progress: 181180/181180 (100%) - 24418 spectra/s] 7.4s | postprocessing 0.3 s
  8. Saliva_D2_desaparicion_Slot2-53_1_3559.d loading 99%1074.3 s | deisotoping 6.0 s [progress: 164889/164889 (100%) - 23458 spectra/s] 7.0s | postprocessing 0.2 s
  9. Saliva_D3_desaparicion_Slot2-54_1_3561.d loading 99%1195.3 s | deisotoping 7.5 s [progress: 182494/182494 (100%) - 24339 spectra/s] 7.5s | postprocessing 0.3 s
  10. Saliva_R1_recurrencia_Slot2-1_1_3563.d loading 99%730.6 s | deisotoping 2.0 s [progress: 109245/109245 (100%) - 27976 spectra/s] 3.9s | postprocessing 0.1 s
  11. Saliva_R2_recurrencia_Slot2-2_1_3565.d loading 99%1025.1 s | deisotoping 4.3 s [progress: 156844/156844 (100%) - 26215 spectra/s] 6.0s | postprocessing 0.2 s
  12. Saliva_R3_recurrencia_Slot2-3_1_3567.d loading 99%1041.9 s | deisotoping 4.6 s [progress: 157227/157227 (100%) - 26009 spectra/s] 6.0s | postprocessing 0.2 s ***FIRST SEARCH DONE IN 221.913 MIN**
*****MASS CALIBRATION** ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 -7.21 2.86 0.02 2.40 -6.24 4.71 -0.77 4.35
002 -6.95 2.83 -0.03 2.31 -6.01 4.68 -0.81 4.31
003 -6.69 2.83 -0.00 2.37 -5.59 4.73 -0.70 4.29
004 -7.09 2.80 0.02 2.30 -6.12 4.58 -0.79 4.23
005 -6.92 2.92 -0.07 2.40 -5.98 4.67 -0.65 4.29
006 -7.61 2.79 -0.01 2.27 -7.12 4.71 -0.86 4.35
007 -6.58 2.85 -0.03 2.32 -5.55 4.67 -0.74 4.20
008 -6.86 2.88 0.01 2.33 -6.08 4.68 -0.80 4.32
009 -6.37 2.86 0.03 2.32 -5.37 4.58 -0.67 4.20
010 -7.48 2.37 -0.13 2.01 -5.75 5.17 -0.95 4.87
011 -6.81 2.71 0.03 2.20 -6.10 4.85 -0.86 4.44
012 -7.14 2.69 -0.03 2.31 -6.29 4.75 -0.79 4.44
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 141206 150200 155317 156692 155339 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- -------
Peaks 500_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- -------
Count 156098 158294 157694 skip rest
------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 157632
------- -------
------- -------
Rm P. 1
------- -------
Count 159339
------- -------

New fragment_mass_tolerance = 15 PPM New use_topN_peaks = 200 New minimum_ratio = 0.000000 New intensity_transform = 0 New remove_precursor_peak = 1 **MASS CALIBRATION DONE IN 18.704 MIN***

****MAIN SEARCH**** Checking database... Parameters: num_threads = 12 database_name = D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas decoyprefix = rev precursor_mass_lower = -50.0 precursor_mass_upper = 50.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = true isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y diagnostic_intensity_filter = 0.0 Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279 diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.0656/138.055/126.055/163.060096/512.197375/292.1026925/274.0921325/657.2349/243.026426/405.079246/485.045576/308.09761 search_enzyme_name = trypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = P num_enzyme_termini = 1 allowed_missed_cleavage = 1 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 200 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 remove_precursor_peak = 1 remove_precursor_range = -1.50,1.50 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.99490 M 3 variable_mod_02 = 42.01060 [^ 1 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 Number of unique peptides of length 7: 3381957 of length 8: 3294902 of length 9: 3133209 of length 10: 2964686 of length 11: 2796208 of length 12: 2632076 of length 13: 2468027 of length 14: 2313949 of length 15: 2166114 of length 16: 2028052 of length 17: 1898107 of length 18: 1774994 of length 19: 1656893 of length 20: 1547402 of length 21: 1445016 of length 22: 1350190 of length 23: 1259982 of length 24: 1175878 of length 25: 1096780 of length 26: 1024263 of length 27: 955049 of length 28: 889734 of length 29: 828974 of length 30: 772224 of length 31: 718917 of length 32: 668801 of length 33: 623099 of length 34: 580106 of length 35: 540700 of length 36: 503499 of length 37: 468994 of length 38: 437330 of length 39: 408173 of length 40: 380991 of length 41: 354214 of length 42: 326990 of length 43: 294052 of length 44: 252005 of length 45: 201320 of length 46: 149208 of length 47: 102757 of length 48: 66358 of length 49: 41065 of length 50: 24580 In total 51997825 peptides. Generated 80327019 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment tolerance 0.08 Da. 3172029920 fragments to be searched in 4 slices (47.27 GB total) Operating on slice 1 of 4: Fragment index slice generated in 6.08 s

