System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK .NET Core Info: 6.0.11 Version info: FragPipe version 21.1 MSFragger version 4.0 IonQuant version 1.10.12 Philosopher version 5.1.0 LCMS files: Experiment/Group: CM_1 (if "spectral library generation" is enabled, all files will be analyzed together) - D:\DATA_MAUD\CM_1_RA2_1_31922.mzML DDA Experiment/Group: CM_3 (if "spectral library generation" is enabled, all files will be analyzed together) - D:\DATA_MAUD\CM_3_RA3_1_31923.mzML DDA Experiment/Group: CM_4 (if "spectral library generation" is enabled, all files will be analyzed together) - D:\DATA_MAUD\CM_4_RA4_1_31925.mzML DDA Experiment/Group: CM_5 (if "spectral library generation" is enabled, all files will be analyzed together) - D:\DATA_MAUD\CM_5_RA5_1_31926.mzML DDA Experiment/Group: E1_1 (if "spectral library generation" is enabled, all files will be analyzed together) - D:\DATA_MAUD\E1_1_RA6_1_31928.mzML DDA Experiment/Group: E1_4 (if "spectral library generation" is enabled, all files will be analyzed together) - D:\DATA_MAUD\E1_4_RA7_1_31929.mzML DDA Experiment/Group: E1_5 (if "spectral library generation" is enabled, all files will be analyzed together) - D:\DATA_MAUD\E1_5_RA8_1_31930.mzML DDA Experiment/Group: E2_1 (if "spectral library generation" is enabled, all files will be analyzed together) - D:\DATA_MAUD\E2_1_RB1_1_31932.mzML DDA Experiment/Group: E2_3 (if "spectral library generation" is enabled, all files will be analyzed together) - D:\DATA_MAUD\E2_3_RB2_1_31933.mzML DDA Experiment/Group: E2_4 (if "spectral library generation" is enabled, all files will be analyzed together) - D:\DATA_MAUD\E2_4_RB3_1_31935.mzML DDA Experiment/Group: E2_5 (if "spectral library generation" is enabled, all files will be analyzed together) - D:\DATA_MAUD\E2_5_RB4_1_31936.mzML DDA 130 commands to execute: CheckCentroid C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -Xmx3G -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid D:\DATA_MAUD\CM_1_RA2_1_31922.mzML 11 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\13ad578d-d78c-4c4a-8e43-a7923d1a1071 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\94ad0f05-86f4-4249-b881-ccfe9f3ad01d WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E1_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E1_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\3af6cf0d-a31e-4f8c-8f5e-ab6d46cd163e WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\50e82806-db83-46c4-ad69-8b7372eb4549 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E1_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E1_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\08ad0f17-a581-4079-ad1c-c8a7e304e851 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\4c642cea-d58c-4af6-875a-87a5e7b0ab19 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\8f8bf91c-826f-47aa-874b-04cf90f6980a WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E1_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E1_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\3144d218-0b2b-4923-bd95-f670a40f134a WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\c0a233b3-38a7-49c4-8840-b809a42ac9d0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\33cef2f4-ecb8-47d5-9877-4408af8b9547 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\4fcfd6e1-987c-49ac-8d0b-a8d012e6f622 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\79677a70-51f3-4f52-972f-c6669db70534 MSFragger [Work dir: D:\DATA_MAUD\Results] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx3G C:\Users\lucas\Desktop\FragPipe\MSFragger-4.0\MSFragger-4.0.jar D:\DATA_MAUD\Results\fragger.params D:\DATA_MAUD\CM_1_RA2_1_31922.mzML D:\DATA_MAUD\CM_3_RA3_1_31923.mzML D:\DATA_MAUD\CM_4_RA4_1_31925.mzML D:\DATA_MAUD\CM_5_RA5_1_31926.mzML D:\DATA_MAUD\E1_1_RA6_1_31928.mzML D:\DATA_MAUD\E1_4_RA7_1_31929.mzML D:\DATA_MAUD\E1_5_RA8_1_31930.mzML D:\DATA_MAUD\E2_1_RB1_1_31932.mzML D:\DATA_MAUD\E2_3_RB2_1_31933.mzML D:\DATA_MAUD\E2_4_RB3_1_31935.mzML D:\DATA_MAUD\E2_5_RB4_1_31936.mzML MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_1_RA2_1_31922.pepXML D:\DATA_MAUD\Results\CM_1\CM_1_RA2_1_31922.pepXML MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_1_RA2_1_31922.pin D:\DATA_MAUD\Results\CM_1\CM_1_RA2_1_31922.pin MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_3_RA3_1_31923.pepXML D:\DATA_MAUD\Results\CM_3\CM_3_RA3_1_31923.pepXML MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_3_RA3_1_31923.pin D:\DATA_MAUD\Results\CM_3\CM_3_RA3_1_31923.pin MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_4_RA4_1_31925.pepXML D:\DATA_MAUD\Results\CM_4\CM_4_RA4_1_31925.pepXML MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_4_RA4_1_31925.pin D:\DATA_MAUD\Results\CM_4\CM_4_RA4_1_31925.pin MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_5_RA5_1_31926.pepXML D:\DATA_MAUD\Results\CM_5\CM_5_RA5_1_31926.pepXML MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_5_RA5_1_31926.pin D:\DATA_MAUD\Results\CM_5\CM_5_RA5_1_31926.pin MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E1_1_RA6_1_31928.pepXML D:\DATA_MAUD\Results\E1_1\E1_1_RA6_1_31928.pepXML MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E1_1_RA6_1_31928.pin D:\DATA_MAUD\Results\E1_1\E1_1_RA6_1_31928.pin MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E1_4_RA7_1_31929.pepXML D:\DATA_MAUD\Results\E1_4\E1_4_RA7_1_31929.pepXML MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E1_4_RA7_1_31929.pin D:\DATA_MAUD\Results\E1_4\E1_4_RA7_1_31929.pin MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E1_5_RA8_1_31930.pepXML D:\DATA_MAUD\Results\E1_5\E1_5_RA8_1_31930.pepXML MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E1_5_RA8_1_31930.pin D:\DATA_MAUD\Results\E1_5\E1_5_RA8_1_31930.pin MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_1_RB1_1_31932.pepXML D:\DATA_MAUD\Results\E2_1\E2_1_RB1_1_31932.pepXML MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_1_RB1_1_31932.pin D:\DATA_MAUD\Results\E2_1\E2_1_RB1_1_31932.pin MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_3_RB2_1_31933.pepXML D:\DATA_MAUD\Results\E2_3\E2_3_RB2_1_31933.pepXML MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_3_RB2_1_31933.pin D:\DATA_MAUD\Results\E2_3\E2_3_RB2_1_31933.pin MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_4_RB3_1_31935.pepXML D:\DATA_MAUD\Results\E2_4\E2_4_RB3_1_31935.pepXML MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_4_RB3_1_31935.pin D:\DATA_MAUD\Results\E2_4\E2_4_RB3_1_31935.pin MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_5_RB4_1_31936.pepXML D:\DATA_MAUD\Results\E2_5\E2_5_RB4_1_31936.pepXML MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_5_RB4_1_31936.pin D:\DATA_MAUD\Results\E2_5\E2_5_RB4_1_31936.pin MSBooster [Work dir: D:\DATA_MAUD\Results] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -Xmx3G -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\msbooster-1.1.28.jar;C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\batmass-io-1.30.0.jar Features.MainClass --paramsList D:\DATA_MAUD\Results\msbooster_params.txt Percolator [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms CM_1_RA2_1_31922_percolator_target_psms.tsv --decoy-results-psms CM_1_RA2_1_31922_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CM_1_RA2_1_31922_edited.pin Percolator [Work dir: D:\DATA_MAUD\Results\CM_5] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms CM_5_RA5_1_31926_percolator_target_psms.tsv --decoy-results-psms CM_5_RA5_1_31926_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CM_5_RA5_1_31926_edited.pin Percolator [Work dir: D:\DATA_MAUD\Results\E1_4] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E1_4_RA7_1_31929_percolator_target_psms.tsv --decoy-results-psms E1_4_RA7_1_31929_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E1_4_RA7_1_31929_edited.pin Percolator [Work dir: D:\DATA_MAUD\Results\E1_5] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E1_5_RA8_1_31930_percolator_target_psms.tsv --decoy-results-psms E1_5_RA8_1_31930_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E1_5_RA8_1_31930_edited.pin Percolator [Work dir: D:\DATA_MAUD\Results\CM_3] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms CM_3_RA3_1_31923_percolator_target_psms.tsv --decoy-results-psms CM_3_RA3_1_31923_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CM_3_RA3_1_31923_edited.pin Percolator [Work dir: D:\DATA_MAUD\Results\CM_4] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms CM_4_RA4_1_31925_percolator_target_psms.tsv --decoy-results-psms CM_4_RA4_1_31925_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CM_4_RA4_1_31925_edited.pin Percolator [Work dir: D:\DATA_MAUD\Results\E2_3] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E2_3_RB2_1_31933_percolator_target_psms.tsv --decoy-results-psms E2_3_RB2_1_31933_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E2_3_RB2_1_31933_edited.pin Percolator [Work dir: D:\DATA_MAUD\Results\E2_1] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E2_1_RB1_1_31932_percolator_target_psms.tsv --decoy-results-psms E2_1_RB1_1_31932_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E2_1_RB1_1_31932_edited.pin Percolator [Work dir: D:\DATA_MAUD\Results\E1_1] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E1_1_RA6_1_31928_percolator_target_psms.tsv --decoy-results-psms E1_1_RA6_1_31928_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E1_1_RA6_1_31928_edited.pin Percolator [Work dir: D:\DATA_MAUD\Results\E2_4] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E2_4_RB3_1_31935_percolator_target_psms.tsv --decoy-results-psms E2_4_RB3_1_31935_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E2_4_RB3_1_31935_edited.pin Percolator [Work dir: D:\DATA_MAUD\Results\E2_5] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E2_5_RB4_1_31936_percolator_target_psms.tsv --decoy-results-psms E2_5_RB4_1_31936_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E2_5_RB4_1_31936_edited.pin Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CM_1_RA2_1_31922.pin CM_1_RA2_1_31922 CM_1_RA2_1_31922_percolator_target_psms.tsv CM_1_RA2_1_31922_percolator_decoy_psms.tsv interact-CM_1_RA2_1_31922 DDA 0.5 D:\DATA_MAUD\CM_1_RA2_1_31922.mzML Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_1\CM_1_RA2_1_31922_percolator_target_psms.tsv Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_1\CM_1_RA2_1_31922_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\CM_5] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CM_5_RA5_1_31926.pin CM_5_RA5_1_31926 CM_5_RA5_1_31926_percolator_target_psms.tsv CM_5_RA5_1_31926_percolator_decoy_psms.tsv interact-CM_5_RA5_1_31926 DDA 0.5 D:\DATA_MAUD\CM_5_RA5_1_31926.mzML Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_5\CM_5_RA5_1_31926_percolator_target_psms.tsv Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_5\CM_5_RA5_1_31926_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E1_4] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E1_4_RA7_1_31929.pin E1_4_RA7_1_31929 E1_4_RA7_1_31929_percolator_target_psms.tsv E1_4_RA7_1_31929_percolator_decoy_psms.tsv interact-E1_4_RA7_1_31929 DDA 0.5 D:\DATA_MAUD\E1_4_RA7_1_31929.mzML Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E1_4\E1_4_RA7_1_31929_percolator_target_psms.tsv Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E1_4\E1_4_RA7_1_31929_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E1_5] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E1_5_RA8_1_31930.pin E1_5_RA8_1_31930 E1_5_RA8_1_31930_percolator_target_psms.tsv E1_5_RA8_1_31930_percolator_decoy_psms.tsv interact-E1_5_RA8_1_31930 DDA 0.5 D:\DATA_MAUD\E1_5_RA8_1_31930.mzML Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E1_5\E1_5_RA8_1_31930_percolator_target_psms.tsv Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E1_5\E1_5_RA8_1_31930_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\CM_3] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CM_3_RA3_1_31923.pin CM_3_RA3_1_31923 CM_3_RA3_1_31923_percolator_target_psms.tsv CM_3_RA3_1_31923_percolator_decoy_psms.tsv interact-CM_3_RA3_1_31923 DDA 0.5 