System OS: Windows 11, Architecture: AMD64 Java Info: 21.0.1, OpenJDK 64-Bit Server VM, Azul Systems, Inc. .NET Core Info: 6.0.26 Version info: FragPipe version 21.1 MSFragger version 4.0 IonQuant version 1.10.12 Philosopher version 5.1.0 LCMS files: Experiment/Group: EV_1 (if "spectral library generation" is enabled, all files will be analyzed together) - U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.raw DDA Experiment/Group: EV_2 (if "spectral library generation" is enabled, all files will be analyzed together) - U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2.raw DDA Experiment/Group: EV_3 (if "spectral library generation" is enabled, all files will be analyzed together) - U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3.raw DDA Experiment/Group: RNF220_1 (if "spectral library generation" is enabled, all files will be analyzed together) - U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4.raw DDA Experiment/Group: RNF220_2 (if "spectral library generation" is enabled, all files will be analyzed together) - U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5.raw DDA Experiment/Group: RNF220_3 (if "spectral library generation" is enabled, all files will be analyzed together) - U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6.raw DDA Experiment/Group: TOPORS_1 (if "spectral library generation" is enabled, all files will be analyzed together) - U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7.raw DDA Experiment/Group: TOPORS_2 (if "spectral library generation" is enabled, all files will be analyzed together) - U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8.raw DDA Experiment/Group: TOPORS_3 (if "spectral library generation" is enabled, all files will be analyzed together) - U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9.raw DDA 110 commands to execute: CheckCentroid java -Xmx20G -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;C:\Users\Public\fragpipe(21.1)\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.raw 7 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\dc832aa8-bcf6-4c75-9d31-c72df0e86ce7 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\699b885f-8750-4e9a-a94f-881dae753cb5 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\63ffa047-882b-4c91-9518-1e8140feb8f1 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\23d11891-9177-4c28-b901-c1d38276322f WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\c48b7041-b82d-4a29-a2cd-d49497c6f46f WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\7bc71061-230b-4e04-b7e8-9d94caf027eb WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\57a542a5-0f97-4b58-ad69-5a9b3bcc2030 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\0b6b3c6a-539e-47af-b3a5-4ca66e0153c6 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\045031a0-625a-44a7-8613-9219eb1e82e9 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\66545b3f-9e32-4af7-9ac5-dd75e17f3397 MSFragger [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] java -jar -Dfile.encoding=UTF-8 -Xmx20G C:\Users\Public\fragpipe(21.1)\tools\MSFragger-4.0\MSFragger-4.0.jar U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\fragger.params U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9.raw MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1\20230602_PHCOQEHF_PC1131-Emanuele_1.pepXML MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1\20230602_PHCOQEHF_PC1131-Emanuele_1.pin MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2\20230602_PHCOQEHF_PC1131-Emanuele_2.pepXML MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2\20230602_PHCOQEHF_PC1131-Emanuele_2.pin MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3\20230602_PHCOQEHF_PC1131-Emanuele_3.pepXML MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3\20230602_PHCOQEHF_PC1131-Emanuele_3.pin MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1\20230602_PHCOQEHF_PC1131-Emanuele_4.pepXML MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1\20230602_PHCOQEHF_PC1131-Emanuele_4.pin MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2\20230602_PHCOQEHF_PC1131-Emanuele_5.pepXML MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2\20230602_PHCOQEHF_PC1131-Emanuele_5.pin MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3\20230602_PHCOQEHF_PC1131-Emanuele_6.pepXML MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3\20230602_PHCOQEHF_PC1131-Emanuele_6.pin MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1\20230602_PHCOQEHF_PC1131-Emanuele_7.pepXML MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1\20230602_PHCOQEHF_PC1131-Emanuele_7.pin MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2\20230602_PHCOQEHF_PC1131-Emanuele_8.pepXML MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2\20230602_PHCOQEHF_PC1131-Emanuele_8.pin MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\20230602_PHCOQEHF_PC1131-Emanuele_9.pepXML MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\20230602_PHCOQEHF_PC1131-Emanuele_9.pin MSBooster [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] java -Xmx20G -cp C:\Users\Public\fragpipe(21.1)\tools\msbooster-1.1.28.jar;C:\Users\Public\fragpipe(21.1)\tools\batmass-io-1.30.0.jar Features.MainClass --paramsList U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\msbooster_params.txt Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_2_edited.pin Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_1_edited.pin Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_4_edited.pin Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_5_edited.pin Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_6_edited.pin Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_7_edited.pin Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_8_edited.pin Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_9_edited.pin Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_3_edited.pin Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_2.pin 20230602_PHCOQEHF_PC1131-Emanuele_2 20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_2 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2_uncalibrated.mzML Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2\20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_target_psms.tsv Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2\20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_1.pin 20230602_PHCOQEHF_PC1131-Emanuele_1 20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_1 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1_uncalibrated.mzML Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1\20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_target_psms.tsv Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1\20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_4.pin 20230602_PHCOQEHF_PC1131-Emanuele_4 20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_4 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4_uncalibrated.mzML Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1\20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_target_psms.tsv Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1\20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_5.pin 20230602_PHCOQEHF_PC1131-Emanuele_5 20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_5 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5_uncalibrated.mzML Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2\20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_target_psms.tsv Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2\20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_6.pin 20230602_PHCOQEHF_PC1131-Emanuele_6 20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_6 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6_uncalibrated.mzML Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3\20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_target_psms.tsv Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3\20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_7.pin 20230602_PHCOQEHF_PC1131-Emanuele_7 20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_7 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7_uncalibrated.mzML Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1\20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_target_psms.tsv Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1\20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_8.pin 20230602_PHCOQEHF_PC1131-Emanuele_8 20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_8 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8_uncalibrated.mzML Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2\20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_target_psms.tsv Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2\20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_9.pin 20230602_PHCOQEHF_PC1131-Emanuele_9 20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_9 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9_uncalibrated.mzML Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_target_psms.tsv Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_3.pin 20230602_PHCOQEHF_PC1131-Emanuele_3 20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_3 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3_uncalibrated.mzML Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3\20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_target_psms.tsv Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3\20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_decoy_psms.tsv ProteinProphet [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate U:\slyon\fragpipe_seaches\PC1131\2023-07-31-decoys-reviewed-contam-UP000005640.fas --prefix rev_ PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --razor PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PTMShepherd [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] java -Xmx20G -Dlibs.thermo.dir=C:\Users\Public\fragpipe(21.1)\tools\MSFragger-4.0\ext\thermo -cp C:\Users\Public\fragpipe(21.1)\tools\ptmshepherd-2.0.6.jar;C:\Users\Public\fragpipe(21.1)\tools\batmass-io-1.30.0.jar;C:\Users\Public\fragpipe(21.1)\tools\commons-math3-3.6.1.jar;C:\Users\Public\fragpipe(21.1)\tools\hipparchus-1.8\hipparchus-core-1.8.jar;C:\Users\Public\fragpipe(21.1)\tools\hipparchus-1.8\hipparchus-stat-1.8.jar edu.umich.andykong.ptmshepherd.PTMShepherd "U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\shepherd.config" WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck AppendFile java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.util.AppendToFile U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\modmasses_ionquant.txt U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\glyco_masses_list.txt IonQuant [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] java -Xmx20G -Dlibs.bruker.dir=C:\Users\Public\fragpipe(21.1)\tools\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=C:\Users\Public\fragpipe(21.1)\tools\MSFragger-4.0\ext\thermo -cp C:\Users\Public\fragpipe(21.1)\tools\jfreechart-1.5.3.jar;C:\Users\Public\fragpipe(21.1)\tools\batmass-io-1.30.0.jar;C:\Users\Public\fragpipe(21.1)\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 7 --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 1 --locprob 0.75 --uniqueness 0 --multidir . --filelist U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\filelist_ionquant.txt --modlist U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\modmasses_ionquant.txt ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [CheckCentroid], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [WorkspaceCleanInit], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] Cmd: [WorkspaceCleanInit], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] Cmd: [WorkspaceCleanInit], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] Cmd: [WorkspaceCleanInit], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [WorkspaceCleanInit], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] Cmd: [WorkspaceCleanInit], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] Cmd: [WorkspaceCleanInit], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] Cmd: [WorkspaceCleanInit], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] Cmd: [WorkspaceCleanInit], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] Cmd: [WorkspaceCleanInit], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] Cmd: [MSFragger], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [MSBooster], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [Percolator], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [ProteinProphet], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [PhilosopherDbAnnotate], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [PhilosopherFilter], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [PhilosopherReport], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [PTMShepherd], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [WorkspaceClean], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] Cmd: [WorkspaceClean], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] Cmd: [WorkspaceClean], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] Cmd: [WorkspaceClean], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [WorkspaceClean], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] Cmd: [WorkspaceClean], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] Cmd: [WorkspaceClean], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] Cmd: [WorkspaceClean], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] Cmd: [WorkspaceClean], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] Cmd: [WorkspaceClean], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] Cmd: [AppendFile], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] Cmd: [IonQuant], Work dir: [U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of U:\slyon\fragpipe_seaches\PC1131\2023-07-31-decoys-reviewed-contam-UP000005640.fas~~~~~~~ >contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries OX=9940 GN=KRT15 PE=2 SV=1 >rev_sp|O43526|KCNQ2_HUMAN Potassium voltage-gated channel subfamily KQT member 2 OS=Homo sapiens OX=9606 GN=KCNQ2 PE=1 SV=2 >rev_sp|P0DMR1|HNRC4_HUMAN Heterogeneous nuclear ribonucleoprotein C-like 4 OS=Homo sapiens OX=9606 GN=HNRNPCL4 PE=3 SV=1 >rev_sp|P49721|PSB2_HUMAN Proteasome subunit beta type-2 OS=Homo sapiens OX=9606 GN=PSMB2 PE=1 SV=1 >rev_sp|Q14157|UBP2L_HUMAN Ubiquitin-associated protein 2-like OS=Homo sapiens OX=9606 GN=UBAP2L PE=1 SV=2 >rev_sp|Q68DX3|FRPD2_HUMAN FERM and PDZ domain-containing protein 2 OS=Homo sapiens OX=9606 GN=FRMPD2 PE=1 SV=3 >rev_sp|Q8IWE5|PKHM2_HUMAN Pleckstrin homology domain-containing family M member 2 OS=Homo sapiens OX=9606 GN=PLEKHM2 PE=1 SV=2 >rev_sp|Q8WVK7|SKA2_HUMAN Spindle and kinetochore-associated