  1. Saliva_A1_AFTA_Slot2-46_1_3547.mzBIN_calibrated 1.4 s [progress: 169770/169770 (100%) - 8021 spectra/s] 21.2s
  2. Saliva_A2_AFTA_Slot2-47_1_3545.mzBIN_calibrated 12.4 s [progress: 180112/180112 (100%) - 7817 spectra/s] 23.0s
  3. Saliva_A3_AFTA_Slot2-48_1_3549.mzBIN_calibrated 1.5 s [progress: 179845/179845 (100%) - 7447 spectra/s] 24.2s
  4. Saliva_C1_ControlSano_Slot2-49_1_3551.mzBIN_calibrated 12.2 s [progress: 180140/180140 (100%) - 8196 spectra/s] 22.0s
  5. Saliva_C2_ControlSano_Slot2-50_1_3553.mzBIN_calibrated 1.3 s [progress: 167010/167010 (100%) - 8069 spectra/s] 20.7s
  6. Saliva_C3_ControlSano_Slot2-51_1_3555.mzBIN_calibrated 12.7 s [progress: 174992/174992 (100%) - 7768 spectra/s] 22.5s
  7. Saliva_D1_desaparicion_Slot2-52_1_3557.mzBIN_calibrated 1.5 s [progress: 180673/180673 (100%) - 7690 spectra/s] 23.5s
  8. Saliva_D2_desaparicion_Slot2-53_1_3559.mzBIN_calibrated 11.9 s [progress: 164464/164464 (100%) - 7952 spectra/s] 20.7s
  9. Saliva_D3_desaparicion_Slot2-54_1_3561.mzBIN_calibrated 1.5 s [progress: 182029/182029 (100%) - 7562 spectra/s] 24.1s
  10. Saliva_R1_recurrencia_Slot2-1_1_3563.mzBIN_calibrated 2.1 s [progress: 108653/108653 (100%) - 7644 spectra/s] 14.2s
  11. Saliva_R2_recurrencia_Slot2-2_1_3565.mzBIN_calibrated 2.2 s [progress: 156128/156128 (100%) - 7509 spectra/s] 20.8s
  12. Saliva_R3_recurrencia_Slot2-3_1_3567.mzBIN_calibrated 2.6 s [progress: 156710/156710 (100%) - 8045 spectra/s] 19.5s Operating on slice 2 of 4: Fragment index slice generated in 5.41 s
  13. Saliva_A1_AFTA_Slot2-46_1_3547.mzBIN_calibrated 1.6 s [progress: 169770/169770 (100%) - 10233 spectra/s] 16.6s
  14. Saliva_A2_AFTA_Slot2-47_1_3545.mzBIN_calibrated 1.6 s [progress: 180112/180112 (100%) - 10194 spectra/s] 17.7s
  15. Saliva_A3_AFTA_Slot2-48_1_3549.mzBIN_calibrated 1.5 s [progress: 179845/179845 (100%) - 10117 spectra/s] 17.8s
  16. Saliva_C1_ControlSano_Slot2-49_1_3551.mzBIN_calibrated 1.6 s [progress: 180140/180140 (100%) - 10133 spectra/s] 17.8s
  17. Saliva_C2_ControlSano_Slot2-50_1_3553.mzBIN_calibrated 1.4 s [progress: 167010/167010 (100%) - 10607 spectra/s] 15.7s
  18. Saliva_C3_ControlSano_Slot2-51_1_3555.mzBIN_calibrated 1.6 s [progress: 174992/174992 (100%) - 10156 spectra/s] 17.2s
  19. Saliva_D1_desaparicion_Slot2-52_1_3557.mzBIN_calibrated 1.5 s [progress: 180673/180673 (100%) - 9802 spectra/s] 18.4s
  20. Saliva_D2_desaparicion_Slot2-53_1_3559.mzBIN_calibrated 1.4 s [progress: 164464/164464 (100%) - 10231 spectra/s] 16.1s
  21. Saliva_D3_desaparicion_Slot2-54_1_3561.mzBIN_calibrated 1.6 s [progress: 182029/182029 (100%) - 9943 spectra/s] 18.3s
  22. Saliva_R1_recurrencia_Slot2-1_1_3563.mzBIN_calibrated 0.9 s [progress: 108653/108653 (100%) - 12245 spectra/s] 8.9s
  23. Saliva_R2_recurrencia_Slot2-2_1_3565.mzBIN_calibrated 1.3 s [progress: 156128/156128 (100%) - 10887 spectra/s] 14.3s
  24. Saliva_R3_recurrencia_Slot2-3_1_3567.mzBIN_calibrated 1.4 s [progress: 156710/156710 (100%) - 10976 spectra/s] 14.3s Operating on slice 3 of 4: Fragment index slice generated in 6.26 s
  25. Saliva_A1_AFTA_Slot2-46_1_3547.mzBIN_calibrated 1.6 s [progress: 169770/169770 (100%) - 14263 spectra/s] 11.9s
  26. Saliva_A2_AFTA_Slot2-47_1_3545.mzBIN_calibrated 1.5 s [progress: 180112/180112 (100%) - 15032 spectra/s] 12.0s
  27. Saliva_A3_AFTA_Slot2-48_1_3549.mzBIN_calibrated 1.5 s [progress: 179845/179845 (100%) - 14779 spectra/s] 12.2s
  28. Saliva_C1_ControlSano_Slot2-49_1_3551.mzBIN_calibrated 1.5 s [progress: 180140/180140 (100%) - 14505 spectra/s] 12.4s
  29. Saliva_C2_ControlSano_Slot2-50_1_3553.mzBIN_calibrated 1.4 s [progress: 167010/167010 (100%) - 14665 spectra/s] 11.4s
  30. Saliva_C3_ControlSano_Slot2-51_1_3555.mzBIN_calibrated 1.4 s [progress: 174992/174992 (100%) - 14957 spectra/s] 11.7s
  31. Saliva_D1_desaparicion_Slot2-52_1_3557.mzBIN_calibrated 1.6 s [progress: 180673/180673 (100%) - 14772 spectra/s] 12.2s
  32. Saliva_D2_desaparicion_Slot2-53_1_3559.mzBIN_calibrated 1.3 s [progress: 164464/164464 (100%) - 14324 spectra/s] 11.5s
  33. Saliva_D3_desaparicion_Slot2-54_1_3561.mzBIN_calibrated 1.5 s [progress: 182029/182029 (100%) - 14638 spectra/s] 12.4s
  34. Saliva_R1_recurrencia_Slot2-1_1_3563.mzBIN_calibrated 0.9 s [progress: 108653/108653 (100%) - 17610 spectra/s] 6.2s
  35. Saliva_R2_recurrencia_Slot2-2_1_3565.mzBIN_calibrated 1.3 s [progress: 156128/156128 (100%) - 15889 spectra/s] 9.8s
  36. Saliva_R3_recurrencia_Slot2-3_1_3567.mzBIN_calibrated 1.4 s [progress: 156710/156710 (100%) - 15246 spectra/s] 10.3s Operating on slice 4 of 4: Fragment index slice generated in 7.26 s
  37. Saliva_A1_AFTA_Slot2-46_1_3547.mzBIN_calibrated 1.4 s [progress: 169770/169770 (100%) - 18204 spectra/s] 9.3s | postprocessing 4.8 s
  38. Saliva_A2_AFTA_Slot2-47_1_3545.mzBIN_calibrated 1.4 s [progress: 180112/180112 (100%) - 19609 spectra/s] 9.2s | postprocessing 6.0 s
  39. Saliva_A3_AFTA_Slot2-48_1_3549.mzBIN_calibrated 1.4 s [progress: 179845/179845 (100%) - 19317 spectra/s] 9.3s | postprocessing 5.7 s
  40. Saliva_C1_ControlSano_Slot2-49_1_3551.mzBIN_calibrated 1.4 s [progress: 180140/180140 (100%) - 19091 spectra/s] 9.4s | postprocessing 4.9 s
  41. Saliva_C2_ControlSano_Slot2-50_1_3553.mzBIN_calibrated 1.3 s [progress: 167010/167010 (100%) - 19618 spectra/s] 8.5s | postprocessing 4.4 s
  42. Saliva_C3_ControlSano_Slot2-51_1_3555.mzBIN_calibrated 1.4 s [progress: 174992/174992 (100%) - 18274 spectra/s] 9.6s | postprocessing 4.8 s
  43. Saliva_D1_desaparicion_Slot2-52_1_3557.mzBIN_calibrated 1.5 s [progress: 180673/180673 (100%) - 19309 spectra/s] 9.4s | postprocessing 5.0 s
  44. Saliva_D2_desaparicion_Slot2-53_1_3559.mzBIN_calibrated 1.3 s [progress: 164464/164464 (100%) - 19424 spectra/s] 8.5s | postprocessing 4.5 s
  45. Saliva_D3_desaparicion_Slot2-54_1_3561.mzBIN_calibrated 1.5 s [progress: 182029/182029 (100%) - 18645 spectra/s] 9.8s | postprocessing 5.0 s
  46. Saliva_R1_recurrencia_Slot2-1_1_3563.mzBIN_calibrated 0.9 s [progress: 108653/108653 (100%) - 24493 spectra/s] 4.4s | postprocessing 2.9 s
  47. Saliva_R2_recurrencia_Slot2-2_1_3565.mzBIN_calibrated 1.3 s [progress: 156128/156128 (100%) - 21042 spectra/s] 7.4s | postprocessing 4.2 s
  48. Saliva_R3_recurrencia_Slot2-3_1_3567.mzBIN_calibrated 1.4 s [progress: 156710/156710 (100%) - 20432 spectra/s] 7.7s | postprocessing 4.2 s MAIN SEARCH DONE IN 15.530 MIN

***TOTAL TIME 256.147 MIN**** Process 'MsFragger' finished, exit code: 0 MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML Process 'MsFragger' finished, exit code: 0 MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML Process 'MsFragger' finished, exit code: 0 MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML Process 'MsFragger' finished, exit code: 0 MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML Process 'MsFragger' finished, exit code: 0 MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML Process 'MsFragger' finished, exit code: 0 MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML Process 'MsFragger' finished, exit code: 0 MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML Process 'MsFragger' finished, exit code: 0 MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML Process 'MsFragger' finished, exit code: 0 MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML Process 'MsFragger' finished, exit code: 0 MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_A1_AFTA_Slot2-46_1_3547.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\Saliva_A1_AFTA_Slot2-46_1_3547.pepXML Process 'MsFragger' finished, exit code: 0 MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_A2_AFTA_Slot2-47_1_3545.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\Saliva_A2_AFTA_Slot2-47_1_3545.pepXML Process 'MsFragger' finished, exit code: 0 MsFragger D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\ProteomicaAftas\Experimentar\Saliva_A3_AFTA_Slot2-48_1_3549.pepXML D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\Saliva_A3_AFTA_Slot2-48_1_3549.pepXML Process 'MsFragger' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\fragpipe-Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck Process 'PeptideProphet: Workspace init' finished, exit code: 0 INFO[20:22:48] Executing Workspace v3.2.7
INFO[20:22:48] Creating workspace
INFO[20:22:48] Done
PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\fragpipe-Saliva_A1_AFTA_Slot2-46_1_3547.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck Process 'PeptideProphet: Workspace init' finished, exit code: 0 INFO[20:22:49] Executing Workspace v3.2.7
INFO[20:22:49] Creating workspace
INFO[20:22:49] Done
PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\fragpipe-Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[20:22:49] Executing Workspace v3.2.7
INFO[20:22:49] Creating workspace
INFO[20:22:49] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\fragpipe-Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[20:22:49] Executing Workspace v3.2.7
INFO[20:22:49] Creating workspace
INFO[20:22:49] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\fragpipe-Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[20:22:49] Executing Workspace v3.2.7
INFO[20:22:49] Creating workspace
INFO[20:22:49] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\fragpipe-Saliva_A2_AFTA_Slot2-47_1_3545.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[20:22:49] Executing Workspace v3.2.7
INFO[20:22:49] Creating workspace
INFO[20:22:49] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\fragpipe-Saliva_A3_AFTA_Slot2-48_1_3549.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[20:22:50] Executing Workspace v3.2.7
INFO[20:22:50] Creating workspace
INFO[20:22:50] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\fragpipe-Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[20:22:50] Executing Workspace v3.2.7
INFO[20:22:50] Creating workspace
INFO[20:22:50] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\fragpipe-Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[20:22:50] Executing Workspace v3.2.7
INFO[20:22:50] Creating workspace
INFO[20:22:50] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\fragpipe-Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[20:22:50] Executing Workspace v3.2.7
INFO[20:22:50] Creating workspace
INFO[20:22:50] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\fragpipe-Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck Process 'PeptideProphet: Workspace init' finished, exit code: 0 INFO[20:22:50] Executing Workspace v3.2.7
INFO[20:22:50] Creating workspace
INFO[20:22:50] Done
PeptideProphet: Workspace init [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\fragpipe-Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --init --nocheck INFO[20:22:51] Executing Workspace v3.2.7
INFO[20:22:51] Creating workspace
INFO[20:22:51] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\fragpipe-Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\fragpipe-Saliva_A1_AFTA_Slot2-46_1_3547.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_A1_AFTA_Slot2-46_1_3547.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\fragpipe-Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\fragpipe-Saliva_A2_AFTA_Slot2-47_1_3545.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_A2_AFTA_Slot2-47_1_3545.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\fragpipe-Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\fragpipe-Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\fragpipe-Saliva_A3_AFTA_Slot2-48_1_3549.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_A3_AFTA_Slot2-48_1_3549.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\fragpipe-Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\fragpipe-Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\fragpipe-Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\fragpipe-Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML INFO[20:22:51] Executing PeptideProphet v3.2.7
INFO[20:22:51] Executing PeptideProphet v3.2.7
INFO[20:22:51] Executing PeptideProphet v3.2.7
INFO[20:22:51] Executing PeptideProphet v3.2.7
INFO[20:22:51] Executing PeptideProphet v3.2.7
INFO[20:22:51] Executing PeptideProphet v3.2.7
INFO[20:22:51] Executing PeptideProphet v3.2.7
INFO[20:22:51] Executing PeptideProphet v3.2.7
INFO[20:22:51] Executing PeptideProphet v3.2.7
INFO[20:22:51] Executing PeptideProphet v3.2.7
INFO[20:22:51] Executing PeptideProphet v3.2.7
C:\TPP\bin\mkdir.exe: cannot create directory C:/tmp': File exists C:\TPP\bin\mkdir.exe: cannot create directoryC:/tmp': File exists C:\TPP\bin\mkdir.exe: cannot create directory C:/tmp': File exists C:\TPP\bin\mkdir.exe: cannot create directoryC:/tmp': File exists C:\TPP\bin\mkdir.exe: cannot create directory C:/tmp': File exists C:\TPP\bin\mkdir.exe: cannot create directoryC:/tmp': File exists C:\TPP\bin\mkdir.exe: cannot create directory C:/tmp': File exists C:\TPP\bin\mkdir.exe: cannot create directoryC:/tmp': File exists Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1/Saliva_R1_recurrencia_Slot2-1_1_3563.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1/Saliva_R1_recurrencia_Slot2-1_1_3563.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1/Saliva_R1_recurrencia_Slot2-1_1_3563.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1/Saliva_R1_recurrencia_Slot2-1_1_3563.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1/Saliva_R1_recurrencia_Slot2-1_1_3563.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1/Saliva_R1_recurrencia_Slot2-1_1_3563.mzML in msms_run_summary tag... file 1: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2/Saliva_R2_recurrencia_Slot2-2_1_3565.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2/Saliva_R2_recurrencia_Slot2-2_1_3565.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2/Saliva_R2_recurrencia_Slot2-2_1_3565.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2/Saliva_R2_recurrencia_Slot2-2_1_3565.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2/Saliva_R2_recurrencia_Slot2-2_1_3565.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2/Saliva_R2_recurrencia_Slot2-2_1_3565.mzML in msms_run_summary tag...