D:\DATA_MAUD\CM_3_RA3_1_31923.mzML Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_3\CM_3_RA3_1_31923_percolator_target_psms.tsv Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_3\CM_3_RA3_1_31923_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\CM_4] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CM_4_RA4_1_31925.pin CM_4_RA4_1_31925 CM_4_RA4_1_31925_percolator_target_psms.tsv CM_4_RA4_1_31925_percolator_decoy_psms.tsv interact-CM_4_RA4_1_31925 DDA 0.5 D:\DATA_MAUD\CM_4_RA4_1_31925.mzML Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_4\CM_4_RA4_1_31925_percolator_target_psms.tsv Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_4\CM_4_RA4_1_31925_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E2_3] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E2_3_RB2_1_31933.pin E2_3_RB2_1_31933 E2_3_RB2_1_31933_percolator_target_psms.tsv E2_3_RB2_1_31933_percolator_decoy_psms.tsv interact-E2_3_RB2_1_31933 DDA 0.5 D:\DATA_MAUD\E2_3_RB2_1_31933.mzML Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_3\E2_3_RB2_1_31933_percolator_target_psms.tsv Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_3\E2_3_RB2_1_31933_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E2_1] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E2_1_RB1_1_31932.pin E2_1_RB1_1_31932 E2_1_RB1_1_31932_percolator_target_psms.tsv E2_1_RB1_1_31932_percolator_decoy_psms.tsv interact-E2_1_RB1_1_31932 DDA 0.5 D:\DATA_MAUD\E2_1_RB1_1_31932.mzML Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_1\E2_1_RB1_1_31932_percolator_target_psms.tsv Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_1\E2_1_RB1_1_31932_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E1_1] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E1_1_RA6_1_31928.pin E1_1_RA6_1_31928 E1_1_RA6_1_31928_percolator_target_psms.tsv E1_1_RA6_1_31928_percolator_decoy_psms.tsv interact-E1_1_RA6_1_31928 DDA 0.5 D:\DATA_MAUD\E1_1_RA6_1_31928.mzML Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E1_1\E1_1_RA6_1_31928_percolator_target_psms.tsv Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E1_1\E1_1_RA6_1_31928_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E2_4] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E2_4_RB3_1_31935.pin E2_4_RB3_1_31935 E2_4_RB3_1_31935_percolator_target_psms.tsv E2_4_RB3_1_31935_percolator_decoy_psms.tsv interact-E2_4_RB3_1_31935 DDA 0.5 D:\DATA_MAUD\E2_4_RB3_1_31935.mzML Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_4\E2_4_RB3_1_31935_percolator_target_psms.tsv Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_4\E2_4_RB3_1_31935_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E2_5] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E2_5_RB4_1_31936.pin E2_5_RB4_1_31936 E2_5_RB4_1_31936_percolator_target_psms.tsv E2_5_RB4_1_31936_percolator_decoy_psms.tsv interact-E2_5_RB4_1_31936 DDA 0.5 D:\DATA_MAUD\E2_5_RB4_1_31936.mzML Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_5\E2_5_RB4_1_31936_percolator_target_psms.tsv Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_5\E2_5_RB4_1_31936_percolator_decoy_psms.tsv ProteinProphet [Work dir: D:\DATA_MAUD\Results] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\DATA_MAUD\Results\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe database --annotate C:\Users\lucas\Desktop\FragPipe\2024-05-02-decoys-Hbt_salinarum_NRC_1_Membrane_Proteome.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\DATA_MAUD\Results\CM_1 --protxml D:\DATA_MAUD\Results\combined.prot.xml --razor PhilosopherFilter [Work dir: D:\DATA_MAUD\Results\CM_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\DATA_MAUD\Results\CM_3 --dbbin D:\DATA_MAUD\Results\CM_1 --protxml D:\DATA_MAUD\Results\combined.prot.xml --probin D:\DATA_MAUD\Results\CM_1 --razor PhilosopherFilter [Work dir: D:\DATA_MAUD\Results\CM_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\DATA_MAUD\Results\CM_4 --dbbin D:\DATA_MAUD\Results\CM_1 --protxml D:\DATA_MAUD\Results\combined.prot.xml --probin D:\DATA_MAUD\Results\CM_1 --razor PhilosopherFilter [Work dir: D:\DATA_MAUD\Results\CM_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\DATA_MAUD\Results\CM_5 --dbbin D:\DATA_MAUD\Results\CM_1 --protxml D:\DATA_MAUD\Results\combined.prot.xml --probin D:\DATA_MAUD\Results\CM_1 --razor PhilosopherFilter [Work dir: D:\DATA_MAUD\Results\E1_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\DATA_MAUD\Results\E1_1 --dbbin D:\DATA_MAUD\Results\CM_1 --protxml D:\DATA_MAUD\Results\combined.prot.xml --probin D:\DATA_MAUD\Results\CM_1 --razor PhilosopherFilter [Work dir: D:\DATA_MAUD\Results\E1_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\DATA_MAUD\Results\E1_4 --dbbin D:\DATA_MAUD\Results\CM_1 --protxml D:\DATA_MAUD\Results\combined.prot.xml --probin D:\DATA_MAUD\Results\CM_1 --razor PhilosopherFilter [Work dir: D:\DATA_MAUD\Results\E1_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\DATA_MAUD\Results\E1_5 --dbbin D:\DATA_MAUD\Results\CM_1 --protxml D:\DATA_MAUD\Results\combined.prot.xml --probin D:\DATA_MAUD\Results\CM_1 --razor PhilosopherFilter [Work dir: D:\DATA_MAUD\Results\E2_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\DATA_MAUD\Results\E2_1 --dbbin D:\DATA_MAUD\Results\CM_1 --protxml D:\DATA_MAUD\Results\combined.prot.xml --probin D:\DATA_MAUD\Results\CM_1 --razor PhilosopherFilter [Work dir: D:\DATA_MAUD\Results\E2_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\DATA_MAUD\Results\E2_3 --dbbin D:\DATA_MAUD\Results\CM_1 --protxml D:\DATA_MAUD\Results\combined.prot.xml --probin D:\DATA_MAUD\Results\CM_1 --razor PhilosopherFilter [Work dir: D:\DATA_MAUD\Results\E2_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\DATA_MAUD\Results\E2_4 --dbbin D:\DATA_MAUD\Results\CM_1 --protxml D:\DATA_MAUD\Results\combined.prot.xml --probin D:\DATA_MAUD\Results\CM_1 --razor PhilosopherFilter [Work dir: D:\DATA_MAUD\Results\E2_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\DATA_MAUD\Results\E2_5 --dbbin D:\DATA_MAUD\Results\CM_1 --protxml D:\DATA_MAUD\Results\combined.prot.xml --probin D:\DATA_MAUD\Results\CM_1 --razor PhilosopherReport [Work dir: D:\DATA_MAUD\Results\CM_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\DATA_MAUD\Results\E1_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\DATA_MAUD\Results\E2_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\DATA_MAUD\Results\E1_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\DATA_MAUD\Results\E2_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\DATA_MAUD\Results\E2_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\DATA_MAUD\Results\E1_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\DATA_MAUD\Results\E2_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\DATA_MAUD\Results\CM_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\DATA_MAUD\Results\CM_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe report WorkspaceClean [Work dir: D:\DATA_MAUD\Results] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\DATA_MAUD\Results\CM_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\DATA_MAUD\Results\E1_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\DATA_MAUD\Results\E2_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\DATA_MAUD\Results\E1_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\DATA_MAUD\Results\E2_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\DATA_MAUD\Results\E2_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\DATA_MAUD\Results\E1_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\DATA_MAUD\Results\E2_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\DATA_MAUD\Results\CM_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\DATA_MAUD\Results\CM_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck IonQuant [Work dir: D:\DATA_MAUD\Results] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -Xmx3G -Dlibs.bruker.dir=C:\Users\lucas\Desktop\FragPipe\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=C:\Users\lucas\Desktop\FragPipe\MSFragger-4.0\ext\thermo -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\jfreechart-1.5.3.jar;C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\batmass-io-1.30.0.jar;C:\Users\lucas\Desktop\FragPipe\IonQuant-1.10.12\IonQuant-1.10.12.jar ionquant.IonQuant --threads 11 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist D:\DATA_MAUD\Results\filelist_ionquant.txt --modlist D:\DATA_MAUD\Results\modmasses_ionquant.txt ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [D:\DATA_MAUD\Results] Cmd: [CheckCentroid], Work dir: [D:\DATA_MAUD\Results] Cmd: [WorkspaceCleanInit], Work dir: [D:\DATA_MAUD\Results] Cmd: [WorkspaceCleanInit], Work dir: [D:\DATA_MAUD\Results\CM_5] Cmd: [WorkspaceCleanInit], Work dir: [D:\DATA_MAUD\Results\E1_4] Cmd: [WorkspaceCleanInit], Work dir: [D:\DATA_MAUD\Results\E2_3] Cmd: [WorkspaceCleanInit], Work dir: [D:\DATA_MAUD\Results\E1_5] Cmd: [WorkspaceCleanInit], Work dir: [D:\DATA_MAUD\Results\E2_4] Cmd: [WorkspaceCleanInit], Work dir: [D:\DATA_MAUD\Results\E2_5] Cmd: [WorkspaceCleanInit], Work dir: [D:\DATA_MAUD\Results\E1_1] Cmd: [WorkspaceCleanInit], Work dir: [D:\DATA_MAUD\Results\E2_1] Cmd: [WorkspaceCleanInit], Work dir: [D:\DATA_MAUD\Results\CM_4] Cmd: [WorkspaceCleanInit], Work dir: [D:\DATA_MAUD\Results\CM_3] Cmd: [WorkspaceCleanInit], Work dir: [D:\DATA_MAUD\Results\CM_1] Cmd: [MSFragger], Work dir: [D:\DATA_MAUD\Results] Cmd: [MSBooster], Work dir: [D:\DATA_MAUD\Results] Cmd: [Percolator], Work dir: [D:\DATA_MAUD\Results] Cmd: [ProteinProphet], Work dir: [D:\DATA_MAUD\Results] Cmd: [PhilosopherDbAnnotate], Work dir: [D:\DATA_MAUD\Results] Cmd: [PhilosopherFilter], Work dir: [D:\DATA_MAUD\Results] Cmd: [PhilosopherReport], Work dir: [D:\DATA_MAUD\Results] Cmd: [WorkspaceClean], Work dir: [D:\DATA_MAUD\Results] Cmd: [WorkspaceClean], Work dir: [D:\DATA_MAUD\Results\CM_5] Cmd: [WorkspaceClean], Work dir: [D:\DATA_MAUD\Results\E1_4] Cmd: [WorkspaceClean], Work dir: [D:\DATA_MAUD\Results\E2_3] Cmd: [WorkspaceClean], Work dir: [D:\DATA_MAUD\Results\E1_5] Cmd: [WorkspaceClean], Work dir: [D:\DATA_MAUD\Results\E2_4] Cmd: [WorkspaceClean], Work dir: [D:\DATA_MAUD\Results\E2_5] Cmd: [WorkspaceClean], Work dir: [D:\DATA_MAUD\Results\E1_1] Cmd: [WorkspaceClean], Work dir: [D:\DATA_MAUD\Results\E2_1] Cmd: [WorkspaceClean], Work dir: [D:\DATA_MAUD\Results\CM_4] Cmd: [WorkspaceClean], Work dir: [D:\DATA_MAUD\Results\CM_3] Cmd: [WorkspaceClean], Work dir: [D:\DATA_MAUD\Results\CM_1] Cmd: [IonQuant], Work dir: [D:\DATA_MAUD\Results] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of C:\Users\lucas\Desktop\FragPipe\2024-05-02-decoys-Hbt_salinarum_NRC_1_Membrane_Proteome.fasta.fas~~~~~~~ >rev_sp|P02945|BACR_HALSA Bacteriorhodopsin OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=bop PE=1 SV=2 >rev_tr|O54559|O54559_HALSA DUF4341/DUF395 family protein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_6061H PE=4 SV=1 >rev_tr|Q9HMD5|Q9HMD5_HALSA Uncharacterized protein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_2594C PE=4 SV=1 >rev_tr|Q9HMZ5|Q9HMZ5_HALSA Biotin transport protein BioY OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=bioY PE=4 SV=1 >rev_tr|Q9HNI9|Q9HNI9_HALSA ABC-type transport system permease protein(Probable substrate phosphate/phosphonate) OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=phnE PE=4 SV=1 >rev_tr|Q9HPF3|Q9HPF3_HALSA Uncharacterized protein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_1664H PE=4 SV=1 >rev_tr|Q9HQ92|Q9HQ92_HALSA Secreted glycoprotein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_1270H PE=4 SV=1 >rev_tr|Q9HR07|Q9HR07_HALSA Glycosyltransferase RgtA/B/C/D-like domain-containing protein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_0920H PE=4 SV=1 >rev_tr|Q9HRL2|Q9HRL2_HALSA F420H2:quinone oxidoreductase chain M OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=nuoM PE=3 SV=1 >rev_tr|Q9HS26|Q9HS26_HALSA Na+/H+ antiporter OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=nhaC1 PE=4 SV=1 >rev_tr|Q9HSV6|Q9HSV6_HALSA O-antigen ligase OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_0057H PE=4 SV=1 >tr|O51960|O51960_HALSA Vng6008h OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_6008H PE=4 SV=1 >tr|Q9HM71|Q9HM71_HALSA Probable secreted glycoprotein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_2677H