protein 2 OS=Homo sapiens OX=9606 GN=SKA2 PE=1 SV=1 >rev_sp|Q9BRG1|VPS25_HUMAN Vacuolar protein-sorting-associated protein 25 OS=Homo sapiens OX=9606 GN=VPS25 PE=1 SV=1 >rev_sp|Q9NUQ2|PLCE_HUMAN 1-acyl-sn-glycerol-3-phosphate acyltransferase epsilon OS=Homo sapiens OX=9606 GN=AGPAT5 PE=1 SV=3 >rev_sp|Q9Y6N3|CLCA3_HUMAN Calcium-activated chloride channel regulator family member 3 OS=Homo sapiens OX=9606 GN=CLCA3P PE=1 SV=1 >sp|O43676|NDUB3_HUMAN NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 OS=Homo sapiens OX=9606 GN=NDUFB3 PE=1 SV=3 >sp|P0DP08|HVD82_HUMAN Immunoglobulin heavy variable 4-38-2 OS=Homo sapiens OX=9606 GN=IGHV4-38-2 PE=3 SV=1 >sp|P49902|5NTC_HUMAN Cytosolic purine 5'-nucleotidase OS=Homo sapiens OX=9606 GN=NT5C2 PE=1 SV=1 >sp|Q14264|ENR1_HUMAN Endogenous retrovirus group 3 member 1 Env polyprotein OS=Homo sapiens OX=9606 GN=ERV3-1 PE=2 SV=2 >sp|Q6B0K9|HBM_HUMAN Hemoglobin subunit mu OS=Homo sapiens OX=9606 GN=HBM PE=1 SV=1 >sp|Q8IWZ4|TRI48_HUMAN E3 ubiquitin-protein ligase TRIM48 OS=Homo sapiens OX=9606 GN=TRIM48 PE=1 SV=3 >sp|Q8WWB5|PIHD2_HUMAN PIH1 domain-containing protein 2 OS=Homo sapiens OX=9606 GN=PIH1D2 PE=1 SV=1 >sp|Q9BRV8|SIKE1_HUMAN Suppressor of IKBKE 1 OS=Homo sapiens OX=9606 GN=SIKE1 PE=1 SV=1 >sp|Q9NVE5|UBP40_HUMAN Ubiquitin carboxyl-terminal hydrolase 40 OS=Homo sapiens OX=9606 GN=USP40 PE=1 SV=3 >sp|Q9Y6Z2|CF123_HUMAN Uncharacterized protein encoded by LINC01558 OS=Homo sapiens OX=9606 GN=LINC01558 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=U\:\\slyon\\fragpipe_seaches\\PC1131\\2023-07-31-decoys-reviewed-contam-UP000005640.fas crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.medium= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=QuantUMS (high precision) 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\\Public\\fragpipe(21.1)\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe fragpipe-config.bin-ionquant=C\:\\Users\\Public\\fragpipe(21.1)\\tools\\IonQuant-1.10.12.jar fragpipe-config.bin-msfragger=C\:\\Users\\Public\\fragpipe(21.1)\\tools\\MSFragger-4.0\\MSFragger-4.0.jar fragpipe-config.bin-philosopher=C\:\\Users\\Public\\fragpipe(21.1)\\tools\\philosopher_v5.1.0_windows_amd64\\philosopher.exe fragpipe-config.bin-python=C\:\\Users\\slyon\\AppData\\Local\\Programs\\Python\\Python39\\python.exe 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=1 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.add_topN_complementary=0 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=7 msfragger.fragment_ion_series=b,y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.group_variable=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.mass_offsets_detailed= msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.01 msfragger.misc.fragger.clear-mz-hi=0 msfragger.misc.fragger.clear-mz-lo=0 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=500 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin msfragger.misc.fragger.enzyme-dropdown-2=null msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=2 msfragger.output_format=pepXML_pin msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.output_report_topN_dda_plus=5 msfragger.output_report_topN_dia1=5 msfragger.output_report_topN_dia2=3 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2= msfragger.search_enzyme_name_1=stricttrypsin msfragger.search_enzyme_name_2=null msfragger.search_enzyme_nocut_1= msfragger.search_enzyme_nocut_2= msfragger.search_enzyme_sense_1=C msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 0.0,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=true 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.diagextract_mode=false ptmshepherd.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=00.2 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=00.1 ptmshepherd.diagmine_fragMinSpecDiff=00.1 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_mode=false ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=00.2 ptmshepherd.glyco_adducts= ptmshepherd.glyco_fdr=1.00 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_mode=false ptmshepherd.glyco_ppm_tol=50 ptmshepherd.glycodatabase= ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=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=true 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.dont-run-fq-lq=false tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=-1 tmtintegrator.groupby=0 tmtintegrator.log2transformed=true tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=0 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=false tmtintegrator.tolerance=20 tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=false workdir=U\:\\slyon\\fragpipe_seaches\\PC1131_testOutput_run2 workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=false workflow.ram=0 workflow.threads=7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid java -Xmx20G -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;C:\Users\Public\fragpipe(21.1)\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.raw 7 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[20:44:25] Executing Workspace v5.1.0 INFO[20:44:25] Removing workspace INFO[20:44:25] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\dc832aa8-bcf6-4c75-9d31-c72df0e86ce7 INFO[20:44:25] Executing Workspace v5.1.0 INFO[20:44:25] Creating workspace INFO[20:44:25] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[20:44:26] Executing Workspace v5.1.0 INFO[20:44:26] Removing workspace INFO[20:44:26] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\699b885f-8750-4e9a-a94f-881dae753cb5 INFO[20:44:26] Executing Workspace v5.1.0 INFO[20:44:26] Creating workspace INFO[20:44:26] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[20:44:26] Executing Workspace v5.1.0 INFO[20:44:26] Removing workspace INFO[20:44:26] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\63ffa047-882b-4c91-9518-1e8140feb8f1 INFO[20:44:26] Executing Workspace v5.1.0 INFO[20:44:26] Creating workspace INFO[20:44:26] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[20:44:26] Executing Workspace v5.1.0 INFO[20:44:26] Removing workspace INFO[20:44:26] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\23d11891-9177-4c28-b901-c1d38276322f INFO[20:44:27] Executing Workspace v5.1.0 INFO[20:44:27] Creating workspace INFO[20:44:27] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[20:44:27] Executing Workspace v5.1.0 INFO[20:44:27] Removing workspace INFO[20:44:27] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\c48b7041-b82d-4a29-a2cd-d49497c6f46f INFO[20:44:27] Executing Workspace v5.1.0 INFO[20:44:27] Creating workspace INFO[20:44:27] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[20:44:27] Executing Workspace v5.1.0 INFO[20:44:27] Removing workspace INFO[20:44:27] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\7bc71061-230b-4e04-b7e8-9d94caf027eb INFO[20:44:27] Executing Workspace v5.1.0 INFO[20:44:27] Creating workspace INFO[20:44:27] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[20:44:28] Executing Workspace v5.1.0 INFO[20:44:28] Removing workspace INFO[20:44:28] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\57a542a5-0f97-4b58-ad69-5a9b3bcc2030 INFO[20:44:28] Executing Workspace v5.1.0 INFO[20:44:28] Creating workspace INFO[20:44:28] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[20:44:28] Executing Workspace v5.1.0 INFO[20:44:28] Removing workspace INFO[20:44:28] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\0b6b3c6a-539e-47af-b3a5-4ca66e0153c6 INFO[20:44:28] Executing Workspace v5.1.0 INFO[20:44:28] Creating workspace INFO[20:44:28] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[20:44:28] Executing Workspace v5.1.0 INFO[20:44:28] Removing workspace INFO[20:44:28] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\045031a0-625a-44a7-8613-9219eb1e82e9 INFO[20:44:29] Executing Workspace v5.1.0 INFO[20:44:29] Creating workspace INFO[20:44:29] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[20:44:29] Executing Workspace v5.1.0 INFO[20:44:29] Removing workspace INFO[20:44:29] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\slyon\AppData\Local\Temp\66545b3f-9e32-4af7-9ac5-dd75e17f3397 INFO[20:44:29] Executing Workspace v5.1.0 INFO[20:44:29] Creating workspace INFO[20:44:29] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] java -jar -Dfile.encoding=UTF-8 -Xmx20G C:\Users\Public\fragpipe(21.1)\tools\MSFragger-4.0\MSFragger-4.0.jar U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\fragger.params U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8.raw U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9.raw MSFragger version MSFragger-4.0 Batmass-IO version 1.30.0 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 11, Architecture: AMD64 Java Info: 21.0.1, OpenJDK 64-Bit Server VM, Azul Systems, Inc. JVM started with 20 GB memory Checking database... Checking spectral files... U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2.raw: Scans = 39871; Isolation sizes = [1.6] U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.raw: Scans = 47325; Isolation sizes = [1.6] U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8.raw: Scans = 51446; Isolation sizes = [1.6] U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6.raw: Scans = 53681; Isolation sizes = [1.6] U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7.raw: Scans = 49237; Isolation sizes = [1.6] U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4.raw: Scans = 56506; Isolation sizes = [1.6] U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3.raw: Scans = 52571; Isolation sizes = [1.6] U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9.raw: Scans = 45767; Isolation sizes = [1.6] U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5.raw: Scans = 58782; Isolation sizes = [1.6] ***********************************FIRST SEARCH************************************ Parameters: num_threads = 7 database_name = U:\slyon\fragpipe_seaches\PC1131\2023-07-31-decoys-reviewed-contam-UP000005640.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 0 override_charge = 0 precursor_charge_low = 2 precursor_charge_high = 3 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 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 = 0.0 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 Number of unique peptides of length 7: 290097 of length 8: 281127 of length 9: 280388 of length 10: 264672 of length 11: 251284 of length 12: 240446 of length 13: 234310 of length 14: 219646 of length 15: 208300 of length 16: 194628 of length 17: 182068 of length 18: 174871 of length 19: 171627 of length 20: 153726 of length 21: 146973 of length 22: 137907 of length 23: 128654 of length 24: 122000 of length 25: 114701 of length 26: 106855 of length 27: 101783 of length 28: 97200 of length 29: 88400 of length 30: 83874 of length 31: 78617 of length 32: 74478 of length 33: 69680 of length 34: 65280 of length 35: 59129 of length 36: 57563 of length 37: 52296 of length 38: 49252 of length 39: 44395 of length 40: 42239 of length 41: 39335 of length 42: 36337 of length 43: 30461 of length 44: 24675 of length 45: 18980 of length 46: 12396 of length 47: 7817 of length 48: 4500 of length 49: 2437 of length 50: 1487 In total 5046891 peptides. Generated 7932163 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 323461980 fragments to be searched in 1 slices (4.82 GB total) Operating on slice 1 of 1: Fragment index slice generated in 3.96 s 001. 20230602_PHCOQEHF_PC1131-Emanuele_1.raw 141.8 s | deisotoping 0.3 s [progress: 35790/35790 (100%) - 19170 spectra/s] 1.9s | postprocessing 0.4 s 002. 20230602_PHCOQEHF_PC1131-Emanuele_2.raw 52.0 s | deisotoping 0.0 s [progress: 28309/28309 (100%) - 64339 spectra/s] 0.4s | postprocessing 0.2 s 003. 20230602_PHCOQEHF_PC1131-Emanuele_3.raw 132.0 s | deisotoping 0.3 s [progress: 41476/41476 (100%) - 41980 spectra/s] 1.0s | postprocessing 0.2 s 004. 20230602_PHCOQEHF_PC1131-Emanuele_4.raw 122.9 s | deisotoping 0.2 s [progress: 48507/48507 (100%) - 39695 spectra/s] 1.2s | postprocessing 0.2 s 005. 20230602_PHCOQEHF_PC1131-Emanuele_5.raw 132.5 s | deisotoping 0.1 s [progress: 53045/53045 (100%) - 31878 spectra/s] 1.7s | postprocessing 0.3 s 006. 20230602_PHCOQEHF_PC1131-Emanuele_6.raw 119.2 s | deisotoping 0.0 s [progress: 42776/42776 (100%) - 38676 spectra/s] 1.1s | postprocessing 0.2 s 007. 20230602_PHCOQEHF_PC1131-Emanuele_7.raw 144.8 s | deisotoping 0.0 s [progress: 40187/40187 (100%) - 40268 spectra/s] 1.0s | postprocessing 0.2 s 008. 20230602_PHCOQEHF_PC1131-Emanuele_8.raw 150.9 s | deisotoping 0.0 s [progress: 39852/39852 (100%) - 44778 spectra/s] 0.9s | postprocessing 0.4 s 009. 20230602_PHCOQEHF_PC1131-Emanuele_9.raw 176.9 s | deisotoping 0.0 s [progress: 36591/36591 (100%) - 47153 spectra/s] 0.8s | postprocessing 0.2 s ***************************FIRST SEARCH DONE IN 20.484 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | 1.09 1.40 | -0.01 0.88 | -0.53 3.25 | -0.01 3.17 002 | 1.03 1.22 | -0.06 0.74 | -0.47 3.30 | -0.01 3.23 003 | 1.07 1.61 | -0.04 0.92 | -0.57 3.27 | 0.01 3.23 004 | 0.75 1.88 | 0.06 1.11 | -0.98 3.19 | -0.02 3.10 005 | 0.70 2.07 | -0.01 1.25 | -1.00 3.20 | -0.00 3.14 006 | 0.80 1.84 | -0.00 1.19 | -0.85 3.29 | -0.03 3.23 007 | 0.75 1.94 | -0.03 1.15 | -0.90 3.32 | -0.01 3.22 008 | 0.89 1.65 | -0.02 1.07 | -0.80 3.22 | -0.06 3.17 009 | 0.95 1.59 | -0.10 1.07 | -0.65 3.24 | -0.02 3.22 -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|-------|-------|------- MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 -------|-------|-------|-------|-------|-------|-------|-------|------- Count | skip | 19925| 20448| 20394| skip rest -------|-------|-------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 -------|-------|-------|-------|-------|-------|------- Count | 20477| 20475| skip rest -------|-------|-------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 20674 -------|------- -------|------- Rm P. | 0 -------|------- Count | 20608 -------|------- New fragment_mass_tolerance = 10.000000 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 18.854 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 7 database_name = U:\slyon\fragpipe_seaches\PC1131\2023-07-31-decoys-reviewed-contam-UP000005640.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 = 10.