command "C:\TPP\bin\mkdir.exe -p C:/tmp" failed: Operation not permitted file 1: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3/Saliva_R3_recurrencia_Slot2-3_1_3567.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3/Saliva_R3_recurrencia_Slot2-3_1_3567.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3/Saliva_R3_recurrencia_Slot2-3_1_3567.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3/Saliva_R3_recurrencia_Slot2-3_1_3567.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3/Saliva_R3_recurrencia_Slot2-3_1_3567.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3/Saliva_R3_recurrencia_Slot2-3_1_3567.mzML in msms_run_summary tag...

command "C:\TPP\bin\mkdir.exe -p C:/tmp" failed: Operation not permitted file 1: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2/Saliva_C2_ControlSano_Slot2-50_1_3553.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2/Saliva_C2_ControlSano_Slot2-50_1_3553.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2/Saliva_C2_ControlSano_Slot2-50_1_3553.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2/Saliva_C2_ControlSano_Slot2-50_1_3553.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2/Saliva_C2_ControlSano_Slot2-50_1_3553.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2/Saliva_C2_ControlSano_Slot2-50_1_3553.mzML in msms_run_summary tag... file 1: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2/Saliva_D2_desaparicion_Slot2-53_1_3559.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2/Saliva_D2_desaparicion_Slot2-53_1_3559.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2/Saliva_D2_desaparicion_Slot2-53_1_3559.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2/Saliva_D2_desaparicion_Slot2-53_1_3559.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2/Saliva_D2_desaparicion_Slot2-53_1_3559.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2/Saliva_D2_desaparicion_Slot2-53_1_3559.mzML in msms_run_summary tag...

command "C:\TPP\bin\mkdir.exe -p C:/tmp" failed: Operation not permitted file 1: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3/Saliva_D3_desaparicion_Slot2-54_1_3561.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3/Saliva_D3_desaparicion_Slot2-54_1_3561.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3/Saliva_D3_desaparicion_Slot2-54_1_3561.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3/Saliva_D3_desaparicion_Slot2-54_1_3561.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3/Saliva_D3_desaparicion_Slot2-54_1_3561.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3/Saliva_D3_desaparicion_Slot2-54_1_3561.mzML in msms_run_summary tag...

command "C:\TPP\bin\mkdir.exe -p C:/tmp" failed: Operation not permitted file 1: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1/Saliva_C1_ControlSano_Slot2-49_1_3551.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1/Saliva_C1_ControlSano_Slot2-49_1_3551.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1/Saliva_C1_ControlSano_Slot2-49_1_3551.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1/Saliva_C1_ControlSano_Slot2-49_1_3551.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1/Saliva_C1_ControlSano_Slot2-49_1_3551.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1/Saliva_C1_ControlSano_Slot2-49_1_3551.mzML in msms_run_summary tag...

command "C:\TPP\bin\mkdir.exe -p C:/tmp" failed: Operation not permitted file 1: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1/Saliva_A1_AFTA_Slot2-46_1_3547.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1/Saliva_A1_AFTA_Slot2-46_1_3547.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1/Saliva_A1_AFTA_Slot2-46_1_3547.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1/Saliva_A1_AFTA_Slot2-46_1_3547.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1/Saliva_A1_AFTA_Slot2-46_1_3547.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1/Saliva_A1_AFTA_Slot2-46_1_3547.mzML in msms_run_summary tag...

command "C:\TPP\bin\mkdir.exe -p C:/tmp" failed: Operation not permitted file 1: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\Saliva_A1_AFTA_Slot2-46_1_3547.pepXML Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3/Saliva_A3_AFTA_Slot2-48_1_3549.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3/Saliva_A3_AFTA_Slot2-48_1_3549.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3/Saliva_A3_AFTA_Slot2-48_1_3549.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3/Saliva_A3_AFTA_Slot2-48_1_3549.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3/Saliva_A3_AFTA_Slot2-48_1_3549.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3/Saliva_A3_AFTA_Slot2-48_1_3549.mzML in msms_run_summary tag...

command "C:\TPP\bin\mkdir.exe -p C:/tmp" failed: Operation not permitted file 1: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\Saliva_A3_AFTA_Slot2-48_1_3549.pepXML Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2/Saliva_A2_AFTA_Slot2-47_1_3545.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2/Saliva_A2_AFTA_Slot2-47_1_3545.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2/Saliva_A2_AFTA_Slot2-47_1_3545.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2/Saliva_A2_AFTA_Slot2-47_1_3545.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2/Saliva_A2_AFTA_Slot2-47_1_3545.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2/Saliva_A2_AFTA_Slot2-47_1_3545.mzML in msms_run_summary tag...

command "C:\TPP\bin\mkdir.exe -p C:/tmp" failed: Operation not permitted file 1: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\Saliva_A2_AFTA_Slot2-47_1_3545.pepXML Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3/Saliva_C3_ControlSano_Slot2-51_1_3555.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3/Saliva_C3_ControlSano_Slot2-51_1_3555.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3/Saliva_C3_ControlSano_Slot2-51_1_3555.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3/Saliva_C3_ControlSano_Slot2-51_1_3555.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3/Saliva_C3_ControlSano_Slot2-51_1_3555.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3/Saliva_C3_ControlSano_Slot2-51_1_3555.mzML in msms_run_summary tag... file 1: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML processed altogether 88841 results processed altogether 129544 results processed altogether 130728 results processed altogether 141137 results processed altogether 136889 results processed altogether 151084 results processed altogether 142199 results processed altogether 151720 results processed altogether 152949 results processed altogether 154518 results processed altogether 149268 results INFO: Results written to file: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\interact-Saliva_R1_recurrencia_Slot2-1_1_3563.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using search_offsets in ACCMASS mixture distr: 0 init with X! Tandem trypsin

INFO: Processing standard MixtureModel ... Initialising statistical models ... using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using searchoffsets in ACCMASS mixture distr: 0 init with X! Tandem trypsin using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using search_offsets in ACCMASS mixture distr: 0 init with X! Tandem trypsin

INFO: Processing standard MixtureModel ... Initialising statistical models ...