PE=4 SV=1 >tr|Q9HMX4|Q9HMX4_HALSA Uncharacterized protein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_2342H PE=4 SV=1 >tr|Q9HNG4|Q9HNG4_HALSA Xanthine/uracil permease family transportprotein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=uraA PE=3 SV=1 >tr|Q9HPA3|Q9HPA3_HALSA Potassium channel domain-containing protein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_1732C PE=4 SV=1 >tr|Q9HQ34|Q9HQ34_HALSA DMT superfamily transport protein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_1350C PE=4 SV=1 >tr|Q9HQW3|Q9HQW3_HALSA Glycerophosphoryl diester phosphodiesterase membrane domain-containing protein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_0979H PE=4 SV=1 >tr|Q9HRJ9|Q9HRJ9_HALSA cytochrome-c oxidase OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=coxB1 PE=3 SV=1 >tr|Q9HRX5|Q9HRX5_HALSA Multidrug resistance protein homolog OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=yfmO1 PE=4 SV=1 >tr|Q9HSP2|Q9HSP2_HALSA Uncharacterized protein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=VNG_0141H PE=4 SV=1 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v21.1ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=C\:\\Users\\lucas\\Desktop\\FragPipe\\2024-05-02-decoys-Hbt_salinarum_NRC_1_Membrane_Proteome.fasta.fas Table.editor=Y crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.medium= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=QuantUMS (high accuracy) diann.run-dia-nn=false diann.run-dia-plex=false diann.run-specific-protein-q-value=false diann.unrelated-runs=false diann.use-predicted-spectra=true diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fpop.fpop-tmt=false fpop.label_control= fpop.label_fpop= fpop.region_size=1 fpop.run-fpop=false fpop.subtract-control=false fragpipe-config.bin-diann=C\:\\Users\\lucas\\Desktop\\FragPipe\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe fragpipe-config.bin-ionquant=C\:\\Users\\lucas\\Desktop\\FragPipe\\IonQuant-1.10.12\\IonQuant-1.10.12.jar fragpipe-config.bin-msfragger=C\:\\Users\\lucas\\Desktop\\FragPipe\\MSFragger-4.0\\MSFragger-4.0.jar fragpipe-config.bin-philosopher=C\:\\Users\\lucas\\Desktop\\FragPipe\\Philosopher\\philosopher.exe fragpipe-config.bin-python=D\:\\Anaconda\\python freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.heavy= ionquant.imtol=0.05 ionquant.ionfdr=0.01 ionquant.light= ionquant.locprob=0.75 ionquant.maxlfq=1 ionquant.mbr=1 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=10 ionquant.medium= ionquant.minfreq=0 ionquant.minions=2 ionquant.minisotopes=2 ionquant.minscans=3 ionquant.mztol=10 ionquant.normalization=1 ionquant.peptidefdr=1 ionquant.proteinfdr=1 ionquant.requantify=1 ionquant.rttol=0.4 ionquant.run-ionquant=true ionquant.tp=0 ionquant.uniqueness=0 ionquant.use-labeling=false ionquant.use-lfq=true ionquant.writeindex=0 msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.run-msbooster=true msbooster.use-correlated-features=false msfragger.Y_type_masses= msfragger.activation_types=all msfragger.allowed_missed_cleavage_1=2 msfragger.allowed_missed_cleavage_2=2 msfragger.calibrate_mass=2 msfragger.check_spectral_files=true msfragger.clip_nTerm_M=true msfragger.deisotope=1 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) msfragger.deneutralloss=1 msfragger.diagnostic_fragments= msfragger.diagnostic_intensity_filter=0 msfragger.digest_max_length=50 msfragger.digest_min_length=1 msfragger.fragment_ion_series=b,y msfragger.fragment_mass_tolerance=0.05 msfragger.fragment_mass_units=0 msfragger.group_variable=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0.0 msfragger.mass_offsets_detailed= msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.01 msfragger.misc.fragger.clear-mz-hi=0 msfragger.misc.fragger.clear-mz-lo=0 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=100 msfragger.misc.fragger.enzyme-dropdown-1=trypsin msfragger.misc.fragger.enzyme-dropdown-2=null msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=2 msfragger.output_format=pepXML_pin msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.output_report_topN_dda_plus=5 msfragger.output_report_topN_dia1=5 msfragger.override_charge=false msfragger.precursor_mass_lower=-5 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=5 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2= msfragger.search_enzyme_name_1=trypsin msfragger.search_enzyme_name_2=null msfragger.search_enzyme_nocut_1=P msfragger.search_enzyme_nocut_2= msfragger.search_enzyme_sense_1=C msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 msfragger.track_zero_topN=0 msfragger.use_all_mods_in_first_search=false msfragger.use_detailed_offsets=false msfragger.use_topN_peaks=150 msfragger.write_calibrated_mzml=false msfragger.write_uncalibrated_mgf=false msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 opair.activation1=HCD opair.activation2=ETD opair.filterOxonium=true opair.glyco_db= opair.max_glycans=4 opair.max_isotope_error=2 opair.min_isotope_error=0 opair.ms1_tol=20 opair.ms2_tol=20 opair.oxonium_filtering_file= opair.oxonium_minimum_intensity=0.05 opair.reverse_scan_order=false opair.run-opair=false opair.single_scan_type=false peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore peptide-prophet.combine-pepxml=false peptide-prophet.run-peptide-prophet=false percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc percolator.keep-tsv-files=false percolator.min-prob=0.5 percolator.run-percolator=true phi-report.dont-use-prot-proph-file=false phi-report.filter=--sequential --prot 0.01 phi-report.pep-level-summary=false phi-report.philosoher-msstats=false phi-report.print-decoys=false phi-report.prot-level-summary=false phi-report.remove-contaminants=false phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 protein-prophet.run-protein-prophet=true ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5 ptmprophet.run-ptmprophet=false ptmshepherd.adv_params=false ptmshepherd.annotation-common=false ptmshepherd.annotation-custom=false ptmshepherd.annotation-glyco=false ptmshepherd.annotation-unimod=true ptmshepherd.annotation_file= ptmshepherd.annotation_tol=0.01 ptmshepherd.cap_y_ions= ptmshepherd.decoy_type=1 ptmshepherd.diag_ions= ptmshepherd.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=00.2 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=00.1 ptmshepherd.diagmine_fragMinSpecDiff=00.1 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=00.2 ptmshepherd.glyco_adducts= ptmshepherd.glyco_fdr=1.00 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_ppm_tol=50 ptmshepherd.glycodatabase= ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=false ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=false ptmshepherd.localization_allowed_res= ptmshepherd.localization_background=4 ptmshepherd.max_adducts=0 ptmshepherd.n_glyco=true ptmshepherd.normalization-psms=true ptmshepherd.normalization-scans=false ptmshepherd.output_extended=false ptmshepherd.peakpicking_mass_units=0 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=0.002 ptmshepherd.precursor_mass_units=0 ptmshepherd.precursor_tol=0.01 ptmshepherd.print_decoys=false ptmshepherd.prob_dhexOx=2,0.5,0.1 ptmshepherd.prob_dhexY=2,0.5 ptmshepherd.prob_neuacOx=2,0.05,0.2 ptmshepherd.prob_neugcOx=2,0.05,0.2 ptmshepherd.prob_phosphoOx=2,0.05,0.2 ptmshepherd.prob_regY=5,0.5 ptmshepherd.prob_sulfoOx=2,0.05,0.2 ptmshepherd.remainder_masses= ptmshepherd.remove_glycan_delta_mass=true ptmshepherd.run-shepherd=false ptmshepherd.run_diagextract_mode=false ptmshepherd.run_diagmine_mode=false ptmshepherd.run_glyco_mode=false ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses= quantitation.run-label-free-quant=true run-psm-validation=true run-validation-tab=true saintexpress.fragpipe.cmd-opts= saintexpress.max-replicates=10 saintexpress.run-saint-express=false saintexpress.virtual-controls=100 speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.rt_lowess_fraction=0 speclibgen.easypqp.fragment.a=false speclibgen.easypqp.fragment.b=true speclibgen.easypqp.fragment.c=false speclibgen.easypqp.fragment.x=false speclibgen.easypqp.fragment.y=true speclibgen.easypqp.fragment.z=false speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.neutral_loss=false speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=false tab-run.delete_calibrated_mzml=false tab-run.delete_temp_files=false tab-run.sub_mzml_prob_threshold=0.5 tab-run.write_sub_mzml=false tmtintegrator.add_Ref=-1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=true tmtintegrator.best_psm=true tmtintegrator.channel_num=TMT-6 tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=-1 tmtintegrator.groupby=0 tmtintegrator.log2transformed=true tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=0 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=false tmtintegrator.tolerance=20 tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=false workdir=D\:\\DATA_MAUD\\Results workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.ram=0 workflow.threads=11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -Xmx3G -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid D:\DATA_MAUD\CM_1_RA2_1_31922.mzML 11 Done in 1,4 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck INFO[11:49:21] Executing Workspace v5.1.0 INFO[11:49:22] Removing workspace INFO[11:49:22] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\13ad578d-d78c-4c4a-8e43-a7923d1a1071 INFO[11:49:22] Executing Workspace v5.1.0 INFO[11:49:22] Creating workspace INFO[11:49:22] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck INFO[11:49:22] Executing Workspace v5.1.0 INFO[11:49:22] Removing workspace INFO[11:49:22] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\94ad0f05-86f4-4249-b881-ccfe9f3ad01d INFO[11:49:23] Executing Workspace v5.1.0 INFO[11:49:23] Creating workspace INFO[11:49:23] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E1_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck INFO[11:49:23] Executing Workspace v5.1.0 INFO[11:49:23] Removing workspace INFO[11:49:23] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E1_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\3af6cf0d-a31e-4f8c-8f5e-ab6d46cd163e INFO[11:49:24] Executing Workspace v5.1.0 INFO[11:49:24] Creating workspace INFO[11:49:24] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck INFO[11:49:24] Executing Workspace v5.1.0 INFO[11:49:24] Removing workspace INFO[11:49:24] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\50e82806-db83-46c4-ad69-8b7372eb4549 INFO[11:49:24] Executing Workspace v5.1.0 INFO[11:49:24] Creating workspace INFO[11:49:24] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E1_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck INFO[11:49:25] Executing Workspace v5.1.0 INFO[11:49:25] Removing workspace INFO[11:49:25] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E1_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\08ad0f17-a581-4079-ad1c-c8a7e304e851 INFO[11:49:25] Executing Workspace v5.1.0 INFO[11:49:25] Creating workspace INFO[11:49:25] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck INFO[11:49:26] Executing Workspace v5.1.0 INFO[11:49:26] Removing workspace INFO[11:49:26] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\4c642cea-d58c-4af6-875a-87a5e7b0ab19 INFO[11:49:26] Executing Workspace v5.1.0 INFO[11:49:26] Creating workspace INFO[11:49:26] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck INFO[11:49:26] Executing Workspace v5.1.0 INFO[11:49:27] Removing workspace INFO[11:49:27] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_5] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\8f8bf91c-826f-47aa-874b-04cf90f6980a INFO[11:49:27] Executing Workspace v5.1.0 INFO[11:49:27] Creating workspace INFO[11:49:27] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E1_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck INFO[11:49:27] Executing Workspace v5.1.0 INFO[11:49:27] Removing workspace INFO[11:49:27] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E1_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\3144d218-0b2b-4923-bd95-f670a40f134a INFO[11:49:28] Executing Workspace v5.1.0 INFO[11:49:28] Creating