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1/2 mass_offsets = 0.0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 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 = 0.0 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 Number of unique peptides of length 7: 290097 of length 8: 281127 of length 9: 280388 of length 10: 264672 of length 11: 251284 of length 12: 240446 of length 13: 234310 of length 14: 219646 of length 15: 208300 of length 16: 194628 of length 17: 182068 of length 18: 174871 of length 19: 171627 of length 20: 153726 of length 21: 146973 of length 22: 137907 of length 23: 128654 of length 24: 122000 of length 25: 114701 of length 26: 106855 of length 27: 101783 of length 28: 97200 of length 29: 88400 of length 30: 83874 of length 31: 78617 of length 32: 74478 of length 33: 69680 of length 34: 65280 of length 35: 59129 of length 36: 57563 of length 37: 52296 of length 38: 49252 of length 39: 44395 of length 40: 42239 of length 41: 39335 of length 42: 36337 of length 43: 30461 of length 44: 24675 of length 45: 18980 of length 46: 12396 of length 47: 7817 of length 48: 4500 of length 49: 2437 of length 50: 1487 In total 5046891 peptides. Generated 7932163 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.05 Da. 323461980 fragments to be searched in 1 slices (4.82 GB total) Operating on slice 1 of 1: Fragment index slice generated in 3.94 s 001. 20230602_PHCOQEHF_PC1131-Emanuele_1.mzBIN_calibrated 0.9 s [progress: 34011/34011 (100%) - 38387 spectra/s] 0.9s | remapping alternative proteins and postprocessing 6.3 s 002. 20230602_PHCOQEHF_PC1131-Emanuele_2.mzBIN_calibrated 0.5 s [progress: 26720/26720 (100%) - 48318 spectra/s] 0.6s | remapping alternative proteins and postprocessing 4.6 s 003. 20230602_PHCOQEHF_PC1131-Emanuele_3.mzBIN_calibrated 1.1 s [progress: 39764/39764 (100%) - 35823 spectra/s] 1.1s | remapping alternative proteins and postprocessing 6.8 s 004. 20230602_PHCOQEHF_PC1131-Emanuele_4.mzBIN_calibrated 1.1 s [progress: 46954/46954 (100%) - 28167 spectra/s] 1.7s | remapping alternative proteins and postprocessing 8.5 s 005. 20230602_PHCOQEHF_PC1131-Emanuele_5.mzBIN_calibrated 1.2 s [progress: 51651/51651 (100%) - 27387 spectra/s] 1.9s | remapping alternative proteins and postprocessing 9.4 s 006. 20230602_PHCOQEHF_PC1131-Emanuele_6.mzBIN_calibrated 0.9 s [progress: 41118/41118 (100%) - 33703 spectra/s] 1.2s | remapping alternative proteins and postprocessing 7.6 s 007. 20230602_PHCOQEHF_PC1131-Emanuele_7.mzBIN_calibrated 0.8 s [progress: 38700/38700 (100%) - 31773 spectra/s] 1.2s | remapping alternative proteins and postprocessing 6.9 s 008. 20230602_PHCOQEHF_PC1131-Emanuele_8.mzBIN_calibrated 0.9 s [progress: 38232/38232 (100%) - 34381 spectra/s] 1.1s | remapping alternative proteins and postprocessing 6.6 s 009. 20230602_PHCOQEHF_PC1131-Emanuele_9.mzBIN_calibrated 0.6 s [progress: 35201/35201 (100%) - 35413 spectra/s] 1.0s | remapping alternative proteins and postprocessing 6.0 s ***************************MAIN SEARCH DONE IN 1.569 MIN*************************** *******************************TOTAL TIME 40.906 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1\20230602_PHCOQEHF_PC1131-Emanuele_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1\20230602_PHCOQEHF_PC1131-Emanuele_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2\20230602_PHCOQEHF_PC1131-Emanuele_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2\20230602_PHCOQEHF_PC1131-Emanuele_2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3\20230602_PHCOQEHF_PC1131-Emanuele_3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3\20230602_PHCOQEHF_PC1131-Emanuele_3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1\20230602_PHCOQEHF_PC1131-Emanuele_4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1\20230602_PHCOQEHF_PC1131-Emanuele_4.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2\20230602_PHCOQEHF_PC1131-Emanuele_5.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2\20230602_PHCOQEHF_PC1131-Emanuele_5.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3\20230602_PHCOQEHF_PC1131-Emanuele_6.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3\20230602_PHCOQEHF_PC1131-Emanuele_6.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1\20230602_PHCOQEHF_PC1131-Emanuele_7.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1\20230602_PHCOQEHF_PC1131-Emanuele_7.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2\20230602_PHCOQEHF_PC1131-Emanuele_8.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2\20230602_PHCOQEHF_PC1131-Emanuele_8.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9.pepXML U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\20230602_PHCOQEHF_PC1131-Emanuele_9.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar;/C:/Users/Public/fragpipe(21.1)/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9.pin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\20230602_PHCOQEHF_PC1131-Emanuele_9.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] java -Xmx20G -cp C:\Users\Public\fragpipe(21.1)\tools\msbooster-1.1.28.jar;C:\Users\Public\fragpipe(21.1)\tools\batmass-io-1.30.0.jar Features.MainClass --paramsList U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\msbooster_params.txt MSBooster v1.1.28 Using 7 threads 88785 unique peptides from 230084 PSMs createFull input file generation took 5701 milliseconds Input file at U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\spectraRT_full.tsv Generating input file for DIA-NN 88785 unique peptides from 230084 PSMs Writing DIA-NN input file Diann input file generation took 4242 milliseconds Input file at U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\spectraRT.tsv Generating DIA-NN predictions C:\Users\Public\fragpipe(21.1)\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\spectraRT.tsv --predict --threads 7 --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: Fri Jan 26 21:25:49 2024 CPU: GenuineIntel Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz 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 7 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 U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_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 88785 precursors in 83078 elution groups. [0:00] Encoding peptides for spectra and RTs prediction [0:00] Predicting spectra and IMs [0:27] Predicting RTs [0:35] Decoding predicted spectra and IMs [0:36] Decoding RTs [0:36] Saving the list of predictions to U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\spectraRT.predicted.bin Finished Done generating DIA-NN predictions Model running took 50633 milliseconds Generating edited pin with following features: [unweightedSpectralEntropy, deltaRTLOESS] Loading predicted spectra Processing U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 3486 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 U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1\20230602_PHCOQEHF_PC1131-Emanuele_1_edited.pin Processing U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 1866 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 U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2\20230602_PHCOQEHF_PC1131-Emanuele_2_edited.pin Processing U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3\20230602_PHCOQEHF_PC1131-Emanuele_3_edited.pin Processing U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1\20230602_PHCOQEHF_PC1131-Emanuele_4_edited.pin Processing U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2\20230602_PHCOQEHF_PC1131-Emanuele_5_edited.pin Processing U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3\20230602_PHCOQEHF_PC1131-Emanuele_6_edited.pin Processing U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1\20230602_PHCOQEHF_PC1131-Emanuele_7_edited.pin Processing U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 5000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2\20230602_PHCOQEHF_PC1131-Emanuele_8_edited.pin Processing U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 4401 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 U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\20230602_PHCOQEHF_PC1131-Emanuele_9_edited.pin Feature calculation and edited pin writing done in 84929 ms Process 'MSBooster' finished, exit code: 0 Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_2_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\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_2_edited.pin Started Fri Jan 26 21:27:55 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20230602_PHCOQEHF_PC1131-Emanuele_2_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 14267 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 12033 positives and 2234 negatives, size ratio=5.3863 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 5518 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 5475 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 5545 training set positives with q<0.01 in that direction. Found 8212 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.1940 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 9657 PSMs with q<0.01 Iteration 2: Estimated 9740 PSMs with q<0.01 Iteration 3: Estimated 9745 PSMs with q<0.01 Iteration 4: Estimated 9751 PSMs with q<0.01 Iteration 5: Estimated 9752 PSMs with q<0.01 Iteration 6: Estimated 9753 PSMs with q<0.01 Iteration 7: Estimated 9752 PSMs with q<0.01 Iteration 8: Estimated 9755 PSMs with q<0.01 Iteration 9: Estimated 9755 PSMs with q<0.01 Iteration 10: Estimated 9754 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 -0.3612 -0.2958 -0.2772 abs_ppm -0.0124 0.0047 0.0356 isotope_errors 0.0507 -0.2159 -0.7629 log10_evalue 0.1856 0.2011 0.0299 hyperscore 1.1251 0.8957 0.6371 delta_hyperscore 1.6845 2.0837 0.7879 matched_ion_num -0.7444 -0.7878 -0.5239 complementary_ions -0.1024 -0.3464 -0.0845 ion_series 0.0330 0.1216 -0.0084 weighted_average_abs_fragment_ppm -0.1487 -0.1170 -0.1432 length_7 -0.0522 -0.0726 -0.0459 length_8 0.1040 0.0827 0.0967 length_9_30 0.1749 0.2302 0.1690 length_31 0.0000 0.0000 0.0000 ntt -0.0907 -0.1714 -0.3029 nmc 0.0000 0.0000 0.0000 charge_1 -0.0568 -0.0764 -0.1296 charge_2 -0.0134 0.0046 0.0797 charge_3 0.1256 0.1291 0.1032 charge_4 0.1326 0.1378 0.0768 charge_5 0.0220 0.0261 0.0051 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 0.0878 0.2442 0.1409 15.9949M 1.4120 1.4068 1.2830 unweighted_spectral_entropy -0.9937 -1.0424 -0.8598 delta_RT_loess 1.4176 1.1240 1.0624 m0 Found 9710 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 12033 target PSMs and 2234 decoy PSMs. Calculating q values. Final list yields 9713 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 3.7430 cpu seconds or 4 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_1_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\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_1_edited.pin Started Fri Jan 26 21:28:13 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20230602_PHCOQEHF_PC1131-Emanuele_1_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 20927 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 17211 positives and 3716 negatives, size ratio=4.63159 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 7810 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 7828 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 7748 training set positives with q<0.01 in that direction. Found 11625 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2620 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 13264 PSMs with q<0.01 Iteration 2: Estimated 13416 PSMs with q<0.01 Iteration 3: Estimated 13421 PSMs with q<0.01 Iteration 4: Estimated 13419 PSMs with q<0.01 Iteration 5: Estimated 13418 PSMs with q<0.01 Iteration 6: Estimated 13414 PSMs with q<0.01 Iteration 7: Estimated 13415 PSMs with q<0.01 Iteration 8: Estimated 13416 PSMs with q<0.01 Iteration 9: Estimated 13417 PSMs with q<0.01 Iteration 10: Estimated 13417 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 -0.3278 -0.3605 -0.3236 abs_ppm 0.0772 0.0408 0.0430 isotope_errors -0.5718 -0.8845 -0.5383 log10_evalue 0.4030 0.3767 0.4538 hyperscore 0.8261 0.9254 0.8687 delta_hyperscore 0.8227 1.4514 0.6919 matched_ion_num -0.7080 -0.8655 -0.5471 complementary_ions 0.0517 -0.3033 0.0353 ion_series 0.1009 0.0757 0.0942 weighted_average_abs_fragment_ppm -0.1169 -0.1366 -0.1063 length_7 -0.0307 -0.0417 -0.0238 length_8 0.0731 0.0878 0.0701 length_9_30 0.1405 0.1720 0.1012 length_31 0.0000 0.0000 0.0000 ntt -0.0541 -0.0502 -0.0932 nmc 0.0000 0.0000 0.0000 charge_1 -0.0715 -0.0139 -0.0458 charge_2 0.0100 -0.0561 -0.0285 charge_3 0.1026 0.1004 0.0960 charge_4 0.0747 0.1500 0.1667 charge_5 0.0798 0.0065 0.0938 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 0.1330 0.0646 0.1181 15.9949M 1.3838 1.6053 1.3153 unweighted_spectral_entropy -1.0116 -1.1479 -1.0152 delta_RT_loess 1.0771 1.4134 1.0200 m0 Found 13384 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 17211 target PSMs and 3716 decoy PSMs. Calculating q values. Final list yields 13385 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 4.3330 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_4_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\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_4_edited.pin Started Fri Jan 26 21:28:39 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20230602_PHCOQEHF_PC1131-Emanuele_4_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 32557 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 27509 positives and 5048 negatives, size ratio=5.44948 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 13735 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 13782 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 13655 training set positives with q<0.01 in that direction. Found 20517 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.4180 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 22188 PSMs with q<0.01 Iteration 2: Estimated 22292 PSMs with q<0.01 Iteration 3: Estimated 22315 PSMs with q<0.01 Iteration 4: Estimated 22319 PSMs with q<0.01 Iteration 5: Estimated 22317 PSMs with q<0.01 Iteration 6: Estimated 22317 PSMs with q<0.01 Iteration 7: Estimated 22316 PSMs with q<0.01 Iteration 8: Estimated 22317 PSMs with q<0.01 Iteration 9: Estimated 22317 PSMs with q<0.01 Iteration 10: Estimated 22316 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 -0.2184 -0.2931 -0.2721 abs_ppm 0.0056 -0.0644 -0.0209 isotope_errors -0.4852 -0.7454 -0.7639 log10_evalue 1.1957 1.1404 1.5150 hyperscore 1.2898 1.2522 1.0282 delta_hyperscore 0.2629 0.3279 0.0602 matched_ion_num -0.7036 -0.9915 -0.8239 complementary_ions 0.0173 -0.0988 0.0438 ion_series 0.0763 0.1373 0.1679 weighted_average_abs_fragment_ppm -0.1248 -0.1241 -0.1265 length_7 -0.0456 -0.0110 -0.0488 length_8 0.1009 0.0698 0.0842 length_9_30 0.0585 0.0775 0.1170 length_31 0.0000 0.0000 0.0000 ntt -0.1729 -0.1104 -0.1444 nmc 0.0000 0.0000 0.0000 charge_1 -0.0042 0.0724 0.0335 charge_2 -0.0027 -0.0631 -0.0223 charge_3 0.0180 -0.0154 -0.0152 charge_4 -0.0161 -0.0313 -0.0253 charge_5 0.0287 0.0093 -0.0165 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 0.0879 0.0450 0.0771 15.9949M 1.4627 1.4781 1.3940 unweighted_spectral_entropy -0.8529 -0.7467 -0.6575 delta_RT_loess 1.9054 1.9681 2.0360 m0 Found 22292 