INFO: Processing standard MixtureModel ... Initialising statistical models ...

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using searchoffsets in ACCMASS mixture distr: 0 init with X! Tandem trypsin Iterations: .using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using searchoffsets in ACCMASS mixture distr: 0 init with X! Tandem trypsin using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using searchoffsets in ACCMASS mixture distr: 0 init with X! Tandem trypsin using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using searchoffsets in ACCMASS mixture distr: 0 init with X! Tandem trypsin using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using searchoffsets in ACCMASS mixture distr: 0 init with X! Tandem trypsin using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using searchoffsets in ACCMASS mixture distr: 0 init with X! Tandem trypsin using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using searchoffsets in ACCMASS mixture distr: 0 init with X! Tandem trypsin .using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using search_offsets in ACCMASS mixture distr: 0 init with X! Tandem trypsin PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 605 1+, 47507 2+, 49444 3+, 29162 4+, 14419 5+, 0 6+, and 0 7+ spectra. Found 43807 Decoys, and 97330 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 677 1+, 53123 2+, 54804 3+, 30723 4+, 15191 5+, 0 6+, and 0 7+ spectra. Found 51381 Decoys, and 103137 Non-Decoys INFO: Processing standard MixtureModel ... Initialising statistical models ... PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 842 1+, 58334 2+, 52350 3+, 28620 4+, 12803 5+, 0 6+, and 0 7+ spectra. Found 48640 Decoys, and 104309 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 668 1+, 47934 2+, 50552 3+, 28611 4+, 14434 5+, 0 6+, and 0 7+ spectra. Found 44529 Decoys, and 97670 Non-Decoys INFO: Processing standard MixtureModel ... Initialising statistical models ... PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 733 1+, 52283 2+, 52768 3+, 30132 4+, 15168 5+, 0 6+, and 0 7+ spectra. Found 49131 Decoys, and 101953 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... . PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 711 1+, 43715 2+, 48269 3+, 28832 4+, 15362 5+, 0 6+, and 0 7+ spectra. Found 44815 Decoys, and 92074 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 912 1+, 55222 2+, 52319 3+, 28073 4+, 12742 5+, 0 6+, and 0 7+ spectra. Found 46330 Decoys, and 102938 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: . PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 760 1+, 54983 2+, 53201 3+, 29059 4+, 13717 5+, 0 6+, and 0 7+ spectra. Found 46870 Decoys, and 104850 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .....Iterations: .Iterations: .Iterations: ...Iterations: .Iterations: .Iterations: ..Iterations: ..Iterations: ........................10........................................10......10................2010...10...10.....10.101010...10...................... ..WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations .........INFO[20:27:08] Done
Process 'PeptideProphet' finished, exit code: 0 PeptideProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\fragpipe-Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML-temp] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas ..\Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML ....INFO[20:27:11] Executing PeptideProphet v3.2.7
.........Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1/Saliva_D1_desaparicion_Slot2-52_1_3557.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1/Saliva_D1_desaparicion_Slot2-52_1_3557.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1/Saliva_D1_desaparicion_Slot2-52_1_3557.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1/Saliva_D1_desaparicion_Slot2-52_1_3557.d WARNING: cannot open data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1/Saliva_D1_desaparicion_Slot2-52_1_3557.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1/Saliva_D1_desaparicion_Slot2-52_1_3557.mzML in msms_run_summary tag... file 1: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML .......20...20.. processed altogether 151297 results ..............INFO: Results written to file: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\interact-Saliva_D1_desaparicion_Slot2-52_1_3557.pep.xml

20.2020using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using search_offsets in ACCMASS mixture distr: 0 init with X! Tandem trypsin .20.. 20.. PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 706 1+, 51401 2+, 54038 3+, 29699 4+, 15453 5+, 0 6+, and 0 7+ spectra. Found 49686 Decoys, and 101611 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... ..WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations .. ....WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations ......INFO[20:28:34] Done
Process 'PeptideProphet' finished, exit code: 0 ...Iterations: ..INFO[20:28:40] Done
Process 'PeptideProphet' finished, exit code: 0 ...... .....WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations

... WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations ..WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations ....INFO[20:29:02] Done
Process 'PeptideProphet' finished, exit code: 0 ... ..

.INFO[20:29:08] Done
Process 'PeptideProphet' finished, exit code: 0 WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 26 iterations .INFO[20:29:10] Done
Process 'PeptideProphet' finished, exit code: 0 WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations

.WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 28 iterations INFO[20:29:21] Done
Process 'PeptideProphet' finished, exit code: 0 INFO[20:29:23] Done
Process 'PeptideProphet' finished, exit code: 0 INFO[20:29:23] Done
Process 'PeptideProphet' finished, exit code: 0 .INFO[20:29:27] Done
Process 'PeptideProphet' finished, exit code: 0 INFO[20:29:29] Done
Process 'PeptideProphet' finished, exit code: 0 ...10.........20...... WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations INFO[20:32:04] Done
Process 'PeptideProphet' finished, exit code: 0 PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\fragpipe-Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\fragpipe-Saliva_A1_AFTA_Slot2-46_1_3547.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\fragpipe-Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\fragpipe-Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\fragpipe-Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\fragpipe-Saliva_A2_AFTA_Slot2-47_1_3545.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\fragpipe-Saliva_A3_AFTA_Slot2-48_1_3549.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\fragpipe-Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\fragpipe-Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\fragpipe-Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\fragpipe-Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\fragpipe-Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\interact-Saliva_C3_ControlSano_Slot2-51_1_3555.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\interact-Saliva_A1_AFTA_Slot2-46_1_3547.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\interact-Saliva_C1_ControlSano_Slot2-49_1_3551.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\interact-Saliva_R2_recurrencia_Slot2-2_1_3565.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\interact-Saliva_D3_desaparicion_Slot2-54_1_3561.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\interact-Saliva_A2_AFTA_Slot2-47_1_3545.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\interact-Saliva_A3_AFTA_Slot2-48_1_3549.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\interact-Saliva_D2_desaparicion_Slot2-53_1_3559.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\interact-Saliva_R1_recurrencia_Slot2-1_1_3563.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\interact-Saliva_C2_ControlSano_Slot2-50_1_3553.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\interact-Saliva_R3_recurrencia_Slot2-3_1_3567.pep.xml D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\interact-Saliva_D1_desaparicion_Slot2-52_1_3557.pep.xml INFO[20:32:09] Executing ProteinProphet v3.2.7
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) (no FPKM) (using degen pep info) Reading in D:/ProteomicaAftas/2020_06_15_FragPipe13/Control_3/interact-Saliva_C3_ControlSano_Slot2-51_1_3555.pep.xml... ...read in 305 1+, 24909 2+, 21508 3+, 8000 4+, 2181 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/ProteomicaAftas/2020_06_15_FragPipe13/Ulcer_1/interact-Saliva_A1_AFTA_Slot2-46_1_3547.pep.xml... ...read in 179 1+, 22058 2+, 20793 3+, 8160 4+, 2512 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/ProteomicaAftas/2020_06_15_FragPipe13/Control_1/interact-Saliva_C1_ControlSano_Slot2-49_1_3551.pep.xml... ...read in 179 1+, 22600 2+, 20252 3+, 8072 4+, 2555 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/ProteomicaAftas/2020_06_15_FragPipe13/Recurrence_2/interact-Saliva_R2_recurrencia_Slot2-2_1_3565.pep.xml... ...read in 242 1+, 21266 2+, 19969 3+, 7076 4+, 1605 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/ProteomicaAftas/2020_06_15_FragPipe13/Remission_3/interact-Saliva_D3_desaparicion_Slot2-54_1_3561.pep.xml... ...read in 129 1+, 21756 2+, 20176 3+, 7896 4+, 2355 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/ProteomicaAftas/2020_06_15_FragPipe13/Ulcer_2/interact-Saliva_A2_AFTA_Slot2-47_1_3545.pep.xml... ...read in 260 1+, 25241 2+, 20680 3+, 7891 4+, 2238 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/ProteomicaAftas/2020_06_15_FragPipe13/Ulcer_3/interact-Saliva_A3_AFTA_Slot2-48_1_3549.pep.xml... ...read in 222 1+, 25136 2+, 22185 3+, 8565 4+, 2648 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/ProteomicaAftas/2020_06_15_FragPipe13/Remission_2/interact-Saliva_D2_desaparicion_Slot2-53_1_3559.pep.xml... ...read in 165 1+, 22051 2+, 20875 3+, 8414 4+, 2467 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/ProteomicaAftas/2020_06_15_FragPipe13/Recurrence_1/interact-Saliva_R1_recurrencia_Slot2-1_1_3563.pep.xml... ...read in 167 1+, 13848 2+, 13241 3+, 4297 4+, 1330 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/ProteomicaAftas/2020_06_15_FragPipe13/Control_2/interact-Saliva_C2_ControlSano_Slot2-50_1_3553.pep.xml... ...read in 186 1+, 19321 2+, 18667 3+, 7374 4+, 2420 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/ProteomicaAftas/2020_06_15_FragPipe13/Recurrence_3/interact-Saliva_R3_recurrencia_Slot2-3_1_3567.pep.xml... ...read in 191 1+, 18962 2+, 19878 3+, 7508 4+, 2261 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/ProteomicaAftas/2020_06_15_FragPipe13/Remission_1/interact-Saliva_D1_desaparicion_Slot2-52_1_3557.pep.xml... ...read in 175 1+, 21697 2+, 19973 3+, 8041 4+, 2756 5+, 0 6+, 0 7+ spectra with min prob 0.05