workspace INFO[11:49:28] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck INFO[11:49:28] Executing Workspace v5.1.0 INFO[11:49:28] Removing workspace INFO[11:49:28] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\E2_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\c0a233b3-38a7-49c4-8840-b809a42ac9d0 INFO[11:49:29] Executing Workspace v5.1.0 INFO[11:49:29] Creating workspace INFO[11:49:29] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck INFO[11:49:29] Executing Workspace v5.1.0 INFO[11:49:29] Removing workspace INFO[11:49:29] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_4] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\33cef2f4-ecb8-47d5-9877-4408af8b9547 INFO[11:49:29] Executing Workspace v5.1.0 INFO[11:49:29] Creating workspace INFO[11:49:29] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck INFO[11:49:30] Executing Workspace v5.1.0 INFO[11:49:30] Removing workspace INFO[11:49:30] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_3] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\4fcfd6e1-987c-49ac-8d0b-a8d012e6f622 INFO[11:49:30] Executing Workspace v5.1.0 INFO[11:49:30] Creating workspace INFO[11:49:30] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --clean --nocheck INFO[11:49:31] Executing Workspace v5.1.0 INFO[11:49:31] Removing workspace INFO[11:49:31] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe workspace --init --nocheck --temp C:\Users\lucas\AppData\Local\Temp\79677a70-51f3-4f52-972f-c6669db70534 INFO[11:49:31] Executing Workspace v5.1.0 INFO[11:49:31] Creating workspace INFO[11:49:31] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\DATA_MAUD\Results] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx3G C:\Users\lucas\Desktop\FragPipe\MSFragger-4.0\MSFragger-4.0.jar D:\DATA_MAUD\Results\fragger.params D:\DATA_MAUD\CM_1_RA2_1_31922.mzML D:\DATA_MAUD\CM_3_RA3_1_31923.mzML D:\DATA_MAUD\CM_4_RA4_1_31925.mzML D:\DATA_MAUD\CM_5_RA5_1_31926.mzML D:\DATA_MAUD\E1_1_RA6_1_31928.mzML D:\DATA_MAUD\E1_4_RA7_1_31929.mzML D:\DATA_MAUD\E1_5_RA8_1_31930.mzML D:\DATA_MAUD\E2_1_RB1_1_31932.mzML D:\DATA_MAUD\E2_3_RB2_1_31933.mzML D:\DATA_MAUD\E2_4_RB3_1_31935.mzML D:\DATA_MAUD\E2_5_RB4_1_31936.mzML MSFragger version MSFragger-4.0 Batmass-IO version 1.30.0 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 3 GB memory Checking database... Checking spectral files... D:\DATA_MAUD\E1_5_RA8_1_31930.mzML: Scans = 4789; Isolation sizes = [3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3] D:\DATA_MAUD\CM_3_RA3_1_31923.mzML: Scans = 4770; Isolation sizes = [3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3] D:\DATA_MAUD\CM_1_RA2_1_31922.mzML: Scans = 4846; Isolation sizes = [3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4] D:\DATA_MAUD\E2_4_RB3_1_31935.mzML: Scans = 4652; Isolation sizes = [3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3] D:\DATA_MAUD\E1_1_RA6_1_31928.mzML: Scans = 4809; Isolation sizes = [3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3] D:\DATA_MAUD\CM_4_RA4_1_31925.mzML: Scans = 4744; Isolation sizes = [3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3] D:\DATA_MAUD\E1_4_RA7_1_31929.mzML: Scans = 4612; Isolation sizes = [3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3] D:\DATA_MAUD\E2_3_RB2_1_31933.mzML: Scans = 4670; Isolation sizes = [3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3] D:\DATA_MAUD\E2_1_RB1_1_31932.mzML: Scans = 4701; Isolation sizes = [3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3] D:\DATA_MAUD\CM_5_RA5_1_31926.mzML: Scans = 4757; Isolation sizes = [3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3] D:\DATA_MAUD\E2_5_RB4_1_31936.mzML: Scans = 4476; Isolation sizes = [3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3] ***********************************FIRST SEARCH************************************ Parameters: num_threads = 11 database_name = C:\Users\lucas\Desktop\FragPipe\2024-05-02-decoys-Hbt_salinarum_NRC_1_Membrane_Proteome.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 50.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = trypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = P allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 0 override_charge = 0 precursor_charge_low = 2 precursor_charge_high = 3 digest_min_length = 1 digest_max_length = 50 digest_mass_range_low = 100.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.25 Da. 2636950 fragments to be searched in 1 slices (0.04 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.21 s 001. CM_1_RA2_1_31922.mzML 0.9 s | deisotoping 1.4 s [progress: 4811/4811 (100%) - 9920 spectra/s] 0.5s | postprocessing 0.0 s 002. CM_3_RA3_1_31923.mzML 0.6 s | deisotoping 0.0 s [progress: 4736/4736 (100%) - 14528 spectra/s] 0.3s | postprocessing 0.0 s 003. CM_4_RA4_1_31925.mzML 0.5 s | deisotoping 0.0 s [progress: 4705/4705 (100%) - 44810 spectra/s] 0.1s | postprocessing 0.0 s 004. CM_5_RA5_1_31926.mzML 0.6 s | deisotoping 0.0 s [progress: 4714/4714 (100%) - 45327 spectra/s] 0.1s | postprocessing 0.0 s 005. E1_1_RA6_1_31928.mzML 0.6 s | deisotoping 0.0 s [progress: 4766/4766 (100%) - 44542 spectra/s] 0.1s | postprocessing 0.0 s 006. E1_4_RA7_1_31929.mzML 0.5 s | deisotoping 0.0 s [progress: 4582/4582 (100%) - 40549 spectra/s] 0.1s | postprocessing 0.0 s 007. E1_5_RA8_1_31930.mzML 0.6 s | deisotoping 0.4 s [progress: 4745/4745 (100%) - 42748 spectra/s] 0.1s | postprocessing 0.0 s 008. E2_1_RB1_1_31932.mzML 0.6 s | deisotoping 0.0 s [progress: 4655/4655 (100%) - 43102 spectra/s] 0.1s | postprocessing 0.0 s 009. E2_3_RB2_1_31933.mzML 0.5 s | deisotoping 0.0 s [progress: 4627/4627 (100%) - 45363 spectra/s] 0.1s | postprocessing 0.0 s 010. E2_4_RB3_1_31935.mzML 0.6 s | deisotoping 0.0 s [progress: 4612/4612 (100%) - 20589 spectra/s] 0.2s | postprocessing 0.0 s 011. E2_5_RB4_1_31936.mzML 0.5 s | deisotoping 0.0 s [progress: 4430/4430 (100%) - 18536 spectra/s] 0.2s | postprocessing 0.0 s ***************************FIRST SEARCH DONE IN 0.298 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | -0.44 2.03 | -0.15 0.87 | 0.08 5.71 | -0.22 5.55 002 | -0.33 1.67 | -0.12 0.98 | 0.00 5.58 | -0.52 5.36 003 | -2.32 1.87 | -0.10 1.06 | -2.29 5.53 | -0.52 5.32 004 | -3.02 1.50 | -0.21 0.85 | -2.54 5.33 | -0.81 5.36 005 | -2.00 1.42 | -0.28 0.84 | -1.37 5.67 | -0.36 5.59 006 | -3.07 1.45 | -0.02 0.76 | -2.86 5.20 | -0.85 5.17 007 | -3.80 1.49 | -0.04 0.78 | -3.80 5.51 | -0.99 5.43 008 | -3.54 1.54 | -0.05 0.71 | -3.66 5.66 | -0.62 5.41 009 | -4.18 1.59 | -0.09 0.96 | -4.35 5.73 | -1.03 5.55 010 | -4.43 1.77 | -0.08 0.77 | -3.97 5.23 | -0.60 5.05 011 | -3.23 1.49 | -0.17 0.87 | -3.06 5.79 | -1.25 5.71 -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|-------|-------|------- MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 -------|-------|-------|-------|-------|-------|-------|-------|------- Count | skip | skip | skip | 2139| 2152| 2124| skip rest -------|-------|-------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 -------|-------|-------|-------|-------|-------|------- Count | 2091| 2100| 2142| 2152| 2158| 2171 -------|-------|-------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 2151 -------|------- -------|------- Rm P. | 0 -------|------- Count | 2164 -------|------- New fragment_mass_tolerance = 20.000000 PPM New use_topN_peaks = 100 New minimum_ratio = 0.010000 New intensity_transform = 0 New remove_precursor_peak = 1 ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.784 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 11 database_name = C:\Users\lucas\Desktop\FragPipe\2024-05-02-decoys-Hbt_salinarum_NRC_1_Membrane_Proteome.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -5.0 precursor_mass_upper = 5.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1/2 mass_offsets = 0.0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = trypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = P allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 1 digest_max_length = 50 digest_mass_range_low = 100.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 100 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.10 Da. 2636950 fragments to be searched in 1 slices (0.04 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.03 s 001. CM_1_RA2_1_31922.mzBIN_calibrated 0.1 s [progress: 4709/4709 (100%) - 20929 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.4 s 002. CM_3_RA3_1_31923.mzBIN_calibrated 0.1 s [progress: 4617/4617 (100%) - 44394 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.2 s 003. CM_4_RA4_1_31925.mzBIN_calibrated 0.1 s [progress: 4580/4580 (100%) - 43208 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.2 s 004. CM_5_RA5_1_31926.mzBIN_calibrated 0.1 s [progress: 4586/4586 (100%) - 41315 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 005. E1_1_RA6_1_31928.mzBIN_calibrated 0.1 s [progress: 4650/4650 (100%) - 44712 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 006. E1_4_RA7_1_31929.mzBIN_calibrated 0.1 s [progress: 4469/4469 (100%) - 43814 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 007. E1_5_RA8_1_31930.mzBIN_calibrated 0.1 s [progress: 4630/4630 (100%) - 40973 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 008. E2_1_RB1_1_31932.mzBIN_calibrated 0.1 s [progress: 4553/4553 (100%) - 39939 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 009. E2_3_RB2_1_31933.mzBIN_calibrated 0.1 s [progress: 4525/4525 (100%) - 44363 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 010. E2_4_RB3_1_31935.mzBIN_calibrated 0.1 s [progress: 4478/4478 (100%) - 38939 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 011. E2_5_RB4_1_31936.mzBIN_calibrated 0.1 s [progress: 4315/4315 (100%) - 41095 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s ***************************MAIN SEARCH DONE IN 0.071 MIN*************************** *******************************TOTAL TIME 1.153 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_1_RA2_1_31922.pepXML D:\DATA_MAUD\Results\CM_1\CM_1_RA2_1_31922.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_1_RA2_1_31922.pin D:\DATA_MAUD\Results\CM_1\CM_1_RA2_1_31922.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_3_RA3_1_31923.pepXML D:\DATA_MAUD\Results\CM_3\CM_3_RA3_1_31923.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_3_RA3_1_31923.pin D:\DATA_MAUD\Results\CM_3\CM_3_RA3_1_31923.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_4_RA4_1_31925.pepXML D:\DATA_MAUD\Results\CM_4\CM_4_RA4_1_31925.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_4_RA4_1_31925.pin D:\DATA_MAUD\Results\CM_4\CM_4_RA4_1_31925.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_5_RA5_1_31926.pepXML D:\DATA_MAUD\Results\CM_5\CM_5_RA5_1_31926.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\CM_5_RA5_1_31926.pin D:\DATA_MAUD\Results\CM_5\CM_5_RA5_1_31926.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E1_1_RA6_1_31928.pepXML D:\DATA_MAUD\Results\E1_1\E1_1_RA6_1_31928.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E1_1_RA6_1_31928.pin D:\DATA_MAUD\Results\E1_1\E1_1_RA6_1_31928.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E1_4_RA7_1_31929.pepXML D:\DATA_MAUD\Results\E1_4\E1_4_RA7_1_31929.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E1_4_RA7_1_31929.pin D:\DATA_MAUD\Results\E1_4\E1_4_RA7_1_31929.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E1_5_RA8_1_31930.pepXML D:\DATA_MAUD\Results\E1_5\E1_5_RA8_1_31930.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E1_5_RA8_1_31930.pin D:\DATA_MAUD\Results\E1_5\E1_5_RA8_1_31930.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_1_RB1_1_31932.pepXML D:\DATA_MAUD\Results\E2_1\E2_1_RB1_1_31932.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_1_RB1_1_31932.pin D:\DATA_MAUD\Results\E2_1\E2_1_RB1_1_31932.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_3_RB2_1_31933.pepXML D:\DATA_MAUD\Results\E2_3\E2_3_RB2_1_31933.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_3_RB2_1_31933.pin D:\DATA_MAUD\Results\E2_3\E2_3_RB2_1_31933.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_4_RB3_1_31935.pepXML D:\DATA_MAUD\Results\E2_4\E2_4_RB3_1_31935.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_4_RB3_1_31935.pin D:\DATA_MAUD\Results\E2_4\E2_4_RB3_1_31935.