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 27509 target PSMs and 5048 decoy PSMs. Calculating q values. Final list yields 22292 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 9.7260 cpu seconds or 10 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_5_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\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_5_edited.pin Started Fri Jan 26 21:29:23 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20230602_PHCOQEHF_PC1131-Emanuele_5_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 35748 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 29583 positives and 6165 negatives, size ratio=4.79854 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 14519 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 14567 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 14552 training set positives with q<0.01 in that direction. Found 21837 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.4620 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 23274 PSMs with q<0.01 Iteration 2: Estimated 23404 PSMs with q<0.01 Iteration 3: Estimated 23407 PSMs with q<0.01 Iteration 4: Estimated 23396 PSMs with q<0.01 Iteration 5: Estimated 23392 PSMs with q<0.01 Iteration 6: Estimated 23389 PSMs with q<0.01 Iteration 7: Estimated 23389 PSMs with q<0.01 Iteration 8: Estimated 23386 PSMs with q<0.01 Iteration 9: Estimated 23386 PSMs with q<0.01 Iteration 10: Estimated 23387 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 -0.1394 -0.1659 -0.2120 abs_ppm -0.0364 -0.0100 0.0351 isotope_errors -0.9367 -0.5447 -0.9844 log10_evalue 0.1726 0.6994 1.1093 hyperscore 0.7197 1.0321 0.9067 delta_hyperscore 1.1323 0.6112 0.0425 matched_ion_num -0.6869 -0.6650 -0.6757 complementary_ions -0.0866 0.0668 0.0293 ion_series 0.1539 0.0656 0.0775 weighted_average_abs_fragment_ppm -0.0966 -0.1037 -0.1438 length_7 -0.0249 -0.0575 -0.0518 length_8 0.0378 0.0596 0.0735 length_9_30 0.1006 0.1111 0.1332 length_31 0.0000 0.0000 0.0000 ntt -0.1005 -0.0571 -0.1461 nmc 0.0000 0.0000 0.0000 charge_1 -0.0560 -0.0353 -0.0127 charge_2 0.0707 0.0223 0.0382 charge_3 -0.0072 0.0390 -0.0397 charge_4 -0.0267 -0.0159 -0.0262 charge_5 -0.0068 -0.0195 0.0347 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 -0.0060 0.0265 0.0540 15.9949M 1.2815 1.3824 1.5501 unweighted_spectral_entropy -0.7255 -0.5390 -0.5392 delta_RT_loess 1.2809 1.6709 1.7941 m0 Found 23345 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 29583 target PSMs and 6165 decoy PSMs. Calculating q values. Final list yields 23348 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 6.4630 cpu seconds or 7 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_6_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\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_6_edited.pin Started Fri Jan 26 21:30:06 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20230602_PHCOQEHF_PC1131-Emanuele_6_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 28007 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 23666 positives and 4341 negatives, size ratio=5.45174 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 11393 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 11531 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 11474 training set positives with q<0.01 in that direction. Found 17172 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.3650 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 19117 PSMs with q<0.01 Iteration 2: Estimated 19220 PSMs with q<0.01 Iteration 3: Estimated 19219 PSMs with q<0.01 Iteration 4: Estimated 19218 PSMs with q<0.01 Iteration 5: Estimated 19208 PSMs with q<0.01 Iteration 6: Estimated 19211 PSMs with q<0.01 Iteration 7: Estimated 19209 PSMs with q<0.01 Iteration 8: Estimated 19209 PSMs with q<0.01 Iteration 9: Estimated 19208 PSMs with q<0.01 Iteration 10: Estimated 19206 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 -0.2535 -0.2680 -0.2060 abs_ppm 0.0410 0.0470 0.0264 isotope_errors -0.4165 -0.2467 -0.5054 log10_evalue 0.6380 0.9816 0.7397 hyperscore 0.9287 0.8065 0.8856 delta_hyperscore 0.5836 0.3231 0.3686 matched_ion_num -0.5710 -0.5985 -0.5455 complementary_ions -0.1070 -0.0633 -0.0558 ion_series 0.0259 0.0620 0.0366 weighted_average_abs_fragment_ppm -0.0920 -0.1327 -0.1403 length_7 -0.0505 -0.0522 -0.0121 length_8 0.0725 0.0899 0.0808 length_9_30 0.0997 0.1436 0.0980 length_31 0.0000 0.0000 0.0000 ntt -0.1272 -0.1908 -0.0970 nmc 0.0000 0.0000 0.0000 charge_1 -0.0412 -0.0180 -0.0563 charge_2 0.0215 0.0125 0.0471 charge_3 0.0491 0.0226 0.0145 charge_4 0.0006 -0.0179 0.0246 charge_5 -0.0184 -0.0128 0.0119 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 0.1897 0.1509 0.1301 15.9949M 1.1707 1.4055 1.5248 unweighted_spectral_entropy -0.9920 -0.7037 -0.5458 delta_RT_loess 0.6882 1.2998 1.4107 m0 Found 19134 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 23666 target PSMs and 4341 decoy PSMs. Calculating q values. Final list yields 19143 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 6.1530 cpu seconds or 7 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_7_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\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_7_edited.pin Started Fri Jan 26 21:30:46 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20230602_PHCOQEHF_PC1131-Emanuele_7_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 25923 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 21485 positives and 4438 negatives, size ratio=4.84114 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 29 as initial direction. Could separate 10376 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 10238 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 10204 training set positives with q<0.01 in that direction. Found 14590 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.3260 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 16990 PSMs with q<0.01 Iteration 2: Estimated 17069 PSMs with q<0.01 Iteration 3: Estimated 17084 PSMs with q<0.01 Iteration 4: Estimated 17091 PSMs with q<0.01 Iteration 5: Estimated 17090 PSMs with q<0.01 Iteration 6: Estimated 17089 PSMs with q<0.01 Iteration 7: Estimated 17088 PSMs with q<0.01 Iteration 8: Estimated 17089 PSMs with q<0.01 Iteration 9: Estimated 17090 PSMs with q<0.01 Iteration 10: Estimated 17090 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 -0.2145 -0.2928 -0.3386 abs_ppm -0.0044 -0.0008 -0.0133 isotope_errors -0.7290 -0.6371 -0.9865 log10_evalue 0.6020 1.4066 1.4858 hyperscore 0.7477 0.8436 1.0119 delta_hyperscore 0.5726 0.6858 -0.0024 matched_ion_num -0.6650 -1.0903 -0.9241 complementary_ions -0.1380 -0.3489 -0.0446 ion_series 0.0330 0.0413 0.1007 weighted_average_abs_fragment_ppm -0.0881 -0.0800 -0.1403 length_7 0.0263 0.0019 -0.0342 length_8 0.0459 0.0350 0.0765 length_9_30 -0.0020 0.0868 0.1990 length_31 0.0000 0.0000 0.0000 ntt -0.0173 -0.0704 -0.0516 nmc 0.0000 0.0000 0.0000 charge_1 -0.0176 -0.0114 -0.0279 charge_2 -0.0311 -0.0241 -0.0117 charge_3 0.0877 0.0825 0.0784 charge_4 0.0795 0.0115 0.0145 charge_5 0.0064 -0.0351 0.0851 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 0.1856 0.1618 0.1511 15.9949M 1.2444 1.4787 1.5721 unweighted_spectral_entropy -1.0282 -0.9369 -0.9657 delta_RT_loess 0.5099 1.5088 1.7529 m0 Found 17046 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 21485 target PSMs and 4438 decoy PSMs. Calculating q values. Final list yields 17046 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 5.4750 cpu seconds or 6 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_8_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\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_8_edited.pin Started Fri Jan 26 21:31:20 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20230602_PHCOQEHF_PC1131-Emanuele_8_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 25224 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 21075 positives and 4149 negatives, size ratio=5.07954 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 10124 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 10047 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 9922 training set positives with q<0.01 in that direction. Found 15077 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.3210 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 16720 PSMs with q<0.01 Iteration 2: Estimated 16828 PSMs with q<0.01 Iteration 3: Estimated 16833 PSMs with q<0.01 Iteration 4: Estimated 16833 PSMs with q<0.01 Iteration 5: Estimated 16836 PSMs with q<0.01 Iteration 6: Estimated 16835 PSMs with q<0.01 Iteration 7: Estimated 16835 PSMs with q<0.01 Iteration 8: Estimated 16834 PSMs with q<0.01 Iteration 9: Estimated 16835 PSMs with q<0.01 Iteration 10: Estimated 16835 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 -0.2479 -0.2514 -0.2660 abs_ppm 0.0488 0.0121 0.0146 isotope_errors -0.5198 -0.4796 -0.9232 log10_evalue 0.7984 0.8689 0.7011 hyperscore 0.8853 0.6469 0.7762 delta_hyperscore 0.2737 0.3271 0.3472 matched_ion_num -0.6606 -0.6403 -0.8221 complementary_ions 0.0719 0.0540 0.0237 ion_series 0.0423 0.0574 0.0508 weighted_average_abs_fragment_ppm -0.1529 -0.0942 -0.0870 length_7 -0.0171 -0.0284 0.0010 length_8 0.0646 0.0691 0.0463 length_9_30 0.2058 0.0686 0.0551 length_31 0.0000 0.0000 0.0000 ntt -0.0490 -0.1416 -0.0964 nmc 0.0000 0.0000 0.0000 charge_1 -0.0013 -0.0526 -0.0669 charge_2 -0.0393 0.0310 0.0431 charge_3 0.0756 0.0454 0.0516 charge_4 -0.0020 0.0003 -0.0053 charge_5 0.0947 0.0463 0.0620 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 0.1024 0.0757 0.0323 15.9949M 1.4662 1.1695 1.5048 unweighted_spectral_entropy -1.4521 -0.7701 -0.8507 delta_RT_loess 1.0868 1.2347 0.9802 m0 Found 16803 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 21075 target PSMs and 4149 decoy PSMs. Calculating q values. Final list yields 16811 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 4.9280 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_9_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\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_9_edited.pin Started Fri Jan 26 21:31:51 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20230602_PHCOQEHF_PC1131-Emanuele_9_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 22671 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 18913 positives and 3758 negatives, size ratio=5.03273 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 8974 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 8872 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 8883 training set positives with q<0.01 in that direction. Found 13328 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2850 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 14930 PSMs with q<0.01 Iteration 2: Estimated 15025 PSMs with q<0.01 Iteration 3: Estimated 15026 PSMs with q<0.01 Iteration 4: Estimated 15026 PSMs with q<0.01 Iteration 5: Estimated 15030 PSMs with q<0.01 Iteration 6: Estimated 15033 PSMs with q<0.01 Iteration 7: Estimated 15033 PSMs with q<0.01 Iteration 8: Estimated 15033 PSMs with q<0.01 Iteration 9: Estimated 15034 PSMs with q<0.01 Iteration 10: Estimated 15034 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 -0.4005 -0.3697 -0.3482 abs_ppm 0.0701 -0.0669 0.0069 isotope_errors -0.9715 -1.0458 -0.6881 log10_evalue 0.6769 0.5949 0.7523 hyperscore 0.6415 0.7335 0.7001 delta_hyperscore 0.8129 0.8517 0.2262 matched_ion_num -0.9034 -0.8928 -0.7728 complementary_ions -0.1775 -0.1644 0.0192 ion_series 0.0041 0.0402 -0.0175 weighted_average_abs_fragment_ppm -0.1271 -0.1266 -0.1269 length_7 -0.0204 -0.0212 -0.0485 length_8 0.0859 0.0893 0.0962 length_9_30 0.0921 0.0778 0.1387 length_31 0.0000 0.0000 0.0000 ntt -0.0986 -0.1979 0.0033 nmc 0.0000 0.0000 0.0000 charge_1 -0.0162 -0.0390 0.0176 charge_2 -0.0149 0.0047 -0.0177 charge_3 0.0586 0.0752 -0.0138 charge_4 0.0588 0.0500 0.0436 charge_5 0.0266 -0.0206 0.0172 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 0.0434 0.1321 0.0772 15.9949M 1.2883 1.3569 1.2645 unweighted_spectral_entropy -1.2589 -0.8650 -0.7586 delta_RT_loess 1.3205 1.4585 0.8715 m0 Found 15004 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 18913 target PSMs and 3758 decoy PSMs. Calculating q values. Final list yields 15006 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 4.4740 cpu seconds or 4 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] C:\Users\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_3_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\Public\fragpipe(21.1)\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_target_psms.tsv --decoy-results-psms 20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20230602_PHCOQEHF_PC1131-Emanuele_3_edited.pin Started Fri Jan 26 21:32:19 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20230602_PHCOQEHF_PC1131-Emanuele_3_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 24760 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 20477 positives and 4283 negatives, size ratio=4.78099 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 9532 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 9675 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 9675 training set positives with q<0.01 in that direction. Found 14425 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.3160 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 15940 PSMs with q<0.01 Iteration 2: Estimated 16048 PSMs with q<0.01 Iteration 3: Estimated 16064 PSMs with q<0.01 Iteration 4: Estimated 16066 PSMs with q<0.01 Iteration 5: Estimated 16071 PSMs with q<0.01 Iteration 6: Estimated 16073 PSMs with q<0.01 Iteration 7: Estimated 16072 PSMs with q<0.01 Iteration 8: Estimated 16073 PSMs with q<0.01 Iteration 9: Estimated 16073 PSMs with q<0.01 Iteration 10: Estimated 16072 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 -0.2557 -0.2264 -0.2177 abs_ppm 0.0701 -0.0175 -0.0642 isotope_errors -0.6204 -0.7115 -0.6190 log10_evalue 0.3702 0.4548 0.4564 hyperscore 0.7966 0.8583 0.7788 delta_hyperscore 1.2050 1.1751 1.1748 matched_ion_num -0.7576 -0.9248 -0.8331 complementary_ions -0.2048 -0.2410 -0.3233 ion_series -0.0064 0.0063 0.0070 weighted_average_abs_fragment_ppm -0.1327 -0.1007 -0.0973 length_7 -0.0008 -0.0002 -0.0183 length_8 0.0619 0.0398 -0.0033 length_9_30 0.0915 0.0889 0.2383 length_31 0.0000 0.0000 0.0000 ntt -0.0602 -0.1116 -0.1237 nmc 0.0000 0.0000 0.0000 charge_1 -0.0226 -0.0434 -0.0547 charge_2 -0.0193 -0.0023 0.0248 charge_3 0.0589 0.0778 0.0688 charge_4 0.0748 0.0419 0.0117 charge_5 -0.0343 -0.0154 -0.0700 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 0.1800 0.1398 0.1102 15.9949M 1.5517 1.4060 1.3152 unweighted_spectral_entropy -1.0976 -0.9216 -0.9396 delta_RT_loess 1.2820 1.4391 1.2184 