WARNING: Cannot find database specified: "d:/Programas/Programas espectrometr a de masas/Transformar archivos d a mzxl/Fasta philosopher/2020-06-15-decoys-reviewed-contam-UP000005640.fas". Initializing 54875 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% WARNING: Cannot find database "d:/Programas/Programas espectrometr a de masas/Transformar archivos d a mzxl/Fasta philosopher/2020-06-15-decoys-reviewed-contam-UP000005640.fas" for protein lengths and molecular weights. PROTLEN, NORMPROTLEN and PROTMW options are off. Computing degenerate peptides for 17316 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 17834 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 17834 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 17834 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 17834 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 17834 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 16418 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=inf, db_size=0 Calculating sensitivity...and error tables... WARNING: Cannot open DB "d:/Programas/Programas espectrometr a de masas/Transformar archivos d a mzxl/Fasta philosopher/2020-06-15-decoys-reviewed-contam-UP000005640.fas". No coverage information is available. Computing MU for 17834 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%

Finished. INFO[20:35:44] Done
Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:35:46] Executing Database v3.2.7
INFO[20:35:46] Processing database
INFO[20:35:48] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:35:48] Executing Database v3.2.7
INFO[20:35:48] Processing database
Process 'PhilosopherDbAnnotate' finished, exit code: 0 INFO[20:35:50] Done
PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:35:50] Executing Database v3.2.7
INFO[20:35:50] Processing database
INFO[20:35:52] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:35:54] Executing Database v3.2.7
INFO[20:35:54] Processing database
INFO[20:35:56] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:35:56] Executing Database v3.2.7
INFO[20:35:56] Processing database
INFO[20:35:58] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:35:58] Executing Database v3.2.7
INFO[20:35:58] Processing database
Process 'PhilosopherDbAnnotate' finished, exit code: 0 INFO[20:36:00] Done
PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:36:01] Executing Database v3.2.7
INFO[20:36:01] Processing database
Process 'PhilosopherDbAnnotate' finished, exit code: 0 INFO[20:36:04] Done
PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:36:04] Executing Database v3.2.7
INFO[20:36:04] Processing database
INFO[20:36:06] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:36:06] Executing Database v3.2.7
INFO[20:36:06] Processing database
INFO[20:36:08] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:36:10] Executing Database v3.2.7
INFO[20:36:10] Processing database
Process 'PhilosopherDbAnnotate' finished, exit code: 0 INFO[20:36:12] Done
PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:36:12] Executing Database v3.2.7
INFO[20:36:12] Processing database
INFO[20:36:14] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:36:14] Executing Database v3.2.7
INFO[20:36:14] Processing database
INFO[20:36:16] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe database --annotate D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\Fasta philosopher\2020-06-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[20:36:18] Executing Database v3.2.7
INFO[20:36:18] Processing database
INFO[20:36:20] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml INFO[20:36:20] Executing Filter v3.2.7
INFO[20:36:20] Processing peptide identification files
INFO[20:36:25] 1+ Charge profile decoy=37 target=185 INFO[20:36:25] 2+ Charge profile decoy=1535 target=23603 INFO[20:36:25] 3+ Charge profile decoy=570 target=21618 INFO[20:36:25] 4+ Charge profile decoy=187 target=8378 INFO[20:36:25] 5+ Charge profile decoy=81 target=2567 INFO[20:36:25] 6+ Charge profile decoy=0 target=0 INFO[20:36:25] Database search results ions=20874 peptides=16253 psms=58761 INFO[20:36:25] Converged to 1.00 % FDR with 51322 PSMs decoy=517 threshold=0.7111 total=51839 INFO[20:36:26] Converged to 1.00 % FDR with 11621 Peptides decoy=117 threshold=0.9136 total=11738 INFO[20:36:26] Converged to 1.00 % FDR with 16027 Ions decoy=161 threshold=0.8785 total=16188 INFO[20:36:29] Protein inference results decoy=7665 target=8753 INFO[20:36:29] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:36:31] Applying sequential FDR estimation ions=16449 peptides=12101 psms=51140 INFO[20:36:31] Converged to 0.28 % FDR with 50997 PSMs decoy=143 threshold=0.7113 total=51140 INFO[20:36:32] Converged to 0.25 % FDR with 12070 Peptides decoy=31 threshold=0.7116 total=12101 INFO[20:36:32] Converged to 0.25 % FDR with 16407 Ions decoy=42 threshold=0.7116 total=16449 INFO[20:36:32] Post processing identifications
INFO[20:36:34] Mapping modifications
INFO[20:36:41] Processing protein inference
INFO[20:36:44] Assigning protein identifications to layers
INFO[20:36:44] Updating razor PSM assignment to proteins
INFO[20:36:44] Calculating spectral counts
INFO[20:36:44] Saving
INFO[20:36:49] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml INFO[20:36:51] Executing Filter v3.2.7
INFO[20:36:51] Processing peptide identification files
INFO[20:36:56] 1+ Charge profile decoy=31 target=98 INFO[20:36:56] 2+ Charge profile decoy=1438 target=20320 INFO[20:36:56] 3+ Charge profile decoy=640 target=19537 INFO[20:36:56] 4+ Charge profile decoy=207 target=7689 INFO[20:36:56] 5+ Charge profile decoy=72 target=2283 INFO[20:36:56] 6+ Charge profile decoy=0 target=0 INFO[20:36:56] Database search results ions=18882 peptides=14797 psms=52315 INFO[20:36:56] Converged to 1.00 % FDR with 44239 PSMs decoy=446 threshold=0.7922 total=44685 INFO[20:36:57] Converged to 1.00 % FDR with 10554 Peptides decoy=106 threshold=0.9123 total=10660 INFO[20:36:57] Converged to 1.00 % FDR with 14382 Ions decoy=145 threshold=0.8896 total=14527 INFO[20:37:00] Protein inference results decoy=7665 target=8753 INFO[20:37:00] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:37:02] Applying sequential FDR estimation ions=14652 peptides=10851 psms=44237 INFO[20:37:02] Converged to 0.54 % FDR with 43997 PSMs decoy=240 threshold=0.7922 total=44237 INFO[20:37:03] Converged to 0.37 % FDR with 10811 Peptides decoy=40 threshold=0.7925 total=10851 INFO[20:37:03] Converged to 0.37 % FDR with 14598 Ions decoy=54 threshold=0.7925 total=14652 INFO[20:37:03] Post processing identifications
INFO[20:37:04] Mapping modifications
INFO[20:37:11] Processing protein inference
INFO[20:37:13] Assigning protein identifications to layers
INFO[20:37:13] Updating razor PSM assignment to proteins
INFO[20:37:14] Calculating spectral counts
INFO[20:37:14] Saving
INFO[20:37:18] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml INFO[20:37:19] Executing Filter v3.2.7
INFO[20:37:19] Processing peptide identification files
INFO[20:37:24] 1+ Charge profile decoy=39 target=222 INFO[20:37:24] 2+ Charge profile decoy=1607 target=23635 INFO[20:37:24] 3+ Charge profile decoy=485 target=20195 INFO[20:37:24] 4+ Charge profile decoy=174 target=7717 INFO[20:37:24] 5+ Charge profile decoy=61 target=2177 INFO[20:37:24] 6+ Charge profile decoy=0 target=0 INFO[20:37:24] Database search results ions=19503 peptides=15184 psms=56312 INFO[20:37:24] Converged to 1.00 % FDR with 48998 PSMs decoy=494 threshold=0.7052 total=49492 INFO[20:37:25] Converged to 1.00 % FDR with 10605 Peptides decoy=107 threshold=0.9188 total=10712 INFO[20:37:25] Converged to 1.00 % FDR with 14720 Ions decoy=148 threshold=0.8837 total=14868 INFO[20:37:29] Protein inference results decoy=7665 target=8753 INFO[20:37:29] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:37:31] Applying sequential FDR estimation ions=15122 peptides=11049 psms=48840 INFO[20:37:31] Converged to 0.32 % FDR with 48680 PSMs decoy=160 threshold=0.7052 total=48840 INFO[20:37:32] Converged to 0.29 % FDR with 11017 Peptides decoy=32 threshold=0.7053 total=11049 INFO[20:37:32] Converged to 0.28 % FDR with 15079 Ions decoy=43 threshold=0.7053 total=15122 INFO[20:37:32] Post processing identifications
INFO[20:37:34] Mapping modifications
INFO[20:37:40] Processing protein inference
INFO[20:37:43] Assigning protein identifications to layers
INFO[20:37:43] Updating razor PSM assignment to proteins
INFO[20:37:44] Calculating spectral counts
INFO[20:37:44] Saving
INFO[20:37:48] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml INFO[20:37:49] Executing Filter v3.2.7
INFO[20:37:49] Processing peptide identification files
INFO[20:37:53] 1+ Charge profile decoy=32 target=143 INFO[20:37:53] 2+ Charge profile decoy=1401 target=20297 INFO[20:37:53] 3+ Charge profile decoy=582 target=19391 INFO[20:37:53] 4+ Charge profile decoy=222 target=7819 INFO[20:37:53] 5+ Charge profile decoy=87 target=2669 INFO[20:37:53] 6+ Charge profile decoy=0 target=0 INFO[20:37:54] Database search results ions=17646 peptides=13808 psms=52643 INFO[20:37:54] Converged to 1.00 % FDR with 44852 PSMs decoy=452 threshold=0.7673 total=45304 INFO[20:37:54] Converged to 1.00 % FDR with 9385 Peptides decoy=94 threshold=0.9359 total=9479 INFO[20:37:54] Converged to 1.00 % FDR with 12985 Ions decoy=130 threshold=0.9088 total=13115 INFO[20:37:57] Protein inference results decoy=7665 target=8753 INFO[20:37:58] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:37:59] Applying sequential FDR estimation ions=13420 peptides=9847 psms=44777 INFO[20:37:59] Converged to 0.43 % FDR with 44585 PSMs decoy=192 threshold=0.7674 total=44777 INFO[20:38:00] Converged to 0.36 % FDR with 9811 Peptides decoy=36 threshold=0.7674 total=9847 INFO[20:38:00] Converged to 0.38 % FDR with 13369 Ions decoy=51 threshold=0.7674 total=13420 INFO[20:38:00] Post processing identifications