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_5_RB4_1_31936.pepXML D:\DATA_MAUD\Results\E2_5\E2_5_RB4_1_31936.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar;/C:/Users/lucas/Desktop/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\DATA_MAUD\E2_5_RB4_1_31936.pin D:\DATA_MAUD\Results\E2_5\E2_5_RB4_1_31936.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: D:\DATA_MAUD\Results] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -Xmx3G -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\msbooster-1.1.28.jar;C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\batmass-io-1.30.0.jar Features.MainClass --paramsList D:\DATA_MAUD\Results\msbooster_params.txt MSBooster v1.1.28 Using 11 threads 1766 unique peptides from 10973 PSMs createFull input file generation took 291 milliseconds Input file at D:\DATA_MAUD\Results\E2_3\spectraRT_full.tsv Generating input file for DIA-NN 1766 unique peptides from 10973 PSMs Writing DIA-NN input file Diann input file generation took 109 milliseconds Input file at D:\DATA_MAUD\Results\E2_3\spectraRT.tsv Generating DIA-NN predictions C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib D:\DATA_MAUD\Results\E2_3\spectraRT.tsv --predict --threads 11 --strip-unknown-mods --predict-n-frag 100 DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks) Compiled on Sep 15 2022 18:28:57 Current date and time: Tue May 14 11:50:49 2024 CPU: GenuineIntel Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 Logical CPU cores: 12 Predicted spectra will be saved in a binary format Thread number set to 11 DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option Deep learning predictor will predict 100 fragments 0 files will be processed [0:00] Loading spectral library D:\DATA_MAUD\Results\E2_3\spectraRT.tsv [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 1766 precursors in 1402 elution groups. [0:00] Encoding peptides for spectra and RTs prediction [0:00] Predicting spectra and IMs [0:01] Predicting RTs [0:01] Decoding predicted spectra and IMs [0:01] Decoding RTs [0:01] Saving the list of predictions to D:\DATA_MAUD\Results\E2_3\spectraRT.predicted.bin Finished Done generating DIA-NN predictions Model running took 3073 milliseconds Generating edited pin with following features: [unweightedSpectralEntropy, deltaRTLOESS] Loading predicted spectra Processing D:\DATA_MAUD\CM_1_RA2_1_31922.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Not enough high quality PSMs for RT regression with escore cutoff of 3.1622776E-4. Relaxing escore cutoff to 0.01 RT regression using 914 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at D:\DATA_MAUD\Results\CM_1\CM_1_RA2_1_31922_edited.pin Processing D:\DATA_MAUD\CM_3_RA3_1_31923.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 863 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at D:\DATA_MAUD\Results\CM_3\CM_3_RA3_1_31923_edited.pin Processing D:\DATA_MAUD\CM_4_RA4_1_31925.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Not enough high quality PSMs for RT regression with escore cutoff of 0.01. Relaxing escore cutoff to 0.01 RT regression using 766 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at D:\DATA_MAUD\Results\CM_4\CM_4_RA4_1_31925_edited.pin Processing D:\DATA_MAUD\CM_5_RA5_1_31926.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 830 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at D:\DATA_MAUD\Results\CM_5\CM_5_RA5_1_31926_edited.pin Processing D:\DATA_MAUD\E1_1_RA6_1_31928.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Not enough high quality PSMs for RT regression with escore cutoff of 0.01. Relaxing escore cutoff to 0.01 RT regression using 752 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at D:\DATA_MAUD\Results\E1_1\E1_1_RA6_1_31928_edited.pin Processing D:\DATA_MAUD\E1_4_RA7_1_31929.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Not enough high quality PSMs for RT regression with escore cutoff of 0.01. Relaxing escore cutoff to 0.01 RT regression using 648 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at D:\DATA_MAUD\Results\E1_4\E1_4_RA7_1_31929_edited.pin Processing D:\DATA_MAUD\E1_5_RA8_1_31930.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Not enough high quality PSMs for RT regression with escore cutoff of 0.01. Relaxing escore cutoff to 0.01 RT regression using 754 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at D:\DATA_MAUD\Results\E1_5\E1_5_RA8_1_31930_edited.pin Processing D:\DATA_MAUD\E2_1_RB1_1_31932.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Not enough high quality PSMs for RT regression with escore cutoff of 0.01. Relaxing escore cutoff to 0.01 RT regression using 787 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at D:\DATA_MAUD\Results\E2_1\E2_1_RB1_1_31932_edited.pin Processing D:\DATA_MAUD\E2_3_RB2_1_31933.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Not enough high quality PSMs for RT regression with escore cutoff of 0.01. Relaxing escore cutoff to 0.01 RT regression using 667 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at D:\DATA_MAUD\Results\E2_3\E2_3_RB2_1_31933_edited.pin Processing D:\DATA_MAUD\E2_4_RB3_1_31935.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Not enough high quality PSMs for RT regression with escore cutoff of 0.01. Relaxing escore cutoff to 0.01 RT regression using 716 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at D:\DATA_MAUD\Results\E2_4\E2_4_RB3_1_31935_edited.pin Processing D:\DATA_MAUD\E2_5_RB4_1_31936.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Not enough high quality PSMs for RT regression with escore cutoff of 0.01. Relaxing escore cutoff to 0.01 RT regression using 653 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at D:\DATA_MAUD\Results\E2_5\E2_5_RB4_1_31936_edited.pin Feature calculation and edited pin writing done in 10139 ms Process 'MSBooster' finished, exit code: 0 Percolator [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms CM_1_RA2_1_31922_percolator_target_psms.tsv --decoy-results-psms CM_1_RA2_1_31922_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CM_1_RA2_1_31922_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms CM_1_RA2_1_31922_percolator_target_psms.tsv --decoy-results-psms CM_1_RA2_1_31922_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CM_1_RA2_1_31922_edited.pin Started Tue May 14 11:51:00 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CM_1_RA2_1_31922_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess Found 1172 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 1162 positives and 10 negatives, size ratio=116.2 and pi0=1 Warning : the number of negative samples read is too small to perform a correct classification. Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 1 as initial direction. Could separate 774 training set positives with q<0.01 in that direction. Split 2: Selected feature 1 as initial direction. Could separate 774 training set positives with q<0.01 in that direction. Split 3: Selected feature 1 as initial direction. Could separate 776 training set positives with q<0.01 in that direction. Found 0 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.1340 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 1159 PSMs with q<0.01 Iteration 2: Estimated 1159 PSMs with q<0.01 Iteration 3: Estimated 1159 PSMs with q<0.01 Iteration 4: Estimated 1159 PSMs with q<0.01 Iteration 5: Estimated 1159 PSMs with q<0.01 Iteration 6: Estimated 1159 PSMs with q<0.01 Iteration 7: Estimated 1159 PSMs with q<0.01 Iteration 8: Estimated 1159 PSMs with q<0.01 Iteration 9: Estimated 1159 PSMs with q<0.01 Iteration 10: Estimated 1159 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.0816 0.4355 0.4433 abs_ppm 0.4558 0.2593 0.1518 isotope_errors 0.3482 0.2168 -0.6247 log10_evalue 0.2918 0.5294 0.7690 hyperscore -0.0297 0.1542 0.2258 delta_hyperscore 0.0660 0.7208 0.4227 matched_ion_num 0.1015 0.4305 -0.7371 complementary_ions 0.7914 0.7023 0.5567 ion_series -0.0035 0.3492 0.1569 weighted_average_abs_fragment_ppm -0.1346 0.0351 0.1396 length_7 -0.2750 0.0021 -0.1093 length_8 0.2009 0.1016 -0.0097 length_9_30 0.0413 -0.1725 -0.0183 length_31 0.0000 0.0000 0.0000 ntt 0.0056 0.0223 -0.0558 nmc -0.0042 0.0486 0.0606 charge_1 -0.1188 -0.3824 -0.3443 charge_2 0.1122 0.3596 0.3160 charge_3 0.0194 0.0630 0.0636 charge_4 0.0108 -0.0735 -0.0293 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.1846 0.2247 0.3740 15.9949M -0.0750 -0.1021 -0.1049 unweighted_spectral_entropy -0.4804 -0.2290 -0.1731 delta_RT_loess 1.8503 2.5168 2.5863 m0 Found 1126 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 1162 target PSMs and 10 decoy PSMs. Calculating q values. Final list yields 1162 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 8.8590 cpu seconds or 9 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\DATA_MAUD\Results\CM_5] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms CM_5_RA5_1_31926_percolator_target_psms.tsv --decoy-results-psms CM_5_RA5_1_31926_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CM_5_RA5_1_31926_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms CM_5_RA5_1_31926_percolator_target_psms.tsv --decoy-results-psms CM_5_RA5_1_31926_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CM_5_RA5_1_31926_edited.pin Started Tue May 14 11:51:09 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CM_5_RA5_1_31926_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess Found 1080 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 1074 positives and 6 negatives, size ratio=179 and pi0=1 Warning : the number of negative samples read is too small to perform a correct classification. Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 1 as initial direction. Could separate 715 training set positives with q<0.01 in that direction. Split 2: Selected feature 1 as initial direction. Could separate 717 training set positives with q<0.01 in that direction. Split 3: Selected feature 1 as initial direction. Could separate 716 training set positives with q<0.01 in that direction. Found 717 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.0520 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 1074 PSMs with q<0.01 Iteration 2: Estimated 1074 PSMs with q<0.01 Iteration 3: Estimated 1074 PSMs with q<0.01 Iteration 4: Estimated 1074 PSMs with q<0.01 Iteration 5: Estimated 1074 PSMs with q<0.01 Iteration 6: Estimated 1074 PSMs with q<0.01 Iteration 7: Estimated 1074 PSMs with q<0.01 Iteration 8: Estimated 1074 PSMs with q<0.01 Iteration 9: Estimated 1074 PSMs with q<0.01 Iteration 10: Estimated 1074 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank 0.5210 0.3166 -0.0511 abs_ppm -0.5103 -0.6735 -0.0333 isotope_errors -0.3116 -1.0720 -0.8634 log10_evalue 0.0502 0.1612 -0.0316 hyperscore -0.1462 -0.0102 -0.1647 delta_hyperscore 0.3731 0.3868 -0.1047 matched_ion_num 0.1254 -0.5048 0.2826 complementary_ions 0.4984 -0.0405 0.3243 ion_series 0.5327 0.3161 0.4761 weighted_average_abs_fragment_ppm -0.0575 -0.0590 -0.0403 length_7 -0.1223 0.1614 -0.1953 length_8 0.0239 -0.0846 0.0508 length_9_30 0.0973 0.0461 0.0990 length_31 0.0000 0.0000 0.0000 ntt -0.0010 -0.2734 -0.2905 nmc -0.0027 -0.0002 -0.0868 charge_1 -0.2752 -0.2759 -0.1462 charge_2 0.2308 0.1850 0.1054 charge_3 0.1073 0.1953 0.1119 charge_4 -0.0348 -0.0011 -0.0614 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.2153 -0.0629 -0.1593 15.9949M -0.0411 -0.0640 -0.0367 unweighted_spectral_entropy -0.1625 -0.0969 -0.1445 delta_RT_loess 2.0579 1.9947 2.0158 m0 Found 1074 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 1074 target PSMs and 6 decoy PSMs. Calculating q values. Final list yields 1074 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 7.5990 cpu seconds or 7 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\DATA_MAUD\Results\E1_4] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E1_4_RA7_1_31929_percolator_target_psms.tsv --decoy-results-psms E1_4_RA7_1_31929_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E1_4_RA7_1_31929_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E1_4_RA7_1_31929_percolator_target_psms.tsv --decoy-results-psms E1_4_RA7_1_31929_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E1_4_RA7_1_31929_edited.pin Started Tue May 14 11:51:17 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile E1_4_RA7_1_31929_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess Found 902 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 895 positives and 7 negatives, size ratio=127.857 and pi0=1 Warning : the number of negative samples read is too small to perform a correct classification. Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 1 as initial direction. Could separate 597 training set positives with q<0.01 in that direction. Split 2: Selected feature 1 as initial direction. Could separate 596 training set positives with q<0.01 in that direction. Split 3: Selected feature 1 as initial direction. Could separate 597 training set positives with q<0.01 in that direction. Found 0 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.0470 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 894 PSMs with q<0.01 Iteration 2: Estimated 894 PSMs with q<0.01 Iteration 3: Estimated 894 PSMs with q<0.01 Iteration 4: Estimated 894 PSMs with q<0.01 Iteration 5: Estimated 894 PSMs with q<0.01 Iteration 6: Estimated 894 PSMs with q<0.01 Iteration 7: Estimated 894 PSMs with q<0.01 Iteration 8: Estimated 894 PSMs with q<0.01 Iteration 9: Estimated 894 PSMs with q<0.01 Iteration 10: Estimated 894 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2240 0.1592 -0.1239 abs_ppm 0.5998 0.2744 0.5370 isotope_errors -0.7667 -1.3502 -0.7031 log10_evalue 0.0123 -0.1784 0.0835 hyperscore -0.3446 -0.4893 0.0608 delta_hyperscore 1.6875 -0.2033 1.4511 matched_ion_num -0.4088 0.2160 -0.4923 complementary_ions 0.2279 0.4768 0.1527 ion_series 0.2289 0.5798 0.1444 weighted_average_abs_fragment_ppm 0.2389 0.1045 0.1374 length_7 0.0413 -0.0605 -0.0037 length_8 0.0020 0.0328 -0.0368 length_9_30 -0.3238 -0.1099 -0.0878 length_31 0.0000 0.0000 0.0000 ntt 0.2203 0.0212 0.1576 nmc 0.0473 -0.0218 -0.0767 charge_1 -0.1929 -0.1374 -0.2348 charge_2 0.2720 0.1511 0.2310 charge_3 -0.1915 -0.0213 0.0377 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.4347 0.0518 0.2691 15.9949M -0.1052 -0.0848 -0.1043 unweighted_spectral_entropy -0.3363 -0.3035 -0.2192 delta_RT_loess 2.3209 1.8708 2.3021 m0 Found 875 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 895 target PSMs and 7 decoy PSMs. Calculating q values. Final list yields 895 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 8.0130 cpu seconds or 8 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\DATA_MAUD\Results\E1_5] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E1_5_RA8_1_31930_percolator_target_psms.tsv --decoy-results-psms E1_5_RA8_1_31930_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E1_5_RA8_1_31930_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E1_5_RA8_1_31930_percolator_target_psms.tsv --decoy-results-psms E1_5_RA8_1_31930_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E1_5_RA8_1_31930_edited.pin Started Tue May 14 11:51:25 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile E1_5_RA8_1_31930_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess Found 978 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 970 positives and 8 negatives, size ratio=121.25 and pi0=1 Warning : the number of negative samples read is too small to perform a correct classification. Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 1 as initial direction. Could separate 646 training set positives with q<0.01 in that direction. Split 2: Selected feature 1 as initial direction. Could separate 647 training set positives with q<0.01 in that direction. Split 3: Selected feature 1 as initial direction. Could separate 647 training set positives with q<0.01 in that direction. Found 324 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.0550 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 967 PSMs with q<0.01 Iteration 2: Estimated 967 PSMs with q<0.01 Iteration 3: Estimated 967 PSMs with q<0.01 Iteration 4: Estimated 967 PSMs with q<0.01 Iteration 5: Estimated 967 PSMs with q<0.01 Iteration 6: Estimated 967 PSMs with q<0.01 Iteration 7: Estimated 967 PSMs with q<0.01 Iteration 8: Estimated 967 PSMs with q<0.01 Iteration 9: Estimated 967 PSMs with q<0.01 Iteration 10: Estimated 967 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2544 -0.1359 0.1185 abs_ppm 0.3986 0.3639 0.1901 isotope_errors -0.7969 -1.0797 -1.4999 log10_evalue 0.8435 0.7007 -0.1605 hyperscore 0.3704 0.2478 -0.2033 delta_hyperscore 0.2058 0.1454 -0.3753 matched_ion_num -0.3711 -0.3018 0.2361 complementary_ions 0.2966 0.2922 0.0331 ion_series 0.2727 -0.0327 0.0122 weighted_average_abs_fragment_ppm 0.3104 0.2884 0.0847 length_7 0.0094 -0.0627 0.1464 length_8 -0.0055 -0.0529 -0.0489 length_9_30 -0.2808 -0.1384 -0.1165 length_31 0.0000 0.0000 0.0000 ntt 0.2650 0.3269 0.1538 nmc 0.0183 0.0333 0.0062 charge_1 -0.1893 -0.2747 -0.1099 charge_2 0.1725 0.2139 0.0627 charge_3 0.0406 0.1318 0.1014 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.1325 0.1581 0.0926 15.9949M -0.0767 -0.0799 -0.0302 unweighted_spectral_entropy -0.1620 -0.2863 -0.2817 delta_RT_loess 2.3965 2.4988 1.6160 m0 Found 967 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 970 target PSMs and 8 decoy PSMs. Calculating q values. Final list yields 970 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 32.3490 cpu seconds or 33 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\DATA_MAUD\Results\CM_3] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms CM_3_RA3_1_31923_percolator_target_psms.tsv --decoy-results-psms CM_3_RA3_1_31923_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CM_3_RA3_1_31923_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms CM_3_RA3_1_31923_percolator_target_psms.tsv --decoy-results-psms CM_3_RA3_1_31923_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CM_3_RA3_1_31923_edited.pin Started Tue May 14 11:51:58 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CM_3_RA3_1_31923_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess Found 1112 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 1103 positives and 9 negatives, size ratio=122.556 and pi0=1 Warning : the number of negative samples read is too small to perform a correct classification. Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 1 as initial direction. Could separate 734 training set positives with q<0.01 in that direction. Split 2: Selected feature 1 as initial direction. Could separate 737 training set positives with q<0.01 in that direction. Split 3: Selected feature 1 as initial direction. Could separate 735 training set positives with q<0.01 in that direction. Found 737 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.0520 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 1102 PSMs with q<0.01 Iteration 2: Estimated 1102 PSMs with q<0.01 Iteration 3: Estimated 1102 PSMs with q<0.01 Iteration 4: Estimated 1102 PSMs with q<0.01 Iteration 5: Estimated 1102 PSMs with q<0.01 Iteration 6: Estimated 1102 PSMs with q<0.01 Iteration 7: Estimated 1102 PSMs with q<0.01 Iteration 8: Estimated 1102 PSMs with q<0.01 Iteration 9: Estimated 1102 PSMs with q<0.01 Iteration 10: Estimated 1102 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank 0.0799 0.2822 0.2308 abs_ppm 0.5243 -0.0720 0.5527 isotope_errors -0.9363 0.0527 -0.8559 log10_evalue 0.2503 0.1702 0.2048 hyperscore -0.2093 0.1810 -0.2113 delta_hyperscore 0.2224 0.0020 0.2269 matched_ion_num -0.3412 0.3489 -0.2862 complementary_ions 1.0139 0.3317 0.8548 ion_series 0.0075 0.3025 0.0144 weighted_average_abs_fragment_ppm -0.0649 0.1214 -0.1069 length_7 -0.2303 -0.2360 -0.2189 length_8 0.0959 0.0677 0.0699 length_9_30 0.0877 -0.0224 0.1495 length_31 0.0000 0.0000 0.0000 ntt -0.0606 -0.1934 0.2274 nmc 0.1110 -0.0225 0.1460 charge_1 0.1356 -0.1154 0.2068 charge_2 -0.1848 0.0610 -0.2252 charge_3 0.0597 0.1207 -0.0151 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.1586 0.0787 0.2470 15.9949M -0.0605 0.0020 -0.1084 unweighted_spectral_entropy -0.2942 -0.1771 -0.3422 delta_RT_loess 2.4448 1.7662 2.3077 m0 Found 1077 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 1103 target PSMs and 9 decoy PSMs. Calculating q values. Final list yields 1103 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 8.3290 cpu seconds or 8 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\DATA_MAUD\Results\CM_4] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms CM_4_RA4_1_31925_percolator_target_psms.tsv --decoy-results-psms CM_4_RA4_1_31925_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CM_4_RA4_1_31925_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms CM_4_RA4_1_31925_percolator_target_psms.tsv --decoy-results-psms CM_4_RA4_1_31925_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CM_4_RA4_1_31925_edited.pin Started Tue May 14 11:52:06 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CM_4_RA4_1_31925_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess Found 1002 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 988 positives and 14 negatives, size ratio=70.5714 and pi0=1 Warning : the number of negative samples read is too small to perform a correct classification. Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 30 as initial direction. Could separate 659 training set positives with q<0.01 in that direction. Split 2: Selected feature 30 as initial direction. Could separate 658 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 652 training set positives with q<0.01 in that direction. Found 965 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.0510 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 981 PSMs with q<0.01 Iteration 2: Estimated 982 PSMs with q<0.01 Iteration 3: Estimated 983 PSMs with q<0.01 Iteration 4: Estimated 983 PSMs with q<0.01 Iteration 5: Estimated 983 PSMs with q<0.01 Iteration 6: Estimated 983 PSMs with q<0.01 Iteration 7: Estimated 983 PSMs with q<0.01 Iteration 8: Estimated 983 PSMs with q<0.01 Iteration 9: Estimated 983 PSMs with q<0.01 Iteration 10: Estimated 983 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank 0.0306 -0.2273 -0.1274 abs_ppm -0.2720 0.0615 -0.2884 isotope_errors -0.9992 -0.6744 -2.2156 log10_evalue 0.0762 -0.3014 -2.1205 hyperscore -0.1858 1.0980 6.6339 delta_hyperscore 0.5701 -0.1116 1.3854 matched_ion_num -0.0347 0.1970 0.7470 complementary_ions 0.4263 0.1194 1.9009 ion_series 0.3755 0.2248 0.7411 weighted_average_abs_fragment_ppm 0.0622 -0.0245 0.3253 length_7 -0.1364 -0.1684 -0.0482 length_8 -0.1031 0.1118 -0.0074 length_9_30 0.1916 -0.0085 -0.2109 length_31 0.0000 0.0000 0.0000 ntt -0.3055 0.0317 -0.1798 nmc 0.0193 0.0178 -0.1056 charge_1 -0.3228 0.0872 -0.7912 charge_2 0.2900 -0.1379 0.7062 charge_3 0.0893 0.0911 0.2361 charge_4 -0.0694 0.0234 -0.0132 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.2022 0.2229 0.5706 15.9949M -0.0595 -0.1078 -0.0722 unweighted_spectral_entropy -0.3077 -0.1542 -0.5662 delta_RT_loess 2.1970 2.0726 12.1256 m0 Found 981 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 988 target PSMs and 14 decoy PSMs. Calculating q values. Final list yields 978 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 16.9080 cpu seconds or 17 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\DATA_MAUD\Results\E2_3] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E2_3_RB2_1_31933_percolator_target_psms.tsv --decoy-results-psms E2_3_RB2_1_31933_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E2_3_RB2_1_31933_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E2_3_RB2_1_31933_percolator_target_psms.tsv --decoy-results-psms E2_3_RB2_1_31933_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E2_3_RB2_1_31933_edited.pin Started Tue May 14 11:52:23 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile E2_3_RB2_1_31933_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess Found 886 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 875 positives and 11 negatives, size ratio=79.5455 and pi0=1 Warning : the number of negative samples read is too small to perform a correct classification. Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 582 training set positives with q<0.01 in that direction. Split 2: Selected feature 1 as initial direction. Could separate 587 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 578 training set positives with q<0.01 in that direction. Found 578 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.0520 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 871 PSMs with q<0.01 Iteration 2: Estimated 871 PSMs with q<0.01 Iteration 3: Estimated 871 PSMs with q<0.01 Iteration 4: Estimated 871 PSMs with q<0.01 Iteration 5: Estimated 871 PSMs with q<0.01 Iteration 6: Estimated 871 PSMs with q<0.01 Iteration 7: Estimated 871 PSMs with q<0.01 Iteration 8: Estimated 871 PSMs with q<0.01 Iteration 9: Estimated 871 PSMs with q<0.01 Iteration 10: Estimated 871 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank 0.3646 0.2211 0.3207 abs_ppm 0.1408 0.1096 0.0363 isotope_errors -0.7262 -0.2498 -0.4548 log10_evalue 0.3716 0.1980 0.5296 hyperscore 0.2400 0.2347 0.1639 delta_hyperscore 0.1529 -0.0904 0.3536 matched_ion_num -0.7879 0.5447 -0.2969 complementary_ions 0.6795 0.3404 0.6294 ion_series 0.2151 0.4443 0.3013 weighted_average_abs_fragment_ppm 0.1017 -0.1503 0.0228 length_7 -0.0481 -0.1626 -0.0178 length_8 0.0457 0.2097 0.0559 length_9_30 -0.1446 -0.0175 -0.1051 length_31 0.0000 0.0000 0.0000 ntt -0.1347 -0.2519 -0.2167 nmc -0.0560 -0.1244 0.0566 charge_1 -0.2177 -0.0368 -0.3064 charge_2 0.1734 -0.0185 0.2041 charge_3 0.1271 0.1457 0.2003 charge_4 -0.0693 -0.0057 0.0033 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.2458 0.0748 0.1709 15.9949M -0.0693 -0.0674 -0.0693 unweighted_spectral_entropy -0.1442 -0.0148 -0.0438 delta_RT_loess 2.0605 2.0054 2.0627 m0 Found 809 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 875 target PSMs and 11 decoy PSMs. Calculating q values. Final list yields 864 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 10.4510 cpu seconds or 11 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\DATA_MAUD\Results\E2_1] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E2_1_RB1_1_31932_percolator_target_psms.tsv --decoy-results-psms E2_1_RB1_1_31932_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E2_1_RB1_1_31932_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E2_1_RB1_1_31932_percolator_target_psms.tsv --decoy-results-psms E2_1_RB1_1_31932_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E2_1_RB1_1_31932_edited.pin Started Tue May 14 11:52:34 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile E2_1_RB1_1_31932_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess Found 1021 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 1010 positives and 11 negatives, size ratio=91.8182 and pi0=1 Warning : the number of negative samples read is too small to perform a correct classification. Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 669 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 674 training set positives with q<0.01 in that direction. Split 3: Selected feature 1 as initial direction. Could separate 675 training set positives with q<0.01 in that direction. Found 674 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.0530 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 998 PSMs with q<0.01 Iteration 2: Estimated 997 PSMs with q<0.01 Iteration 3: Estimated 997 PSMs with q<0.01 Iteration 4: Estimated 997 PSMs with q<0.01 Iteration 5: Estimated 997 PSMs with q<0.01 Iteration 6: Estimated 997 PSMs with q<0.01 Iteration 7: Estimated 997 PSMs with q<0.01 Iteration 8: Estimated 997 PSMs with q<0.01 Iteration 9: Estimated 997 PSMs with q<0.01 Iteration 10: Estimated 997 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank 0.4700 0.3790 0.1704 abs_ppm -0.3759 0.3089 -0.5093 isotope_errors -0.9477 -0.5536 -1.0941 log10_evalue 0.3782 0.6243 0.1580 hyperscore -0.0144 0.3400 -0.0088 delta_hyperscore 0.4460 0.9058 -0.2530 matched_ion_num -0.4520 -0.6602 -0.0166 complementary_ions 0.2003 0.1940 -0.0109 ion_series 0.0493 0.1449 0.2609 weighted_average_abs_fragment_ppm 0.1397 0.2727 -0.0570 length_7 -0.1259 0.0433 -0.3021 length_8 -0.0805 -0.1157 0.0949 length_9_30 0.1129 -0.1099 0.1860 length_31 0.0000 0.0000 0.0000 ntt 0.0986 0.2947 0.2323 nmc 0.0182 0.0343 0.0402 charge_1 -0.2829 -0.2560 -0.1496 charge_2 0.1982 0.2142 0.1025 charge_3 0.1720 0.0987 0.0857 charge_4 0.0527 -0.0716 0.0443 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.2561 0.2379 0.1503 15.9949M 0.0116 -0.0471 -0.0814 unweighted_spectral_entropy -0.1524 -0.2081 -0.1952 delta_RT_loess 1.8740 2.2859 1.8608 m0 Found 972 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 1010 target PSMs and 11 decoy PSMs. Calculating q values. Final list yields 982 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 13.5870 cpu seconds or 14 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\DATA_MAUD\Results\E1_1] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E1_1_RA6_1_31928_percolator_target_psms.tsv --decoy-results-psms E1_1_RA6_1_31928_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E1_1_RA6_1_31928_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E1_1_RA6_1_31928_percolator_target_psms.tsv --decoy-results-psms E1_1_RA6_1_31928_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E1_1_RA6_1_31928_edited.pin Started Tue May 14 11:52:48 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile E1_1_RA6_1_31928_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess Found 983 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 972 positives and 11 negatives, size ratio=88.3636 and pi0=1 Warning : the number of negative samples read is too small to perform a correct classification. Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 1 as initial direction. Could separate 649 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 647 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 648 training set positives with q<0.01 in that direction. Found 625 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.0490 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 971 PSMs with q<0.01 Iteration 2: Estimated 971 PSMs with q<0.01 Iteration 3: Estimated 971 PSMs with q<0.01 Iteration 4: Estimated 971 PSMs with q<0.01 Iteration 5: Estimated 971 PSMs with q<0.01 Iteration 6: Estimated 971 PSMs with q<0.01 Iteration 7: Estimated 971 PSMs with q<0.01 Iteration 8: Estimated 971 PSMs with q<0.01 Iteration 9: Estimated 971 PSMs with q<0.01 Iteration 10: Estimated 971 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.0063 0.4233 0.1974 abs_ppm -0.1052 0.2139 0.4375 isotope_errors -0.8614 -1.3163 -2.1727 log10_evalue 0.1855 -0.4755 -0.4677 hyperscore 0.0027 -0.6447 -1.0998 delta_hyperscore -0.1860 -0.0107 -0.2117 matched_ion_num 0.0525 -0.1016 -0.2043 complementary_ions 0.8617 0.7005 1.6464 ion_series 0.7377 0.4079 0.8775 weighted_average_abs_fragment_ppm 0.0480 0.0672 0.2477 length_7 -0.0758 -0.1403 -0.1031 length_8 0.0013 -0.0239 0.0636 length_9_30 0.0218 0.0985 -0.2222 length_31 0.0000 0.0000 0.0000 ntt 0.0885 0.0788 -0.1725 nmc -0.0035 0.0292 -0.0987 charge_1 -0.0982 -0.1079 -0.6376 charge_2 0.0776 0.1197 0.7748 charge_3 0.0478 -0.0242 -0.2168 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.2230 0.1168 0.3154 15.9949M -0.0486 0.0432 -0.0585 unweighted_spectral_entropy -0.2682 -0.5665 -0.4967 delta_RT_loess 2.1173 1.7526 3.9143 m0 Found 970 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 972 target PSMs and 11 decoy PSMs. Calculating q values. Final list yields 943 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 4.0700 cpu seconds or 4 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\DATA_MAUD\Results\E2_4] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E2_4_RB3_1_31935_percolator_target_psms.tsv --decoy-results-psms E2_4_RB3_1_31935_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E2_4_RB3_1_31935_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E2_4_RB3_1_31935_percolator_target_psms.tsv --decoy-results-psms E2_4_RB3_1_31935_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E2_4_RB3_1_31935_edited.pin Started Tue May 14 11:52:52 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile E2_4_RB3_1_31935_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess Found 962 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 948 positives and 14 negatives, size ratio=67.7143 and pi0=1 Warning : the number of negative samples read is too small to perform a correct classification. Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 621 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 631 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 635 training set positives with q<0.01 in that direction. Found 885 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.0520 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 939 PSMs with q<0.01 Iteration 2: Estimated 938 PSMs with q<0.01 Iteration 3: Estimated 939 PSMs with q<0.01 Iteration 4: Estimated 939 PSMs with q<0.01 Iteration 5: Estimated 939 PSMs with q<0.01 Iteration 6: Estimated 939 PSMs with q<0.01 Iteration 7: Estimated 939 PSMs with q<0.01 Iteration 8: Estimated 939 PSMs with q<0.01 Iteration 9: Estimated 939 PSMs with q<0.01 Iteration 10: Estimated 939 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank 0.2009 0.6402 0.6175 abs_ppm 0.6497 1.0020 0.3179 isotope_errors -0.2425 -0.2330 -0.4336 log10_evalue 0.0235 -0.0272 0.6753 hyperscore -0.0460 -0.4737 -1.0840 delta_hyperscore 0.1452 1.2855 2.8310 matched_ion_num 0.1879 0.4619 2.2531 complementary_ions 0.8450 1.3681 0.5371 ion_series 0.0438 0.0443 0.2939 weighted_average_abs_fragment_ppm 0.0593 0.2483 0.0570 length_7 -0.0226 -0.1612 -0.3354 length_8 0.0577 0.0208 0.3069 length_9_30 -0.1349 -0.1274 -0.2222 length_31 0.0000 0.0000 0.0000 ntt 0.3310 0.3583 -0.2039 nmc 0.0259 -0.0309 -0.0179 charge_1 -0.2538 -0.6927 -0.1525 charge_2 0.2757 0.6720 0.1246 charge_3 -0.0389 0.0985 0.0770 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.3263 0.5583 1.0288 15.9949M 0.0000 0.0000 0.0000 unweighted_spectral_entropy -0.4904 -1.3110 -0.5183 delta_RT_loess 2.0390 4.8008 7.7336 m0 Found 914 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 948 target PSMs and 14 decoy PSMs. Calculating q values. Final list yields 921 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 3.5600 cpu seconds or 4 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\DATA_MAUD\Results\E2_5] C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E2_5_RB4_1_31936_percolator_target_psms.tsv --decoy-results-psms E2_5_RB4_1_31936_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E2_5_RB4_1_31936_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\lucas\Desktop\FragPipe\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms E2_5_RB4_1_31936_percolator_target_psms.tsv --decoy-results-psms E2_5_RB4_1_31936_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ E2_5_RB4_1_31936_edited.pin Started Tue May 14 11:52:56 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile E2_5_RB4_1_31936_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy delta_RT_loess Found 875 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 865 positives and 10 negatives, size ratio=86.5 and pi0=1 Warning : the number of negative samples read is too small to perform a correct classification. Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 573 training set positives with q<0.01 in that direction. Split 2: Selected feature 30 as initial direction. Could separate 575 training set positives with q<0.01 in that direction. Split 3: Selected feature 1 as initial direction. Could separate 580 training set positives with q<0.01 in that direction. Found 563 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.0510 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 861 PSMs with q<0.01 Iteration 2: Estimated 860 PSMs with q<0.01 Iteration 3: Estimated 861 PSMs with q<0.01 Iteration 4: Estimated 861 PSMs with q<0.01 Iteration 5: Estimated 861 PSMs with q<0.01 Iteration 6: Estimated 861 PSMs with q<0.01 Iteration 7: Estimated 861 PSMs with q<0.01 Iteration 8: Estimated 861 PSMs with q<0.01 Iteration 9: Estimated 861 PSMs with q<0.01 Iteration 10: Estimated 861 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank 0.2515 -0.0480 -0.1101 abs_ppm -0.1946 -0.0171 0.2970 isotope_errors -0.8226 -0.6153 -0.9713 log10_evalue 0.0779 -0.0254 0.1636 hyperscore -0.0024 -0.2137 -0.1474 delta_hyperscore 0.3056 0.4340 -0.3968 matched_ion_num 0.3325 0.8176 -0.2175 complementary_ions 0.4007 0.3835 0.6517 ion_series 0.0435 0.1614 0.2484 weighted_average_abs_fragment_ppm 0.0868 0.1353 -0.0459 length_7 -0.1300 -0.0787 -0.2061 length_8 -0.0036 -0.0418 0.1990 length_9_30 0.0534 0.0180 -0.0666 length_31 0.0000 0.0000 0.0000 ntt -0.0412 -0.0916 -0.2075 nmc -0.0075 -0.0654 0.0078 charge_1 -0.2963 -0.2759 -0.1104 charge_2 0.2312 0.2408 0.0466 charge_3 0.1714 0.1104 0.1534 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.3346 0.3357 0.1860 15.9949M -0.0650 -0.0654 -0.0368 unweighted_spectral_entropy -0.2702 -0.3254 -0.0949 delta_RT_loess 1.9213 1.9347 1.8646 m0 Found 833 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 865 target PSMs and 10 decoy PSMs. Calculating q values. Final list yields 850 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 16.8990 cpu seconds or 17 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CM_1_RA2_1_31922.pin CM_1_RA2_1_31922 CM_1_RA2_1_31922_percolator_target_psms.tsv CM_1_RA2_1_31922_percolator_decoy_psms.tsv interact-CM_1_RA2_1_31922 DDA 0.5 D:\DATA_MAUD\CM_1_RA2_1_31922.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_1\CM_1_RA2_1_31922_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_1\CM_1_RA2_1_31922_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\CM_5] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CM_5_RA5_1_31926.pin CM_5_RA5_1_31926 CM_5_RA5_1_31926_percolator_target_psms.tsv CM_5_RA5_1_31926_percolator_decoy_psms.tsv interact-CM_5_RA5_1_31926 DDA 0.5 D:\DATA_MAUD\CM_5_RA5_1_31926.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_5\CM_5_RA5_1_31926_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_5\CM_5_RA5_1_31926_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E1_4] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E1_4_RA7_1_31929.pin E1_4_RA7_1_31929 E1_4_RA7_1_31929_percolator_target_psms.tsv E1_4_RA7_1_31929_percolator_decoy_psms.tsv interact-E1_4_RA7_1_31929 DDA 0.5 D:\DATA_MAUD\E1_4_RA7_1_31929.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E1_4\E1_4_RA7_1_31929_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E1_4\E1_4_RA7_1_31929_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E1_5] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E1_5_RA8_1_31930.pin E1_5_RA8_1_31930 E1_5_RA8_1_31930_percolator_target_psms.tsv E1_5_RA8_1_31930_percolator_decoy_psms.tsv interact-E1_5_RA8_1_31930 DDA 0.5 D:\DATA_MAUD\E1_5_RA8_1_31930.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E1_5\E1_5_RA8_1_31930_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E1_5\E1_5_RA8_1_31930_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\CM_3] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CM_3_RA3_1_31923.pin CM_3_RA3_1_31923 CM_3_RA3_1_31923_percolator_target_psms.tsv CM_3_RA3_1_31923_percolator_decoy_psms.tsv interact-CM_3_RA3_1_31923 DDA 0.5 D:\DATA_MAUD\CM_3_RA3_1_31923.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_3\CM_3_RA3_1_31923_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_3\CM_3_RA3_1_31923_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\CM_4] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CM_4_RA4_1_31925.pin CM_4_RA4_1_31925 CM_4_RA4_1_31925_percolator_target_psms.tsv CM_4_RA4_1_31925_percolator_decoy_psms.tsv interact-CM_4_RA4_1_31925 DDA 0.5 D:\DATA_MAUD\CM_4_RA4_1_31925.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_4\CM_4_RA4_1_31925_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\CM_4\CM_4_RA4_1_31925_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E2_3] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E2_3_RB2_1_31933.pin E2_3_RB2_1_31933 E2_3_RB2_1_31933_percolator_target_psms.tsv E2_3_RB2_1_31933_percolator_decoy_psms.tsv interact-E2_3_RB2_1_31933 DDA 0.5 D:\DATA_MAUD\E2_3_RB2_1_31933.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_3\E2_3_RB2_1_31933_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_3\E2_3_RB2_1_31933_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E2_1] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E2_1_RB1_1_31932.pin E2_1_RB1_1_31932 E2_1_RB1_1_31932_percolator_target_psms.tsv E2_1_RB1_1_31932_percolator_decoy_psms.tsv interact-E2_1_RB1_1_31932 DDA 0.5 D:\DATA_MAUD\E2_1_RB1_1_31932.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_1\E2_1_RB1_1_31932_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_1\E2_1_RB1_1_31932_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E1_1] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E1_1_RA6_1_31928.pin E1_1_RA6_1_31928 E1_1_RA6_1_31928_percolator_target_psms.tsv E1_1_RA6_1_31928_percolator_decoy_psms.tsv interact-E1_1_RA6_1_31928 DDA 0.5 D:\DATA_MAUD\E1_1_RA6_1_31928.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E1_1\E1_1_RA6_1_31928_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E1_1\E1_1_RA6_1_31928_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E2_4] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E2_4_RB3_1_31935.pin E2_4_RB3_1_31935 E2_4_RB3_1_31935_percolator_target_psms.tsv E2_4_RB3_1_31935_percolator_decoy_psms.tsv interact-E2_4_RB3_1_31935 DDA 0.5 D:\DATA_MAUD\E2_4_RB3_1_31935.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_4\E2_4_RB3_1_31935_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_4\E2_4_RB3_1_31935_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\DATA_MAUD\Results\E2_5] C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML E2_5_RB4_1_31936.pin E2_5_RB4_1_31936 E2_5_RB4_1_31936_percolator_target_psms.tsv E2_5_RB4_1_31936_percolator_decoy_psms.tsv interact-E2_5_RB4_1_31936 DDA 0.5 D:\DATA_MAUD\E2_5_RB4_1_31936.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_5\E2_5_RB4_1_31936_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Users\lucas\Desktop\FragPipe\fragpipe\jre\bin\java.exe -cp C:\Users\lucas\Desktop\FragPipe\fragpipe\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete D:\DATA_MAUD\Results\E2_5\E2_5_RB4_1_31936_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: D:\DATA_MAUD\Results] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\DATA_MAUD\Results\filelist_proteinprophet.txt INFO[11:53:27] Executing ProteinProphet v5.1.0 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64)) (no FPKM) (no groups) (using degen pep info) Reading in D:\DATA_MAUD\Results\CM_1\interact-CM_1_RA2_1_31922.pep.xml... ...read in 4 1+, 658 2+, 435 3+, 74 4+, 1 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\DATA_MAUD\Results\CM_3\interact-CM_3_RA3_1_31923.pep.xml... ...read in 5 1+, 625 2+, 408 3+, 70 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\DATA_MAUD\Results\CM_4\interact-CM_4_RA4_1_31925.pep.xml... ...read in 2 1+, 560 2+, 367 3+, 61 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\DATA_MAUD\Results\CM_5\interact-CM_5_RA5_1_31926.pep.xml... ...read in 2 1+, 603 2+, 404 3+, 68 4+, 1 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\DATA_MAUD\Results\E1_1\interact-E1_1_RA6_1_31928.pep.xml... ...read in 3 1+, 561 2+, 358 3+, 60 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\DATA_MAUD\Results\E1_4\interact-E1_4_RA7_1_31929.pep.xml... ...read in 1 1+, 568 2+, 299 3+, 34 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\DATA_MAUD\Results\E1_5\interact-E1_5_RA8_1_31930.pep.xml... ...read in 4 1+, 563 2+, 352 3+, 57 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\DATA_MAUD\Results\E2_1\interact-E2_1_RB1_1_31932.pep.xml... ...read in 4 1+, 594 2+, 356 3+, 66 4+, 1 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\DATA_MAUD\Results\E2_3\interact-E2_3_RB2_1_31933.pep.xml... ...read in 3 1+, 523 2+, 297 3+, 59 4+, 1 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\DATA_MAUD\Results\E2_4\interact-E2_4_RB3_1_31935.pep.xml... ...read in 2 1+, 584 2+, 327 3+, 44 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\DATA_MAUD\Results\E2_5\interact-E2_5_RB4_1_31936.pep.xml... ...read in 1 1+, 547 2+, 289 3+, 38 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 1760 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database C:\Users\lucas\Desktop\FragPipe\2024-05-02-decoys-Hbt_salinarum_NRC_1_Membrane_Proteome.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:....... Total: 974 Computing degenerate peptides for 262 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 263 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 263 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=1.30264e-05, db_size=576979 Computing MU for 263 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO[11:53:32] Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe database --annotate C:\Users\lucas\Desktop\FragPipe\2024-05-02-decoys-Hbt_salinarum_NRC_1_Membrane_Proteome.fasta.fas --prefix rev_ INFO[11:53:33] Executing Database v5.1.0 INFO[11:53:33] Annotating the database INFO[11:53:33] Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: D:\DATA_MAUD\Results\CM_1] C:\Users\lucas\Desktop\FragPipe\Philosopher\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\DATA_MAUD\Results\CM_1 --protxml D:\DATA_MAUD\Results\combined.prot.xml --razor panic: the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter goroutine 1 [running]: github.com/Nesvilab/philosopher/lib/msg.callLogrus({0xc00012a000, 0x6c}, {0x136c9af?, 0x1?}) /mnt/g/Dropbox/code/philosopher/lib/msg/msg.go:327 +0x2d8 github.com/Nesvilab/philosopher/lib/msg.Custom({0x14d6e60?, 0xc00045e4b0?}, {0x136c9af, 0x5}) /mnt/g/Dropbox/code/philosopher/lib/msg/msg.go:15 +0x68 github.com/Nesvilab/philosopher/lib/fil.ProtXMLFilter({{0x0, 0x0}, {0xc0000b20e8, 0x4}, {0xc0006d8f40, 0x1a}, {0xc00060aa80, 0x105, 0x110}}, 0x3f847ae147ae147b, ...) /mnt/g/Dropbox/code/philosopher/lib/fil/fdr.go:548 +0x8e5 github.com/Nesvilab/philosopher/lib/fil.ProcessProteinIdentifications({{0x0, 0x0}, {0xc0000b20e8, 0x4}, {0xc0006d8f40, 0x1a}, {0xc00060aa80, 0x105, 0x110}}, 0xc0000cd2b0?, ...) /mnt/g/Dropbox/code/philosopher/lib/fil/fil.go:670 +0x5eb github.com/Nesvilab/philosopher/lib/fil.Run({{0xc0000d0330, 0x24}, {0xc0000b0c00, 0x19}, {0xc000126280, 0x46}, {0xc0000d0360, 0x28}, {0xc0000b0c20, 0x1f}, ...}) /mnt/g/Dropbox/code/philosopher/lib/fil/fil.go:97 +0xb06 github.com/Nesvilab/philosopher/cmd.glob..func5(0xc0000d8500?, {0x136c35c?, 0x4?, 0x136c360?}) /mnt/g/Dropbox/code/philosopher/cmd/filter.go:47 +0x4b7 github.com/spf13/cobra.(*Command).execute(0x2fa2180, {0xc00007c320, 0xa, 0xa}) /mnt/g/Dropbox/code/philosopher/vendor/github.com/spf13/cobra/command.go:920 +0x863 github.com/spf13/cobra.(*Command).ExecuteC(0x2fa4120) /mnt/g/Dropbox/code/philosopher/vendor/github.com/spf13/cobra/command.go:1044 +0x3a5 github.com/spf13/cobra.(*Command).Execute(...) /mnt/g/Dropbox/code/philosopher/vendor/github.com/spf13/cobra/command.go:968 github.com/Nesvilab/philosopher/cmd.Execute() /mnt/g/Dropbox/code/philosopher/cmd/root.go:35 +0x1a main.main() /mnt/g/Dropbox/code/philosopher/main.go:23 +0x85 INFO[11:53:33] Executing Filter v5.1.0 INFO[11:53:33] Processing peptide identification files INFO[11:53:33] Parsing D:\DATA_MAUD\Results\CM_1\interact-CM_1_RA2_1_31922.pep.xml INFO[11:53:33] 1+ Charge profile decoy=0 target=4 INFO[11:53:33] 2+ Charge profile decoy=10 target=648 INFO[11:53:33] 3+ Charge profile decoy=0 target=435 INFO[11:53:33] 4+ Charge profile decoy=0 target=74 INFO[11:53:33] 5+ Charge profile decoy=0 target=1 INFO[11:53:33] 6+ Charge profile decoy=0 target=0 INFO[11:53:33] Database search results ions=987 peptides=764 psms=1172 INFO[11:53:33] Converged to 0.86 % FDR with 1162 PSMs decoy=10 threshold=0.900837 total=1172 INFO[11:53:33] Converged to 0.79 % FDR with 758 Peptides decoy=6 threshold=0.900837 total=764 INFO[11:53:33] Converged to 0.61 % FDR with 981 Ions decoy=6 threshold=0.900837 total=987 INFO[11:53:33] Protein inference results decoy=28 target=233 ERRO[11:53:33] the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter Process 'PhilosopherFilter' finished, exit code: 2 Process returned non-zero exit code, stopping ~~~~~~~~~~~~~~~~~~~~ Cancelling 35 remaining tasks