m0 Found 16017 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 20477 target PSMs and 4283 decoy PSMs. Calculating q values. Final list yields 16019 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 4.3860 cpu seconds or 4 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_2.pin 20230602_PHCOQEHF_PC1131-Emanuele_2 20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_2 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2\20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2\20230602_PHCOQEHF_PC1131-Emanuele_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_1.pin 20230602_PHCOQEHF_PC1131-Emanuele_1 20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_1 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1\20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1\20230602_PHCOQEHF_PC1131-Emanuele_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_4.pin 20230602_PHCOQEHF_PC1131-Emanuele_4 20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_4 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1\20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1\20230602_PHCOQEHF_PC1131-Emanuele_4_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_5.pin 20230602_PHCOQEHF_PC1131-Emanuele_5 20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_5 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2\20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2\20230602_PHCOQEHF_PC1131-Emanuele_5_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_6.pin 20230602_PHCOQEHF_PC1131-Emanuele_6 20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_6 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3\20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3\20230602_PHCOQEHF_PC1131-Emanuele_6_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_7.pin 20230602_PHCOQEHF_PC1131-Emanuele_7 20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_7 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1\20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1\20230602_PHCOQEHF_PC1131-Emanuele_7_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_8.pin 20230602_PHCOQEHF_PC1131-Emanuele_8 20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_8 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2\20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2\20230602_PHCOQEHF_PC1131-Emanuele_8_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_9.pin 20230602_PHCOQEHF_PC1131-Emanuele_9 20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_9 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\20230602_PHCOQEHF_PC1131-Emanuele_9_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230602_PHCOQEHF_PC1131-Emanuele_3.pin 20230602_PHCOQEHF_PC1131-Emanuele_3 20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_target_psms.tsv 20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_decoy_psms.tsv interact-20230602_PHCOQEHF_PC1131-Emanuele_3 DDA 0.5 U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3\20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\Public\fragpipe(21.1)\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3\20230602_PHCOQEHF_PC1131-Emanuele_3_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\filelist_proteinprophet.txt INFO[21:33:45] 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 U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1\interact-20230602_PHCOQEHF_PC1131-Emanuele_1.pep.xml... ...read in 0 1+, 8824 2+, 4213 3+, 750 4+, 89 5+, 8 6+, 0 7+ spectra with min prob 0.05 Reading in U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2\interact-20230602_PHCOQEHF_PC1131-Emanuele_2.pep.xml... ...read in 0 1+, 6568 2+, 3023 3+, 506 4+, 35 5+, 5 6+, 0 7+ spectra with min prob 0.05 Reading in U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3\interact-20230602_PHCOQEHF_PC1131-Emanuele_3.pep.xml... ...read in 0 1+, 9675 2+, 5486 3+, 1098 4+, 157 5+, 25 6+, 0 7+ spectra with min prob 0.05 Reading in U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1\interact-20230602_PHCOQEHF_PC1131-Emanuele_4.pep.xml... ...read in 0 1+, 14345 2+, 6878 3+, 1165 4+, 156 5+, 8 6+, 0 7+ spectra with min prob 0.05 Reading in U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2\interact-20230602_PHCOQEHF_PC1131-Emanuele_5.pep.xml... ...read in 0 1+, 14118 2+, 7660 3+, 1550 4+, 287 5+, 21 6+, 0 7+ spectra with min prob 0.05 Reading in U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3\interact-20230602_PHCOQEHF_PC1131-Emanuele_6.pep.xml... ...read in 0 1+, 12921 2+, 5678 3+, 862 4+, 137 5+, 4 6+, 0 7+ spectra with min prob 0.05 Reading in U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1\interact-20230602_PHCOQEHF_PC1131-Emanuele_7.pep.xml... ...read in 0 1+, 11687 2+, 4894 3+, 735 4+, 74 5+, 5 6+, 0 7+ spectra with min prob 0.05 Reading in U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2\interact-20230602_PHCOQEHF_PC1131-Emanuele_8.pep.xml... ...read in 0 1+, 11168 2+, 5107 3+, 857 4+, 105 5+, 10 6+, 0 7+ spectra with min prob 0.05 Reading in U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\interact-20230602_PHCOQEHF_PC1131-Emanuele_9.pep.xml... ...read in 0 1+, 10539 2+, 4314 3+, 582 4+, 35 5+, 4 6+, 0 7+ spectra with min prob 0.05 Initializing 38717 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database U:\slyon\fragpipe_seaches\PC1131\2023-07-31-decoys-reviewed-contam-UP000005640.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9BVL4|SELO_HUMAN : U MSSUTVCLEAAWLPPKSSYSRQRGDAGDAETAEADTAAGAECHYPTELLKLVRRVESFDGREAAEIANQAIYNRLVYKPNNAHMVRVHEAQWAAADGAGELDKDLRARYAQLWDAWHGQNRSQLEAASLQELRSQQEVRELERAIGARTGMLAFLQPNSQALMLMMSLQRPDMQPRFALRLEELSACQEMLRALFEALGPSELEVPFSSLLYFTNTFDAGTLHMTELLKSVLAGDEELEVQVLGLKRRMKQLYHRQFEADFEEALIAEGLELPLEPQLAEALKRLNWRCVEPQKSYAYRGTNDSANCVHDPDYRDLFGFPGYDITLGLISMNDTLNVGHCFGVCQWEAVMRATRRTVERFFAANRQVSDSAHAAQIEPYFSSIVYDLLQVRIDNRGVSPGARGTHEDASKFIEFSGFRIFTSAVRLVVTCQEYKPNGDYFVDRVVTSESTVCAGARTTPVGLHFMAESCLFERISSRLVKRGDAQRSFPTPGAGKLQLEWREGTATCVEGLYMAAGDGLQGAFQGFQHGCYCHAAPEAGPLLANGSFFLAAEAEAERAPPAGLGLLALAPESLAVLRPQRLPTPQVRTFCAGPVPRPASPAGEPGPPPAEVPLARLARNDFRLGALWRPAPEMAAGSLTSRPAPSPSCRGLPLLRAAALSAGLAARYVA ........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .....WARNING: Found the following zero-mass residues in protein entry sp|P07203|GPX1_HUMAN : U MCAARLAAAAAAAQSVYAFSARPLAGGEPVSLGSLRGKVLLIENVASLUGTTVRDYTQMNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGVPLRRYSRRFQTIDIEPDIEALLSQGPSCA ....:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 ......WARNING: Found the following zero-mass residues in protein entry sp|P36969|GPX4_HUMAN : U MSLGRLCRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF ...:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q8IZQ5|SELH_HUMAN : U MAPRGRKRKAEAAVVAVAEKREKLANGGEGMEEATVVIEHCTSURVYGRNAAALSQALRLEAPELPVKVNPTKPRRGSFEVTLLRPDGSSAELWTGIKKGPPRKLKFPEPQEVVEELKKYLS .....33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry sp|Q9BQE4|SELS_HUMAN : U MERQEESLSARPALETEGLRFLHTTVGSLLATYGWYIVFSCILLYVVFQKLSARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQLEEEKRRQKIEMWDSMQEGKSYKGNAKKPQEEDSPGPSTSSVLKRKSDRKPLRGGGYNPLSGEGGGACSWRPGRRGPSSGGUG ........:.........:.........37000 .........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry sp|Q9C0D9|EPT1_HUMAN : U MAGYEYVSPEQLAGFDKYKYSAVDTNPLSLYVMHPFWNTIVKVFPTWLAPNLITFSGFLLVVFNFLLMAYFDPDFYASAPGHKHVPDWVWIVVGILNFVAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKYNTGILFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKNNTLKLNSVYEAMVPLFSPCLLFILSTAWILWSPSDILELHPRVFYFMVGTAFANSTCQLIVCQMSSTRCPTLNWLLVPLFLVVLVVNLGVASYVESILLYTLTTAFTLAHIHYGVRVVKQLSSHFQIYPFSLRKPNSDULGMEEKNIGL .......:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry sp|Q9Y6D0|SELK_HUMAN : U MVYISNGQVLDSRSQSPWRLSLITDFFWGIAEFVVLFFKTLLQQDVKKRRSYGNSSDSRYDDGRGPPGNPPRRMGRINHLRGPSPPPMAGGUGR ........:. Total: 40912 Computing degenerate peptides for 7154 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 7342 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7342 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7342 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7342 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7342 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=2.27839e-05, db_size=45605914 Computing MU for 7342 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO[21:34:07] Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate U:\slyon\fragpipe_seaches\PC1131\2023-07-31-decoys-reviewed-contam-UP000005640.fas --prefix rev_ INFO[21:34:08] Executing Database v5.1.0 INFO[21:34:08] Annotating the database INFO[21:34:11] Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --razor INFO[21:34:11] Executing Filter v5.1.0 INFO[21:34:11] Processing peptide identification files INFO[21:34:11] Parsing U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1\interact-20230602_PHCOQEHF_PC1131-Emanuele_1.pep.xml INFO[21:34:13] 1+ Charge profile decoy=0 target=0 INFO[21:34:13] 2+ Charge profile decoy=183 target=8641 INFO[21:34:13] 3+ Charge profile decoy=49 target=4164 INFO[21:34:13] 4+ Charge profile decoy=14 target=736 INFO[21:34:13] 5+ Charge profile decoy=1 target=88 INFO[21:34:13] 6+ Charge profile decoy=1 target=7 INFO[21:34:13] Database search results ions=10585 peptides=9338 psms=13884 INFO[21:34:13] Converged to 0.99 % FDR with 13385 PSMs decoy=133 threshold=0.724965 total=13518 INFO[21:34:13] Converged to 1.00 % FDR with 8844 Peptides decoy=88 threshold=0.813207 total=8932 INFO[21:34:13] Converged to 1.00 % FDR with 10130 Ions decoy=101 threshold=0.769851 total=10231 INFO[21:34:13] Protein inference results decoy=1295 target=5348 INFO[21:34:14] Converged to 0.99 % FDR with 3851 Proteins decoy=38 threshold=0.987 total=3889 INFO[21:34:15] Applying sequential FDR estimation ions=10107 peptides=8869 psms=13315 INFO[21:34:15] Converged to 0.08 % FDR with 13304 PSMs decoy=11 threshold=0.724965 total=13315 INFO[21:34:15] Converged to 0.10 % FDR with 8860 Peptides decoy=9 threshold=0.724965 total=8869 INFO[21:34:15] Converged to 0.09 % FDR with 10098 Ions decoy=9 threshold=0.724965 total=10107 INFO[21:34:15] Post processing identifications INFO[21:34:16] Assigning protein identifications to layers INFO[21:34:18] Processing protein inference INFO[21:34:18] Synchronizing PSMs and proteins INFO[21:34:18] Final report numbers after FDR filtering, and post-processing ions=10098 peptides=8860 proteins=1855 psms=13304 INFO[21:34:18] Saving INFO[21:34:21] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor INFO[21:34:22] Executing Filter v5.1.0 INFO[21:34:22] Fetching protein inference from U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 INFO[21:34:22] Processing peptide identification files INFO[21:34:22] Parsing U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2\interact-20230602_PHCOQEHF_PC1131-Emanuele_2.pep.xml INFO[21:34:23] 1+ Charge profile decoy=0 target=0 INFO[21:34:23] 2+ Charge profile decoy=145 target=6423 INFO[21:34:23] 3+ Charge profile decoy=52 target=2971 INFO[21:34:23] 4+ Charge profile decoy=12 target=494 INFO[21:34:23] 5+ Charge profile decoy=1 target=34 INFO[21:34:23] 6+ Charge profile decoy=0 target=5 INFO[21:34:23] Database search results ions=7399 peptides=6712 psms=10137 INFO[21:34:23] Converged to 1.00 % FDR with 9716 PSMs decoy=97 threshold=0.748117 total=9813 INFO[21:34:23] Converged to 0.99 % FDR with 6259 Peptides decoy=62 threshold=0.844823 total=6321 INFO[21:34:23] Converged to 0.99 % FDR with 6961 Ions decoy=69 threshold=0.829587 total=7030 INFO[21:34:23] Protein inference results decoy=1295 target=5348 INFO[21:34:23] Converged to 0.99 % FDR with 3851 Proteins decoy=38 threshold=0.987 total=3889 INFO[21:34:25] Applying sequential FDR estimation ions=6978 peptides=6296 psms=9657 INFO[21:34:25] Converged to 0.06 % FDR with 9651 PSMs decoy=6 threshold=0.748117 total=9657 INFO[21:34:25] Converged to 0.10 % FDR with 6290 Peptides decoy=6 threshold=0.748117 total=6296 INFO[21:34:25] Converged to 0.09 % FDR with 6972 Ions decoy=6 threshold=0.748117 total=6978 INFO[21:34:25] Post processing identifications INFO[21:34:25] Assigning protein identifications to layers INFO[21:34:26] Processing protein inference INFO[21:34:26] Synchronizing PSMs and proteins INFO[21:34:26] Final report numbers after FDR filtering, and post-processing ions=6972 peptides=6290 proteins=1405 psms=9651 INFO[21:34:26] Saving INFO[21:34:29] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor INFO[21:34:29] Executing Filter v5.1.0 INFO[21:34:29] Fetching protein inference from U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 INFO[21:34:30] Processing peptide identification files INFO[21:34:30] Parsing U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3\interact-20230602_PHCOQEHF_PC1131-Emanuele_3.pep.xml INFO[21:34:31] 1+ Charge profile decoy=0 target=0 INFO[21:34:31] 2+ Charge profile decoy=177 target=9498 INFO[21:34:31] 3+ Charge profile decoy=66 target=5420 INFO[21:34:31] 4+ Charge profile decoy=14 target=1084 INFO[21:34:31] 5+ Charge profile decoy=1 target=156 INFO[21:34:31] 6+ Charge profile decoy=1 target=24 INFO[21:34:31] Database search results ions=12510 peptides=10848 psms=16441 INFO[21:34:31] Converged to 1.00 % FDR with 16021 PSMs decoy=160 threshold=0.671931 total=16181 INFO[21:34:31] Converged to 1.00 % FDR with 10419 Peptides decoy=104 threshold=0.742059 total=10523 INFO[21:34:31] Converged to 0.99 % FDR with 12091 Ions decoy=120 threshold=0.724086 total=12211 INFO[21:34:31] Protein inference results decoy=1295 target=5348 INFO[21:34:32] Converged to 0.99 % FDR with 3851 Proteins decoy=38 threshold=0.987 total=3889 INFO[21:34:33] Applying sequential FDR estimation ions=12024 peptides=10367 psms=15910 INFO[21:34:33] Converged to 0.07 % FDR with 15899 PSMs decoy=11 threshold=0.672572 total=15910 INFO[21:34:33] Converged to 0.11 % FDR with 10356 Peptides decoy=11 threshold=0.673307 total=10367 INFO[21:34:33] Converged to 0.09 % FDR with 12013 Ions decoy=11 threshold=0.672572 total=12024 INFO[21:34:33] Post processing identifications INFO[21:34:33] Assigning protein identifications to layers INFO[21:34:35] Processing protein inference INFO[21:34:35] Synchronizing PSMs and proteins INFO[21:34:35] Final report numbers after FDR filtering, and post-processing ions=12013 peptides=10356 proteins=1994 psms=15899 INFO[21:34:35] Saving INFO[21:34:40] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor INFO[21:34:40] Executing Filter v5.1.0 INFO[21:34:40] Fetching protein inference from U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 INFO[21:34:40] Processing peptide identification files INFO[21:34:40] Parsing U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1\interact-20230602_PHCOQEHF_PC1131-Emanuele_4.pep.xml INFO[21:34:43] 1+ Charge profile decoy=0 target=0 INFO[21:34:43] 2+ Charge profile decoy=178 target=14167 