INFO[20:38:02] Mapping modifications
INFO[20:38:07] Processing protein inference
INFO[20:38:10] Assigning protein identifications to layers
INFO[20:38:10] Updating razor PSM assignment to proteins
INFO[20:38:10] Calculating spectral counts
INFO[20:38:10] Saving
INFO[20:38:14] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml INFO[20:38:15] Executing Filter v3.2.7
INFO[20:38:15] Processing peptide identification files
INFO[20:38:20] 1+ Charge profile decoy=42 target=149 INFO[20:38:20] 2+ Charge profile decoy=1243 target=17720 INFO[20:38:20] 3+ Charge profile decoy=489 target=19389 INFO[20:38:20] 4+ Charge profile decoy=178 target=7330 INFO[20:38:20] 5+ Charge profile decoy=72 target=2189 INFO[20:38:20] 6+ Charge profile decoy=0 target=0 INFO[20:38:20] Database search results ions=17555 peptides=13736 psms=48801 INFO[20:38:20] Converged to 1.00 % FDR with 42453 PSMs decoy=428 threshold=0.7585 total=42881 INFO[20:38:20] Converged to 1.00 % FDR with 10045 Peptides decoy=101 threshold=0.8977 total=10146 INFO[20:38:20] Converged to 1.00 % FDR with 13657 Ions decoy=137 threshold=0.8732 total=13794 INFO[20:38:23] Protein inference results decoy=7665 target=8753 INFO[20:38:23] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:38:25] Applying sequential FDR estimation ions=13933 peptides=10347 psms=42429 INFO[20:38:25] Converged to 0.47 % FDR with 42228 PSMs decoy=201 threshold=0.7585 total=42429 INFO[20:38:26] Converged to 0.27 % FDR with 10319 Peptides decoy=28 threshold=0.7586 total=10347 INFO[20:38:26] Converged to 0.30 % FDR with 13891 Ions decoy=42 threshold=0.7586 total=13933 INFO[20:38:26] Post processing identifications
INFO[20:38:28] Mapping modifications
INFO[20:38:33] Processing protein inference
INFO[20:38:36] Assigning protein identifications to layers
INFO[20:38:36] Updating razor PSM assignment to proteins
INFO[20:38:36] Calculating spectral counts
INFO[20:38:36] Saving
INFO[20:38:39] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml INFO[20:38:41] Executing Filter v3.2.7
INFO[20:38:41] Processing peptide identification files
INFO[20:38:45] 1+ Charge profile decoy=38 target=141 INFO[20:38:45] 2+ Charge profile decoy=1357 target=20701 INFO[20:38:45] 3+ Charge profile decoy=549 target=20244 INFO[20:38:45] 4+ Charge profile decoy=194 target=7966 INFO[20:38:45] 5+ Charge profile decoy=81 target=2432 INFO[20:38:45] 6+ Charge profile decoy=0 target=0 INFO[20:38:45] Database search results ions=19028 peptides=14930 psms=53703 INFO[20:38:46] Converged to 1.00 % FDR with 47290 PSMs decoy=477 threshold=0.6576 total=47767 INFO[20:38:46] Converged to 1.00 % FDR with 10791 Peptides decoy=108 threshold=0.8926 total=10899 INFO[20:38:46] Converged to 1.00 % FDR with 14669 Ions decoy=148 threshold=0.862 total=14817 INFO[20:38:49] Protein inference results decoy=7665 target=8753 INFO[20:38:49] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:38:51] Applying sequential FDR estimation ions=15026 peptides=11151 psms=47127 INFO[20:38:51] Converged to 0.38 % FDR with 46948 PSMs decoy=179 threshold=0.6576 total=47127 INFO[20:38:52] Converged to 0.30 % FDR with 11117 Peptides decoy=34 threshold=0.6578 total=11151 INFO[20:38:52] Converged to 0.30 % FDR with 14980 Ions decoy=46 threshold=0.6578 total=15026 INFO[20:38:52] Post processing identifications
INFO[20:38:54] Mapping modifications
INFO[20:39:00] Processing protein inference
INFO[20:39:03] Assigning protein identifications to layers
INFO[20:39:03] Updating razor PSM assignment to proteins
INFO[20:39:03] Calculating spectral counts
INFO[20:39:03] Saving
Process 'PhilosopherFilter' finished, exit code: 0 INFO[20:39:08] Done
PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml INFO[20:39:09] Executing Filter v3.2.7
INFO[20:39:09] Processing peptide identification files
INFO[20:39:13] 1+ Charge profile decoy=45 target=197 INFO[20:39:13] 2+ Charge profile decoy=1399 target=19867 INFO[20:39:13] 3+ Charge profile decoy=426 target=19545 INFO[20:39:13] 4+ Charge profile decoy=140 target=6936 INFO[20:39:13] 5+ Charge profile decoy=40 target=1565 INFO[20:39:13] 6+ Charge profile decoy=0 target=0 INFO[20:39:13] Database search results ions=19438 peptides=15037 psms=50160 INFO[20:39:13] Converged to 1.00 % FDR with 44160 PSMs decoy=445 threshold=0.673 total=44605 INFO[20:39:14] Converged to 0.99 % FDR with 10942 Peptides decoy=109 threshold=0.8906 total=11051 INFO[20:39:14] Converged to 1.00 % FDR with 15159 Ions decoy=153 threshold=0.8532 total=15312 INFO[20:39:18] Protein inference results decoy=7665 target=8753 INFO[20:39:18] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:39:19] Applying sequential FDR estimation ions=15549 peptides=11364 psms=43964 INFO[20:39:20] Converged to 0.26 % FDR with 43848 PSMs decoy=116 threshold=0.673 total=43964 INFO[20:39:20] Converged to 0.26 % FDR with 11334 Peptides decoy=30 threshold=0.6734 total=11364 INFO[20:39:20] Converged to 0.22 % FDR with 15514 Ions decoy=35 threshold=0.6734 total=15549 INFO[20:39:20] Post processing identifications
INFO[20:39:22] Mapping modifications
INFO[20:39:28] Processing protein inference
INFO[20:39:31] Assigning protein identifications to layers
INFO[20:39:31] Updating razor PSM assignment to proteins
INFO[20:39:32] Calculating spectral counts
INFO[20:39:32] Saving
INFO[20:39:38] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml INFO[20:39:40] Executing Filter v3.2.7
INFO[20:39:40] Processing peptide identification files
INFO[20:39:42] 1+ Charge profile decoy=38 target=129 INFO[20:39:42] 2+ Charge profile decoy=998 target=12850 INFO[20:39:42] 3+ Charge profile decoy=349 target=12892 INFO[20:39:42] 4+ Charge profile decoy=143 target=4154 INFO[20:39:42] 5+ Charge profile decoy=34 target=1296 INFO[20:39:42] 6+ Charge profile decoy=0 target=0 INFO[20:39:42] Database search results ions=11860 peptides=9409 psms=32883 INFO[20:39:43] Converged to 1.00 % FDR with 27654 PSMs decoy=279 threshold=0.8403 total=27933 INFO[20:39:44] Converged to 1.00 % FDR with 6846 Peptides decoy=69 threshold=0.8913 total=6915 INFO[20:39:44] Converged to 1.00 % FDR with 9151 Ions decoy=92 threshold=0.8661 total=9243 INFO[20:39:48] Protein inference results decoy=7665 target=8753 INFO[20:39:48] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:39:49] Applying sequential FDR estimation ions=9203 peptides=6957 psms=27747 INFO[20:39:49] Converged to 0.68 % FDR with 27559 PSMs decoy=188 threshold=0.8403 total=27747 INFO[20:39:50] Converged to 0.46 % FDR with 6925 Peptides decoy=32 threshold=0.8404 total=6957 INFO[20:39:50] Converged to 0.46 % FDR with 9160 Ions decoy=43 threshold=0.8404 total=9203 INFO[20:39:50] Post processing identifications
INFO[20:39:51] Mapping modifications
INFO[20:39:55] Processing protein inference
INFO[20:39:57] Assigning protein identifications to layers
INFO[20:39:57] Updating razor PSM assignment to proteins
INFO[20:39:58] Calculating spectral counts
INFO[20:39:58] Saving
INFO[20:40:00] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml INFO[20:40:02] Executing Filter v3.2.7
INFO[20:40:02] Processing peptide identification files
INFO[20:40:06] 1+ Charge profile decoy=31 target=148 INFO[20:40:06] 2+ Charge profile decoy=1567 target=21033 INFO[20:40:06] 3+ Charge profile decoy=565 target=19687 INFO[20:40:06] 4+ Charge profile decoy=219 target=7853 INFO[20:40:06] 5+ Charge profile decoy=84 target=2471 INFO[20:40:06] 6+ Charge profile decoy=0 target=0 INFO[20:40:06] Database search results ions=18771 peptides=14600 psms=53658 INFO[20:40:06] Converged to 1.00 % FDR with 45796 PSMs decoy=462 threshold=0.7759 total=46258 INFO[20:40:07] Converged to 1.00 % FDR with 10181 Peptides decoy=102 threshold=0.916 total=10283 INFO[20:40:07] Converged to 1.00 % FDR with 14085 Ions decoy=142 threshold=0.8907 total=14227 INFO[20:40:11] Protein inference results decoy=7665 target=8753 INFO[20:40:11] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:40:13] Applying sequential FDR estimation ions=14439 peptides=10558 psms=45751 INFO[20:40:13] Converged to 0.43 % FDR with 45555 PSMs decoy=196 threshold=0.7759 total=45751 INFO[20:40:13] Converged to 0.37 % FDR with 10519 Peptides decoy=39 threshold=0.7764 total=10558 INFO[20:40:13] Converged to 0.37 % FDR with 14385 Ions decoy=54 threshold=0.7763 total=14439 INFO[20:40:14] Post processing identifications
INFO[20:40:15] Mapping modifications
INFO[20:40:22] Processing protein inference
INFO[20:40:24] Assigning protein identifications to layers
INFO[20:40:24] Updating razor PSM assignment to proteins
INFO[20:40:25] Calculating spectral counts
INFO[20:40:25] Saving
Process 'PhilosopherFilter' finished, exit code: 0 INFO[20:40:29] Done
PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml INFO[20:40:30] Executing Filter v3.2.7
INFO[20:40:30] Processing peptide identification files
INFO[20:40:35] 1+ Charge profile decoy=23 target=142 INFO[20:40:35] 2+ Charge profile decoy=1459 target=20594 INFO[20:40:35] 3+ Charge profile decoy=539 target=20336 INFO[20:40:35] 4+ Charge profile decoy=220 target=8195 INFO[20:40:35] 5+ Charge profile decoy=88 target=2379 INFO[20:40:35] 6+ Charge profile decoy=0 target=0 INFO[20:40:35] Database search results ions=18448 peptides=14538 psms=53975 INFO[20:40:35] Converged to 1.00 % FDR with 46767 PSMs decoy=472 threshold=0.6666 total=47239 INFO[20:40:36] Converged to 1.00 % FDR with 10047 Peptides decoy=101 threshold=0.9053 total=10148 INFO[20:40:36] Converged to 1.00 % FDR with 13810 Ions decoy=139 threshold=0.8673 total=13949 INFO[20:40:39] Protein inference results decoy=7665 target=8753 INFO[20:40:40] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:40:41] Applying sequential FDR estimation ions=14157 peptides=10457 psms=46537 INFO[20:40:41] Converged to 0.27 % FDR with 46408 PSMs decoy=129 threshold=0.6666 total=46537 INFO[20:40:42] Converged to 0.22 % FDR with 10434 Peptides decoy=23 threshold=0.6667 total=10457 INFO[20:40:42] Converged to 0.19 % FDR with 14129 Ions decoy=28 threshold=0.6667 total=14157 INFO[20:40:42] Post processing identifications