INFO[21:34:43] 3+ Charge profile decoy=44 target=6834 INFO[21:34:43] 4+ Charge profile decoy=7 target=1158 INFO[21:34:43] 5+ Charge profile decoy=4 target=152 INFO[21:34:43] 6+ Charge profile decoy=0 target=8 INFO[21:34:43] Database search results ions=18377 peptides=16131 psms=22552 INFO[21:34:43] Converged to 1.00 % FDR with 22292 PSMs decoy=222 threshold=0.537704 total=22514 INFO[21:34:43] Converged to 1.00 % FDR with 15772 Peptides decoy=157 threshold=0.675105 total=15929 INFO[21:34:43] Converged to 1.00 % FDR with 18061 Ions decoy=180 threshold=0.616948 total=18241 INFO[21:34:43] Protein inference results decoy=1295 target=5348 INFO[21:34:43] Converged to 0.99 % FDR with 3851 Proteins decoy=38 threshold=0.987 total=3889 INFO[21:34:44] Applying sequential FDR estimation ions=17973 peptides=15729 psms=22137 INFO[21:34:44] Converged to 0.07 % FDR with 22121 PSMs decoy=16 threshold=0.541163 total=22137 INFO[21:34:44] Converged to 0.10 % FDR with 15714 Peptides decoy=15 threshold=0.542362 total=15729 INFO[21:34:44] Converged to 0.08 % FDR with 17958 Ions decoy=15 threshold=0.542362 total=17973 INFO[21:34:44] Post processing identifications INFO[21:34:44] Assigning protein identifications to layers INFO[21:34:48] Processing protein inference INFO[21:34:48] Synchronizing PSMs and proteins INFO[21:34:48] Final report numbers after FDR filtering, and post-processing ions=17958 peptides=15714 proteins=3026 psms=22121 INFO[21:34:48] Saving INFO[21:34:54] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor INFO[21:34:54] Executing Filter v5.1.0 INFO[21:34:54] Fetching protein inference from U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 INFO[21:34:54] Processing peptide identification files INFO[21:34:54] Parsing U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2\interact-20230602_PHCOQEHF_PC1131-Emanuele_5.pep.xml INFO[21:34:57] 1+ Charge profile decoy=0 target=0 INFO[21:34:57] 2+ Charge profile decoy=190 target=13928 INFO[21:34:57] 3+ Charge profile decoy=44 target=7616 INFO[21:34:57] 4+ Charge profile decoy=16 target=1534 INFO[21:34:57] 5+ Charge profile decoy=2 target=285 INFO[21:34:57] 6+ Charge profile decoy=3 target=18 INFO[21:34:57] Database search results ions=19690 peptides=16469 psms=23636 INFO[21:34:57] Converged to 1.00 % FDR with 23348 PSMs decoy=233 threshold=0.532027 total=23581 INFO[21:34:57] Converged to 1.00 % FDR with 16051 Peptides decoy=160 threshold=0.694508 total=16211 INFO[21:34:57] Converged to 1.00 % FDR with 19365 Ions decoy=193 threshold=0.591106 total=19558 INFO[21:34:57] Protein inference results decoy=1295 target=5348 INFO[21:34:57] Converged to 0.99 % FDR with 3851 Proteins decoy=38 threshold=0.987 total=3889 INFO[21:34:58] Applying sequential FDR estimation ions=19197 peptides=15979 psms=23127 INFO[21:34:58] Converged to 0.08 % FDR with 23108 PSMs decoy=19 threshold=0.532473 total=23127 INFO[21:34:58] Converged to 0.11 % FDR with 15962 Peptides decoy=17 threshold=0.532473 total=15979 INFO[21:34:58] Converged to 0.10 % FDR with 19178 Ions decoy=19 threshold=0.532473 total=19197 INFO[21:34:58] Post processing identifications INFO[21:34:58] Assigning protein identifications to layers INFO[21:35:02] Processing protein inference INFO[21:35:02] Synchronizing PSMs and proteins INFO[21:35:02] Final report numbers after FDR filtering, and post-processing ions=19178 peptides=15962 proteins=3055 psms=23108 INFO[21:35:02] Saving INFO[21:35:08] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor INFO[21:35:08] Executing Filter v5.1.0 INFO[21:35:08] Fetching protein inference from U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 INFO[21:35:09] Processing peptide identification files INFO[21:35:09] Parsing U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3\interact-20230602_PHCOQEHF_PC1131-Emanuele_6.pep.xml INFO[21:35:11] 1+ Charge profile decoy=0 target=0 INFO[21:35:11] 2+ Charge profile decoy=211 target=12710 INFO[21:35:11] 3+ Charge profile decoy=60 target=5618 INFO[21:35:11] 4+ Charge profile decoy=12 target=850 INFO[21:35:11] 5+ Charge profile decoy=6 target=131 INFO[21:35:11] 6+ Charge profile decoy=0 target=4 INFO[21:35:11] Database search results ions=16176 peptides=14190 psms=19602 INFO[21:35:11] Converged to 1.00 % FDR with 19143 PSMs decoy=191 threshold=0.657311 total=19334 INFO[21:35:11] Converged to 0.99 % FDR with 13689 Peptides decoy=136 threshold=0.754115 total=13825 INFO[21:35:11] Converged to 1.00 % FDR with 15720 Ions decoy=157 threshold=0.711925 total=15877 INFO[21:35:11] Protein inference results decoy=1295 target=5348 INFO[21:35:11] Converged to 0.99 % FDR with 3851 Proteins decoy=38 threshold=0.987 total=3889 INFO[21:35:12] Applying sequential FDR estimation ions=15625 peptides=13642 psms=18994 INFO[21:35:12] Converged to 0.09 % FDR with 18977 PSMs decoy=17 threshold=0.657708 total=18994 INFO[21:35:12] Converged to 0.12 % FDR with 13626 Peptides decoy=16 threshold=0.657708 total=13642 INFO[21:35:12] Converged to 0.10 % FDR with 15609 Ions decoy=16 threshold=0.657708 total=15625 INFO[21:35:12] Post processing identifications INFO[21:35:12] Assigning protein identifications to layers INFO[21:35:15] Processing protein inference INFO[21:35:15] Synchronizing PSMs and proteins INFO[21:35:15] Final report numbers after FDR filtering, and post-processing ions=15609 peptides=13626 proteins=2737 psms=18977 INFO[21:35:15] Saving INFO[21:35:20] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor INFO[21:35:21] Executing Filter v5.1.0 INFO[21:35:21] Fetching protein inference from U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 INFO[21:35:21] Processing peptide identification files INFO[21:35:21] Parsing U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1\interact-20230602_PHCOQEHF_PC1131-Emanuele_7.pep.xml INFO[21:35:23] 1+ Charge profile decoy=0 target=0 INFO[21:35:23] 2+ Charge profile decoy=171 target=11516 INFO[21:35:23] 3+ Charge profile decoy=40 target=4854 INFO[21:35:23] 4+ Charge profile decoy=9 target=726 INFO[21:35:23] 5+ Charge profile decoy=2 target=72 INFO[21:35:23] 6+ Charge profile decoy=1 target=4 INFO[21:35:23] Database search results ions=14098 peptides=12368 psms=17395 INFO[21:35:23] Converged to 1.00 % FDR with 17046 PSMs decoy=170 threshold=0.610522 total=17216 INFO[21:35:23] Converged to 0.99 % FDR with 11978 Peptides decoy=119 threshold=0.704357 total=12097 INFO[21:35:23] Converged to 1.00 % FDR with 13738 Ions decoy=137 threshold=0.673452 total=13875 INFO[21:35:23] Protein inference results decoy=1295 target=5348 INFO[21:35:23] Converged to 0.99 % FDR with 3851 Proteins decoy=38 threshold=0.987 total=3889 INFO[21:35:24] Applying sequential FDR estimation ions=13648 peptides=11922 psms=16908 INFO[21:35:24] Converged to 0.05 % FDR with 16899 PSMs decoy=9 threshold=0.612813 total=16908 INFO[21:35:24] Converged to 0.08 % FDR with 11913 Peptides decoy=9 threshold=0.612813 total=11922 INFO[21:35:24] Converged to 0.07 % FDR with 13639 Ions decoy=9 threshold=0.612813 total=13648 INFO[21:35:24] Post processing identifications INFO[21:35:25] Assigning protein identifications to layers INFO[21:35:27] Processing protein inference INFO[21:35:27] Synchronizing PSMs and proteins INFO[21:35:27] Final report numbers after FDR filtering, and post-processing ions=13639 peptides=11913 proteins=2510 psms=16899 INFO[21:35:27] Saving INFO[21:35:32] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor INFO[21:35:32] Executing Filter v5.1.0 INFO[21:35:32] Fetching protein inference from U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 INFO[21:35:33] Processing peptide identification files INFO[21:35:33] Parsing U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2\interact-20230602_PHCOQEHF_PC1131-Emanuele_8.pep.xml INFO[21:35:34] 1+ Charge profile decoy=0 target=0 INFO[21:35:34] 2+ Charge profile decoy=184 target=10984 INFO[21:35:34] 3+ Charge profile decoy=58 target=5049 INFO[21:35:34] 4+ Charge profile decoy=12 target=845 INFO[21:35:34] 5+ Charge profile decoy=5 target=100 INFO[21:35:34] 6+ Charge profile decoy=1 target=9 INFO[21:35:34] Database search results ions=14085 peptides=12085 psms=17247 INFO[21:35:34] Converged to 1.00 % FDR with 16811 PSMs decoy=168 threshold=0.678825 total=16979 INFO[21:35:34] Converged to 1.00 % FDR with 11605 Peptides decoy=116 threshold=0.778911 total=11721 INFO[21:35:34] Converged to 1.00 % FDR with 13633 Ions decoy=136 threshold=0.747069 total=13769 INFO[21:35:34] Protein inference results decoy=1295 target=5348 INFO[21:35:35] Converged to 0.99 % FDR with 3851 Proteins decoy=38 threshold=0.987 total=3889 INFO[21:35:36] Applying sequential FDR estimation ions=13573 peptides=11577 psms=16681 INFO[21:35:36] Converged to 0.10 % FDR with 16665 PSMs decoy=16 threshold=0.679606 total=16681 INFO[21:35:36] Converged to 0.12 % FDR with 11563 Peptides decoy=14 threshold=0.679606 total=11577 INFO[21:35:36] Converged to 0.10 % FDR with 13559 Ions decoy=14 threshold=0.679606 total=13573 INFO[21:35:36] Post processing identifications INFO[21:35:36] Assigning protein identifications to layers INFO[21:35:38] Processing protein inference INFO[21:35:38] Synchronizing PSMs and proteins INFO[21:35:39] Final report numbers after FDR filtering, and post-processing ions=13559 peptides=11563 proteins=2388 psms=16665 INFO[21:35:39] Saving INFO[21:35:43] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3 --dbbin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --protxml U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\combined.prot.xml --probin U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 --razor INFO[21:35:43] Executing Filter v5.1.0 INFO[21:35:43] Fetching protein inference from U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1 INFO[21:35:44] Processing peptide identification files INFO[21:35:44] Parsing U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\interact-20230602_PHCOQEHF_PC1131-Emanuele_9.pep.xml INFO[21:35:45] 1+ Charge profile decoy=0 target=0 INFO[21:35:45] 2+ Charge profile decoy=207 target=10332 INFO[21:35:45] 3+ Charge profile decoy=59 target=4255 INFO[21:35:45] 4+ Charge profile decoy=9 target=573 INFO[21:35:45] 5+ Charge profile decoy=0 target=35 INFO[21:35:45] 6+ Charge profile decoy=0 target=4 INFO[21:35:45] Database search results ions=12352 peptides=11027 psms=15474 INFO[21:35:45] Converged to 1.00 % FDR with 15006 PSMs decoy=150 threshold=0.69889 total=15156 INFO[21:35:45] Converged to 0.99 % FDR with 10562 Peptides decoy=105 threshold=0.763991 total=10667 INFO[21:35:45] Converged to 0.99 % FDR with 11886 Ions decoy=118 threshold=0.745872 total=12004 INFO[21:35:45] Protein inference results decoy=1295 target=5348 INFO[21:35:45] Converged to 0.99 % FDR with 3851 Proteins decoy=38 threshold=0.987 total=3889 INFO[21:35:47] Applying sequential FDR estimation ions=11832 peptides=10520 psms=14902 INFO[21:35:47] Converged to 0.08 % FDR with 14890 PSMs decoy=12 threshold=0.69889 total=14902 INFO[21:35:47] Converged to 0.10 % FDR with 10509 Peptides decoy=11 threshold=0.69889 total=10520 INFO[21:35:47] Converged to 0.09 % FDR with 11821 Ions decoy=11 threshold=0.69889 total=11832 INFO[21:35:47] Post processing identifications INFO[21:35:47] Assigning protein identifications to layers INFO[21:35:49] Processing protein inference INFO[21:35:49] Synchronizing PSMs and proteins INFO[21:35:49] Final report numbers after FDR filtering, and post-processing ions=11821 peptides=10509 proteins=2293 psms=14890 INFO[21:35:49] Saving INFO[21:35:53] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[21:35:53] Executing Report v5.1.0 INFO[21:35:53] Creating reports INFO[21:35:55] Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[21:35:55] Executing Report v5.1.0 INFO[21:35:55] Creating reports INFO[21:35:56] Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[21:35:56] Executing Report v5.1.0 INFO[21:35:56] Creating reports INFO[21:35:58] Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[21:35:58] Executing Report v5.1.0 INFO[21:35:58] Creating reports INFO[21:35:59] Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[21:35:59] Executing Report v5.1.0 INFO[21:35:59] Creating reports INFO[21:36:00] Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[21:36:00] Executing Report v5.1.0 INFO[21:36:00] Creating reports INFO[21:36:01] Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[21:36:02] Executing Report v5.1.0 INFO[21:36:02] Creating reports INFO[21:36:02] Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[21:36:02] Executing Report v5.1.0 INFO[21:36:02] Creating reports INFO[21:36:04] Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[21:36:04] Executing Report v5.1.0 INFO[21:36:04] Creating reports INFO[21:36:05] Done Process 'PhilosopherReport' finished, exit code: 0 PTMShepherd [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] java -Xmx20G -Dlibs.thermo.dir=C:\Users\Public\fragpipe(21.1)\tools\MSFragger-4.0\ext\thermo -cp C:\Users\Public\fragpipe(21.1)\tools\ptmshepherd-2.0.6.jar;C:\Users\Public\fragpipe(21.1)\tools\batmass-io-1.30.0.jar;C:\Users\Public\fragpipe(21.1)\tools\commons-math3-3.6.1.jar;C:\Users\Public\fragpipe(21.1)\tools\hipparchus-1.8\hipparchus-core-1.8.jar;C:\Users\Public\fragpipe(21.1)\tools\hipparchus-1.8\hipparchus-stat-1.8.jar edu.umich.andykong.ptmshepherd.PTMShepherd "U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\shepherd.config" PTM-Shepherd version 2.0.6 (c) 2022 University of Michigan Using Java 21.0.1 on 20480MB memory Finding spectral data Indexing data from EV_1 Indexing data from EV_2 Indexing data from EV_3 Indexing data from RNF220_1 Indexing data from RNF220_2 Indexing data from RNF220_3 Indexing data from TOPORS_1 Indexing data from TOPORS_2 Indexing data from TOPORS_3 Done finding spectral data Caching spectral data Caching data from EV_1 20230602_PHCOQEHF_PC1131-Emanuele_1 - 13304 (5476 ms, 345 ms) Done caching data from EV_1 Caching data from EV_2 20230602_PHCOQEHF_PC1131-Emanuele_2 - 9651 (3529 ms, 173 ms) Done caching data from EV_2 Caching data from EV_3 20230602_PHCOQEHF_PC1131-Emanuele_3 - 15899 (4800 ms, 314 ms) Done caching data from EV_3 Caching data from RNF220_1 20230602_PHCOQEHF_PC1131-Emanuele_4 - 22121 (5301 ms, 486 ms) Done caching data from RNF220_1 Caching data from RNF220_2 20230602_PHCOQEHF_PC1131-Emanuele_5 - 23108 (5881 ms, 580 ms) Done caching data from RNF220_2 Caching data from RNF220_3 20230602_PHCOQEHF_PC1131-Emanuele_6 - 18977 (5098 ms, 392 ms) Done caching data from RNF220_3 Caching data from TOPORS_1 20230602_PHCOQEHF_PC1131-Emanuele_7 - 16899 (4407 ms, 314 ms) Done caching data from TOPORS_1 Caching data from TOPORS_2 20230602_PHCOQEHF_PC1131-Emanuele_8 - 16665 (4486 ms, 298 ms) Done caching data from TOPORS_2 Caching data from TOPORS_3 20230602_PHCOQEHF_PC1131-Emanuele_9 - 14890 (4517 ms, 271 ms) Done caching data from TOPORS_3 Done caching spectral data Counting MS2 scans for dataset EV_1 13304 MS2 scans present in dataset EV_1 Done counting MS2 scans for dataset EV_1 Counting MS2 scans for dataset EV_2 9651 MS2 scans present in dataset EV_2 Done counting MS2 scans for dataset EV_2 Counting MS2 scans for dataset EV_3 15899 MS2 scans present in dataset EV_3 Done counting MS2 scans for dataset EV_3 Counting MS2 scans for dataset RNF220_1 22121 MS2 scans present in dataset RNF220_1 Done counting MS2 scans for dataset RNF220_1 Counting MS2 scans for dataset RNF220_2 23108 MS2 scans present in dataset RNF220_2 Done counting MS2 scans for dataset RNF220_2 Counting MS2 scans for dataset RNF220_3 18977 MS2 scans present in dataset RNF220_3 Done counting MS2 scans for dataset RNF220_3 Counting MS2 scans for dataset TOPORS_1 16899 MS2 scans present in dataset TOPORS_1 Done counting MS2 scans for dataset TOPORS_1 Counting MS2 scans for dataset TOPORS_2 16665 MS2 scans present in dataset TOPORS_2 Done counting MS2 scans for dataset TOPORS_2 Counting MS2 scans for dataset TOPORS_3 14890 MS2 scans present in dataset TOPORS_3 Done counting MS2 scans for dataset TOPORS_3 Creating combined histogram Generated histogram file for dataset EV_1 [-5 - 7] Generated histogram file for dataset EV_2 [-5 - 7] Generated histogram file for dataset EV_3 [-5 - 7] Generated histogram file for dataset RNF220_1 [-5 - 7] Generated histogram file for dataset RNF220_2 [-5 - 7] Generated histogram file for dataset RNF220_3 [-5 - 7] Generated histogram file for dataset TOPORS_1 [-5 - 7] Generated histogram file for dataset TOPORS_2 [-5 - 7] Generated histogram file for dataset TOPORS_3 [-5 - 7] Done creating combined histogram Running peak picking Picked top 20 peaks Removed 8 peaks with insufficient PSMs Created summary table Done running peak picking Annotated summary table Mapping modifications back into PSM lists Created modification summary Begin localization annotation 20230602_PHCOQEHF_PC1131-Emanuele_1 - 13304 lines (769 ms reading, 3069 ms processing) 20230602_PHCOQEHF_PC1131-Emanuele_2 - 9651 lines (376 ms reading, 2259 ms processing) 20230602_PHCOQEHF_PC1131-Emanuele_3 - 15899 lines (706 ms reading, 3499 ms processing) 20230602_PHCOQEHF_PC1131-Emanuele_4 - 22121 lines (658 ms reading, 4864 ms processing) 20230602_PHCOQEHF_PC1131-Emanuele_5 - 23108 lines (753 ms reading, 5272 ms processing) 20230602_PHCOQEHF_PC1131-Emanuele_6 - 18977 lines (619 ms reading, 4304 ms processing) 20230602_PHCOQEHF_PC1131-Emanuele_7 - 16899 lines (950 ms reading, 3671 ms processing) 20230602_PHCOQEHF_PC1131-Emanuele_8 - 16665 lines (518 ms reading, 3664 ms processing) 20230602_PHCOQEHF_PC1131-Emanuele_9 - 14890 lines (450 ms reading, 3213 ms processing) Done Created localization reports Begin similarity and retention time annotation Spectral data read into memory (340 ms reading) 20230602_PHCOQEHF_PC1131-Emanuele_1 - 13304 lines (3802 ms processing) Spectral data read into memory (291 ms reading) 20230602_PHCOQEHF_PC1131-Emanuele_2 - 9651 lines (2563 ms processing) Spectral data read into memory (417 ms reading) 20230602_PHCOQEHF_PC1131-Emanuele_3 - 15899 lines (4445 ms processing) Spectral data read into memory (573 ms reading) 20230602_PHCOQEHF_PC1131-Emanuele_4 - 22121 lines (6406 ms processing) Spectral data read into memory (599 ms reading) 20230602_PHCOQEHF_PC1131-Emanuele_5 - 23108 lines (6819 ms processing) Spectral data read into memory (463 ms reading) 20230602_PHCOQEHF_PC1131-Emanuele_6 - 18977 lines (5323 ms processing) Spectral data read into memory (484 ms reading) 20230602_PHCOQEHF_PC1131-Emanuele_7 - 16899 lines (4844 ms processing) Spectral data read into memory (375 ms reading) 20230602_PHCOQEHF_PC1131-Emanuele_8 - 16665 lines (4610 ms processing) Spectral data read into memory (344 ms reading) 20230602_PHCOQEHF_PC1131-Emanuele_9 - 14890 lines (4067 ms processing) Done Created similarity/RT reports Combining and cleaning reports Writing combined table for dataset EV_1 Writing combined table for dataset EV_2 Writing combined table for dataset EV_3 Writing combined table for dataset RNF220_1 Writing combined table for dataset RNF220_2 Writing combined table for dataset RNF220_3 Writing combined table for dataset TOPORS_1 Writing combined table for dataset TOPORS_2 Writing combined table for dataset TOPORS_3 Beginning glycan assignment Glycan Assignment params: Glycan FDR: 100.0% Mass error (ppm): 50.0 Isotope errors: [-1, 0, 1, 2, 3] Adducts: none Glycan Database size (including adducts): 1666 mode: N-glycan Allowed Sites: N in N-X-S/T sequons only Y ion probability ratio: 5.0,0.50; dHex-containing: 2.0,0.50 Oxonium probability ratios: NeuAc [2.0, 0.05, 0.2]; NeuGc [2.0, 0.05, 0.2]; dHex [2.0, 0.5, 0.1]; Phospho [2.0, 0.05, 0.2]; Sulfo [2.0, 0.05, 0.2] Assigning glycans: 20230602_PHCOQEHF_PC1131-Emanuele_1 - 13304 (294 ms, 363 ms) 20230602_PHCOQEHF_PC1131-Emanuele_2 - 9651 (234 ms, 214 ms) 20230602_PHCOQEHF_PC1131-Emanuele_3 - 15899 (351 ms, 347 ms) 20230602_PHCOQEHF_PC1131-Emanuele_4 - 22121 (609 ms, 487 ms) 20230602_PHCOQEHF_PC1131-Emanuele_5 - 23108 (562 ms, 504 ms) 20230602_PHCOQEHF_PC1131-Emanuele_6 - 18977 (587 ms, 405 ms) 20230602_PHCOQEHF_PC1131-Emanuele_7 - 16899 (423 ms, 401 ms) 20230602_PHCOQEHF_PC1131-Emanuele_8 - 16665 (413 ms, 387 ms) 20230602_PHCOQEHF_PC1131-Emanuele_9 - 14890 (379 ms, 314 ms) Calculating Glycan FDR Calculating Glycan FDR Calculating Glycan FDR Calculating Glycan FDR Calculating Glycan FDR Calculating Glycan FDR Calculating Glycan FDR Calculating Glycan FDR Calculating Glycan FDR Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters Warning: no modified spectra found, no glycans written to PSM table. Check input data and parameters Created glyco reports Done with glycan assignment Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\peaks.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\peaksummary.annotated.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\peaksummary.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\combined.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\combined.histo Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\global.locprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\global.simrtprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_1.locprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_1.simrtprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_1.profile.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_1.histo Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_1.ms2counts Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_2.locprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_2.simrtprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_2.profile.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_2.histo Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_2.ms2counts Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_3.locprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_3.simrtprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_3.profile.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_3.histo Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_3.ms2counts Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_1.locprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_1.simrtprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_1.profile.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_1.histo Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_1.ms2counts Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_2.locprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_2.simrtprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_2.profile.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_2.histo Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_2.ms2counts Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_3.locprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_3.simrtprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_3.profile.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_3.histo Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_3.ms2counts Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_1.locprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_1.simrtprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_1.profile.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_1.histo Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_1.ms2counts Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_2.locprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_2.simrtprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_2.profile.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_2.histo Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_2.ms2counts Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_3.locprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_3.simrtprofile.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_3.profile.tsv Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_3.histo Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_3.ms2counts Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_1.rawlocalize Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_1.rawsimrt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_1.rawglyco Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\20230602_PHCOQEHF_PC1131-Emanuele_1.mzBIN_cache Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_2.rawlocalize Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_2.rawsimrt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_2.rawglyco Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\20230602_PHCOQEHF_PC1131-Emanuele_2.mzBIN_cache Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_3.rawlocalize Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_3.rawsimrt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\EV_3.rawglyco Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\20230602_PHCOQEHF_PC1131-Emanuele_3.mzBIN_cache Deleted file: 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U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_3.rawsimrt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\RNF220_3.rawglyco Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\20230602_PHCOQEHF_PC1131-Emanuele_6.mzBIN_cache Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_1.rawlocalize Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_1.rawsimrt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_1.rawglyco Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\20230602_PHCOQEHF_PC1131-Emanuele_7.mzBIN_cache Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_2.rawlocalize Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_2.rawsimrt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_2.rawglyco Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\20230602_PHCOQEHF_PC1131-Emanuele_8.mzBIN_cache Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_3.rawlocalize Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_3.rawsimrt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\TOPORS_3.rawglyco Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\20230602_PHCOQEHF_PC1131-Emanuele_9.mzBIN_cache Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\cache-3fa75b305f4680.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\cache-6d5e0944f0a0.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\cache-2e04e18f7276c3.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\cache-2a735c92a126dc.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\cache-ba7b108ba811fe.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\cache-b10777868997ae.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\cache-a13ce01f7a2ba3.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\cache-6eeeb1257844a4.txt Deleted file: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\cache-db45d0196b82ba.txt Process 'PTMShepherd' finished, exit code: 0 WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:39:10] Executing Workspace v5.1.0 INFO[21:39:10] Removing workspace INFO[21:39:11] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:39:11] Executing Workspace v5.1.0 INFO[21:39:11] Removing workspace INFO[21:39:11] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:39:11] Executing Workspace v5.1.0 INFO[21:39:11] Removing workspace INFO[21:39:11] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:39:11] Executing Workspace v5.1.0 INFO[21:39:11] Removing workspace INFO[21:39:11] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:39:12] Executing Workspace v5.1.0 INFO[21:39:12] Removing workspace INFO[21:39:12] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:39:12] Executing Workspace v5.1.0 INFO[21:39:12] Removing workspace INFO[21:39:12] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:39:12] Executing Workspace v5.1.0 INFO[21:39:12] Removing workspace INFO[21:39:12] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:39:13] Executing Workspace v5.1.0 INFO[21:39:13] Removing workspace INFO[21:39:13] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:39:13] Executing Workspace v5.1.0 INFO[21:39:13] Removing workspace INFO[21:39:13] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2] C:\Users\Public\fragpipe(21.1)\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:39:13] Executing Workspace v5.1.0 INFO[21:39:13] Removing workspace INFO[21:39:13] Done Process 'WorkspaceClean' finished, exit code: 0 AppendFile java -cp C:\Users\Public\fragpipe(21.1)\lib/* com.dmtavt.fragpipe.util.AppendToFile U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\modmasses_ionquant.txt U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\ptm-shepherd-output\glyco_masses_list.txt Process 'AppendFile' finished, exit code: 0 IonQuant [Work dir: U:\slyon\fragpipe_seaches\PC1131_testOutput_run2] java -Xmx20G -Dlibs.bruker.dir=C:\Users\Public\fragpipe(21.1)\tools\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=C:\Users\Public\fragpipe(21.1)\tools\MSFragger-4.0\ext\thermo -cp C:\Users\Public\fragpipe(21.1)\tools\jfreechart-1.5.3.jar;C:\Users\Public\fragpipe(21.1)\tools\batmass-io-1.30.0.jar;C:\Users\Public\fragpipe(21.1)\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 7 --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 1 --locprob 0.75 --uniqueness 0 --multidir . --filelist U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\filelist_ionquant.txt --modlist U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\modmasses_ionquant.txt IonQuant version IonQuant-1.10.12 Batmass-IO version 1.30.0 timsdata library version timsdata-2-21-0-4 (c) University of Michigan System OS: Windows 11, Architecture: AMD64 Java Info: 21.0.1, OpenJDK 64-Bit Server VM, Azul Systems, Inc. JVM started with 20 GB memory 