INFO[20:40:44] Mapping modifications
INFO[20:40:50] Processing protein inference
INFO[20:40:53] Assigning protein identifications to layers
INFO[20:40:53] Updating razor PSM assignment to proteins
INFO[20:40:53] Calculating spectral counts
INFO[20:40:53] Saving
INFO[20:40:57] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml INFO[20:40:59] Executing Filter v3.2.7
INFO[20:40:59] Processing peptide identification files
INFO[20:41:03] 1+ Charge profile decoy=45 target=141 INFO[20:41:03] 2+ Charge profile decoy=1313 target=18009 INFO[20:41:03] 3+ Charge profile decoy=553 target=18114 INFO[20:41:03] 4+ Charge profile decoy=189 target=7185 INFO[20:41:03] 5+ Charge profile decoy=69 target=2352 INFO[20:41:03] 6+ Charge profile decoy=0 target=0 INFO[20:41:03] Database search results ions=17074 peptides=13303 psms=47970 INFO[20:41:03] Converged to 1.00 % FDR with 41072 PSMs decoy=414 threshold=0.7665 total=41486 INFO[20:41:04] Converged to 1.00 % FDR with 9403 Peptides decoy=94 threshold=0.8962 total=9497 INFO[20:41:04] Converged to 1.00 % FDR with 12859 Ions decoy=129 threshold=0.8812 total=12988 INFO[20:41:08] Protein inference results decoy=7665 target=8753 INFO[20:41:08] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:41:09] Applying sequential FDR estimation ions=13141 peptides=9652 psms=41050 INFO[20:41:09] Converged to 0.45 % FDR with 40865 PSMs decoy=185 threshold=0.7666 total=41050 INFO[20:41:10] Converged to 0.30 % FDR with 9623 Peptides decoy=29 threshold=0.7667 total=9652 INFO[20:41:11] Converged to 0.31 % FDR with 13100 Ions decoy=41 threshold=0.7667 total=13141 INFO[20:41:11] Post processing identifications
INFO[20:41:12] Mapping modifications
INFO[20:41:18] Processing protein inference
INFO[20:41:20] Assigning protein identifications to layers
INFO[20:41:20] Updating razor PSM assignment to proteins
INFO[20:41:21] Calculating spectral counts
INFO[20:41:21] Saving
INFO[20:41:24] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3 --protxml D:\ProteomicaAftas\2020_06_15_FragPipe13\combined.prot.xml INFO[20:41:26] Executing Filter v3.2.7
INFO[20:41:26] Processing peptide identification files
INFO[20:41:31] 1+ Charge profile decoy=53 target=252 INFO[20:41:31] 2+ Charge profile decoy=1558 target=23354 INFO[20:41:31] 3+ Charge profile decoy=521 target=20987 INFO[20:41:31] 4+ Charge profile decoy=185 target=7816 INFO[20:41:31] 5+ Charge profile decoy=60 target=2121 INFO[20:41:31] 6+ Charge profile decoy=0 target=0 INFO[20:41:31] Database search results ions=20607 peptides=16032 psms=56907 INFO[20:41:31] Converged to 1.00 % FDR with 50191 PSMs decoy=506 threshold=0.6419 total=50697 INFO[20:41:32] Converged to 1.00 % FDR with 11475 Peptides decoy=115 threshold=0.8948 total=11590 INFO[20:41:32] Converged to 1.00 % FDR with 15816 Ions decoy=159 threshold=0.8666 total=15975 INFO[20:41:35] Protein inference results decoy=7665 target=8753 INFO[20:41:35] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:41:37] Applying sequential FDR estimation ions=16292 peptides=11921 psms=49960 INFO[20:41:37] Converged to 0.28 % FDR with 49818 PSMs decoy=142 threshold=0.6419 total=49960 INFO[20:41:38] Converged to 0.24 % FDR with 11892 Peptides decoy=29 threshold=0.6419 total=11921 INFO[20:41:38] Converged to 0.23 % FDR with 16254 Ions decoy=38 threshold=0.6419 total=16292 INFO[20:41:39] Post processing identifications
INFO[20:41:40] Mapping modifications
INFO[20:41:47] Processing protein inference
INFO[20:41:50] Assigning protein identifications to layers
INFO[20:41:50] Updating razor PSM assignment to proteins
INFO[20:41:50] Calculating spectral counts
INFO[20:41:50] Saving
INFO[20:41:54] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report INFO[20:41:57] Executing Report v3.2.7
INFO[20:42:00] Creating reports
INFO[20:42:01] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report INFO[20:42:01] Executing Report v3.2.7
INFO[20:42:04] Creating reports
INFO[20:42:06] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report INFO[20:42:08] Executing Report v3.2.7
INFO[20:42:09] Creating reports
INFO[20:42:11] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report INFO[20:42:11] Executing Report v3.2.7
INFO[20:42:14] Creating reports
INFO[20:42:15] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report INFO[20:42:17] Executing Report v3.2.7
INFO[20:42:19] Creating reports
Process 'PhilosopherReport' finished, exit code: 0 INFO[20:42:21] Done
PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report INFO[20:42:22] Executing Report v3.2.7
INFO[20:42:24] Creating reports
INFO[20:42:26] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report INFO[20:42:27] Executing Report v3.2.7
INFO[20:42:30] Creating reports
INFO[20:42:32] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report INFO[20:42:32] Executing Report v3.2.7
INFO[20:42:34] Creating reports
INFO[20:42:36] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report INFO[20:42:37] Executing Report v3.2.7
INFO[20:42:40] Creating reports
INFO[20:42:41] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report INFO[20:42:42] Executing Report v3.2.7
INFO[20:42:44] Creating reports
INFO[20:42:46] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report INFO[20:42:47] Executing Report v3.2.7
INFO[20:42:50] Creating reports
Process 'PhilosopherReport' finished, exit code: 0 INFO[20:42:51] Done
PhilosopherReport [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe report INFO[20:42:51] Executing Report v3.2.7
INFO[20:42:54] Creating reports
INFO[20:42:55] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherAbacus [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windowsamd64\philosopher.exe abacus --razor --reprint --tag rev --protein Ulcer_3 Remission_3 Ulcer_2 Remission_1 Recurrence_3 Ulcer_1 Recurrence_2 Recurrence_1 Control_1 Remission_2 Control_2 Control_3 INFO[20:42:57] Executing Abacus v3.2.7
INFO[20:42:57] Processing combined file
INFO[20:42:59] Converged to 1.03 % FDR with 1354 Proteins decoy=14 threshold=0.9976 total=1368 INFO[20:43:01] Restoring protein results
INFO[20:43:33] Processing spectral counts
INFO[20:43:35] Processing intensities
INFO[20:43:35] Creating Reprint reports
INFO[20:43:36] Done
Process 'PhilosopherAbacus' finished, exit code: 0 IonQuant [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Xmx28G -Dlibs.bruker.dir="D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\MSFragger-3.0\ext\bruker" -Dlibs.thermo.dir="D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\MSFragger-3.0\ext\thermo" -cp "D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\tools\ionquant-1.3.0.jar;D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar" ionquant.IonQuant --threads 12 --ionmobility 1 --mbr 1 --proteinquant 2 --requantify 0 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0.5 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 3 --ionfdr 0.01 --proteinfdr 0.01 --peptidefdr 0.01 --normalization 1 --minisotopes 2 --tp 3 --minfreq 0.5 --minions 2 --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_3\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_3\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_2\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_1\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_3\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Ulcer_1\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_2\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Recurrence_1\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_1\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Remission_2\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_2\psm.tsv --psm D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3\psm.tsv --multidir D:\ProteomicaAftas\2020_06_15_FragPipe13 D:\ProteomicaAftas\Experimentar\Saliva_C3_ControlSano_Slot2-51_1_3555.d Control_3\Saliva_C3_ControlSano_Slot2-51_1_3555.pepXML D:\ProteomicaAftas\Experimentar\Saliva_A1_AFTA_Slot2-46_1_3547.d Ulcer_1\Saliva_A1_AFTA_Slot2-46_1_3547.pepXML D:\ProteomicaAftas\Experimentar\Saliva_C1_ControlSano_Slot2-49_1_3551.d Control_1\Saliva_C1_ControlSano_Slot2-49_1_3551.pepXML D:\ProteomicaAftas\Experimentar\Saliva_R2_recurrencia_Slot2-2_1_3565.d Recurrence_2\Saliva_R2_recurrencia_Slot2-2_1_3565.pepXML D:\ProteomicaAftas\Experimentar\Saliva_D3_desaparicion_Slot2-54_1_3561.d Remission_3\Saliva_D3_desaparicion_Slot2-54_1_3561.pepXML D:\ProteomicaAftas\Experimentar\Saliva_A2_AFTA_Slot2-47_1_3545.d Ulcer_2\Saliva_A2_AFTA_Slot2-47_1_3545.pepXML D:\ProteomicaAftas\Experimentar\Saliva_A3_AFTA_Slot2-48_1_3549.d Ulcer_3\Saliva_A3_AFTA_Slot2-48_1_3549.pepXML D:\ProteomicaAftas\Experimentar\Saliva_D2_desaparicion_Slot2-53_1_3559.d Remission_2\Saliva_D2_desaparicion_Slot2-53_1_3559.pepXML D:\ProteomicaAftas\Experimentar\Saliva_C2_ControlSano_Slot2-50_1_3553.d Control_2\Saliva_C2_ControlSano_Slot2-50_1_3553.pepXML D:\ProteomicaAftas\Experimentar\Saliva_R1_recurrencia_Slot2-1_1_3563.d Recurrence_1\Saliva_R1_recurrencia_Slot2-1_1_3563.pepXML D:\ProteomicaAftas\Experimentar\Saliva_R3_recurrencia_Slot2-3_1_3567.d Recurrence_3\Saliva_R3_recurrencia_Slot2-3_1_3567.pepXML D:\ProteomicaAftas\Experimentar\Saliva_D1_desaparicion_Slot2-52_1_3557.d Remission_1\Saliva_D1_desaparicion_Slot2-52_1_3557.pepXML Error: no se ha encontrado o cargado la clase principal espectrometr�a Process 'IonQuant' finished, exit code: 1 log_2020-06-16_20-46-30.txt Process returned non-zero exit code, stoppingWorkspaceClean [Work dir: D:\ProteomicaAftas\2020_06_15_FragPipe13\Control_3] D:\Programas\Programas espectrometría de masas\Transformar archivos d a mzxl\philosopher_v3.2.7_windows_amd64\philosopher.exe workspace --clean --nocheck


Cancelling 25 remaining tasks
Processing interrupted, stopping WorkspaceClean
fcyu commented 4 years ago

The critical information was masked by a non-English language: "Error: no se ha encontrado o cargado la clase principal espectrometr�a". Could someone translate it for me (google translate's result seems not right)? :sweat_smile:

If let me try, I guess it's because IonQuant cannot find Bruker's library. @cesarrivera could you delete those spaces in your folder name and try again?

Thanks,

Fengchao

cesarrivera commented 4 years ago

Thanks for your quick response! The translation would be: "* Error: main spectrometry class not found or loaded" I deleted all spaces from routes/folders. I am trying again. I will notify the result!

cesarrivera commented 4 years ago

Hello! all samples ran. My doubts now, are the following "warnings" in ProteinProphet:

Process 'PeptideProphet' finished, exit code: 0 WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 28 iterations

WARNING: Found the following zero-mass residues in protein entry rev_sp|O60613|SEP15_HUMAN : U WARNING: Found the following zero-mass residues in protein entry rev_sp|P07203|GPX1_HUMAN : U WARNING: Found the following zero-mass residues in protein entry rev_sp|Q86VQ6|TRXR3_HUMAN : U WARNING: Found the following zero-mass residues in protein entry rev_sp|Q92813|IOD2_HUMAN : UU WARNING: Found the following zero-mass residues in protein entry rev_sp|Q99611|SPS2_HUMAN : U WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9NZV5|SELN_HUMAN : UU WARNING: Found the following zero-mass residues in protein entry sp|P07203|GPX1_HUMAN : U WARNING: Found the following zero-mass residues in protein entry sp|P22352|GPX3_HUMAN : U WARNING: Found the following zero-mass residues in protein entry sp|P49895|IOD1_HUMAN : U WARNING: Found the following zero-mass residues in protein entry sp|P59796|GPX6_HUMAN : U WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U WARNING: Found the following zero-mass residues in protein entry sp|Q86VQ6|TRXR3_HUMAN : U WARNING: Found the following zero-mass residues in protein entry sp|Q99611|SPS2_HUMAN : U WARNING: Found the following zero-mass residues in protein entry sp|Q9NNW7|TRXR2_HUMAN : U WARNING: Found the following zero-mass residues in protein entry sp|Q9NZV6|MSRB1_HUMAN : U

What do they mean? Best regards, César

log_2020-06-17_09-04-09.txt

fcyu commented 4 years ago

Hi @cesarrivera ,

Those warning can be ignored. Your log looks good.

Best,

Fengchao

cesarrivera commented 4 years ago

Thanks for your quick response! Best, César Rivera Universidad de Talca Chile