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 1856.6556 and 1856.6557. Will keep 1856.6557 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 1872.6505 and 1872.6506. Will keep 1872.6506 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 1913.677 and 1913.6771. Will keep 1913.677 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2001.6931 and 2001.6932. Will keep 2001.6932 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2017.688 and 2017.6881. Will keep 2017.688 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2043.74 and 2043.7401. Will keep 2043.74 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2147.751 and 2147.7511. Will keep 2147.751 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2157.783 and 2157.7831. Will keep 2157.783 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2163.7459 and 2163.746. Will keep 2163.746 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2205.7928 and 2205.7929. Will keep 2205.7929 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2303.8409 and 2303.841. Will keep 2303.841 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2407.8518 and 2407.8519. Will keep 2407.8519 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2408.8722 and 2408.8723. Will keep 2408.8723 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2423.8467 and 2423.8468. Will keep 2423.8468 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2424.8671 and 2424.8672. Will keep 2424.8672 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2522.9152 and 2522.9153. Will keep 2522.9153 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2553.9097 and 2553.9098. Will keep 2553.9098 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2569.9046 and 2569.9047. Will keep 2569.9047 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2586.9199 and 2586.92. Will keep 2586.92 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2602.9148 and 2602.9149. Will keep 2602.9149 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2668.9731 and 2668.9732. Will keep 2668.9732 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2684.968 and 2684.9681. Will keep 2684.968 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2691.9513 and 2691.9514. Will keep 2691.9514 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2699.9676 and 2699.9677. Will keep 2699.9677 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2715.9625 and 2715.9626. Will keep 2715.9626 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2716.9829 and 2716.983. Will keep 2716.983 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2748.9727 and 2748.9728. Will keep 2748.9728 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2804.999 and 2804.9991. Will keep 2804.999 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2805.9943 and 2805.9944. Will keep 2805.9944 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2814.0106 and 2814.0107. Will keep 2814.0107 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2815.031 and 2815.0311. Will keep 2815.031 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2820.9939 and 2820.994. Will keep 2820.994 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2830.0055 and 2830.0056. Will keep 2830.0056 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2847.0208 and 2847.0209. Will keep 2847.0209 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2879.0357 and 2879.0358. Will keep 2879.0358 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2895.0306 and 2895.0307. Will keep 2895.0307 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2911.0256 and 2911.0257. Will keep 2911.0257 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2919.042 and 2919.0421. Will keep 2919.042 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2935.0369 and 2935.037. Will keep 2935.037 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2950.0365 and 2950.0366. Will keep 2950.0366 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2952.0522 and 2952.0523. Will keep 2952.0523 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2960.0685 and 2960.0686. Will keep 2960.0686 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2961.0889 and 2961.089. Will keep 2961.089 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2966.0314 and 2966.0315. Will keep 2966.0315 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2976.0634 and 2976.0635. Will keep 2976.0635 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 2983.0467 and 2983.0468. Will keep 2983.0468 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3056.0631 and 3056.0632. Will keep 3056.0632 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3064.0795 and 3064.0796. Will keep 3064.0796 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3066.1203 and 3066.1204. Will keep 3066.1204 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3097.0897 and 3097.0898. Will keep 3097.0898 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3098.1101 and 3098.1102. Will keep 3098.1102 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3106.1264 and 3106.1265. Will keep 3106.1265 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3112.0893 and 3112.0894. Will keep 3112.0894 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3113.0846 and 3113.0847. Will keep 3113.0847 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3122.1213 and 3122.1214. Will keep 3122.1214 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3171.1265 and 3171.1266. Will keep 3171.1266 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3195.1629 and 3195.163. Will keep 3195.163 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3211.1578 and 3211.1579. Will keep 3211.1579 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3226.1323 and 3226.1324. Will keep 3226.1324 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3227.1527 and 3227.1528. Will keep 3227.1528 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3228.1731 and 3228.1732. Will keep 3228.1732 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3243.1476 and 3243.1477. Will keep 3243.1477 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3244.168 and 3244.1681. Will keep 3244.168 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3259.1425 and 3259.1426. Will keep 3259.1426 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3285.1945 and 3285.1946. Will keep 3285.1946 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3317.1844 and 3317.1845. Will keep 3317.1845 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3372.1902 and 3372.1903. Will keep 3372.1903 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3373.2106 and 3373.2107. Will keep 3373.2107 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3389.2055 and 3389.2056. Will keep 3389.2056 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3405.2004 and 3405.2005. Will keep 3405.2005 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3462.2219 and 3462.222. Will keep 3462.222 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3463.2423 and 3463.2424. Will keep 3463.2424 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3478.2168 and 3478.2169. Will keep 3478.2169 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3518.2481 and 3518.2482. Will keep 3518.2482 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3536.2838 and 3536.2839. Will keep 3536.2839 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3551.2584 and 3551.2585. Will keep 3551.2585 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3566.2329 and 3566.233. Will keep 3566.233 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3567.2533 and 3567.2534. Will keep 3567.2534 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3582.2278 and 3582.2279. Will keep 3582.2279 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3607.2594 and 3607.2595. Will keep 3607.2595 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3608.2798 and 3608.2799. Will keep 3608.2799 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3609.3002 and 3609.3003. Will keep 3609.3003 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3623.2543 and 3623.2544. Will keep 3623.2544 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3624.2747 and 3624.2748. Will keep 3624.2748 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3664.306 and 3664.3061. Will keep 3664.306 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3712.2908 and 3712.2909. Will keep 3712.2909 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3728.2857 and 3728.2858. Will keep 3728.2858 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3739.3632 and 3739.3633. Will keep 3739.3633 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3752.2969 and 3752.297. Will keep 3752.297 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3753.3173 and 3753.3174. Will keep 3753.3174 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3754.3377 and 3754.3378. Will keep 3754.3378 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3768.2918 and 3768.2919. Will keep 3768.2919 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3769.3122 and 3769.3123. Will keep 3769.3123 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3770.3326 and 3770.3327. Will keep 3770.3327 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3842.3538 and 3842.3539. Will keep 3842.3539 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3843.3742 and 3843.3743. Will keep 3843.3743 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3858.3487 and 3858.3488. Will keep 3858.3488 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3859.3691 and 3859.3692. Will keep 3859.3692 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3874.3436 and 3874.3437. Will keep 3874.3437 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3882.3599 and 3882.36. Will keep 3882.36 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3884.4007 and 3884.4008. Will keep 3884.4008 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3898.3548 and 3898.3549. Will keep 3898.3549 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3899.3752 and 3899.3753. Will keep 3899.3753 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3900.3956 and 3900.3957. Will keep 3900.3957 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3901.416 and 3901.4161. Will keep 3901.416 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3914.3497 and 3914.3498. Will keep 3914.3498 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3915.3701 and 3915.3702. Will keep 3915.3702 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3971.3964 and 3971.3965. Will keep 3971.3965 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3972.3916 and 3972.3917. Will keep 3972.3917 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 3988.3865 and 3988.3866. Will keep 3988.3866 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4003.3862 and 4003.3863. Will keep 4003.3863 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4004.4066 and 4004.4067. Will keep 4004.4067 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4013.4433 and 4013.4434. Will keep 4013.4434 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4019.3811 and 4019.3812. Will keep 4019.3812 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4028.4178 and 4028.4179. Will keep 4028.4179 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4029.4382 and 4029.4383. Will keep 4029.4383 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4045.4331 and 4045.4332. Will keep 4045.4332 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4061.428 and 4061.4281. Will keep 4061.428 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4092.3975 and 4092.3976. Will keep 4092.3976 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4104.4954 and 4104.4955. Will keep 4104.4955 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4116.4339 and 4116.434. Will keep 4116.434 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4118.4495 and 4118.4496. Will keep 4118.4496 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4132.4288 and 4132.4289. Will keep 4132.4289 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4134.4444 and 4134.4445. Will keep 4134.4445 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4134.4696 and 4134.4697. Will keep 4134.4697 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4148.4237 and 4148.4238. Will keep 4148.4238 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4149.4441 and 4149.4442. Will keep 4149.4442 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4150.4645 and 4150.4646. Will keep 4150.4646 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4164.4186 and 4164.4187. Will keep 4164.4187 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4165.439 and 4165.4391. Will keep 4165.439 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4174.4757 and 4174.4758. Will keep 4174.4758 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4180.4135 and 4180.4136. Will keep 4180.4136 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4189.4502 and 4189.4503. Will keep 4189.4503 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4190.4706 and 4190.4707. Will keep 4190.4707 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4192.5114 and 4192.5115. Will keep 4192.5115 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4206.4655 and 4206.4656. Will keep 4206.4656 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4208.5063 and 4208.5064. Will keep 4208.5064 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4222.4604 and 4222.4605. Will keep 4222.4605 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4222.4605 and 4222.4606. Will keep 4222.4606 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4238.4554 and 4238.4555. Will keep 4238.4555 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4247.4921 and 4247.4922. Will keep 4247.4922 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4249.5329 and 4249.533. Will keep 4249.533 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4262.4918 and 4262.4919. Will keep 4262.4919 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4263.487 and 4263.4871. Will keep 4263.487 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4263.5122 and 4263.5123. Will keep 4263.5123 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4265.5278 and 4265.5279. Will keep 4265.5279 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4278.4867 and 4278.4868. Will keep 4278.4868 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4279.4819 and 4279.482. Will keep 4279.482 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4294.4816 and 4294.4817. Will keep 4294.4817 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4295.502 and 4295.5021. Will keep 4295.502 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4310.4765 and 4310.4766. Will keep 4310.4766 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4311.4969 and 4311.497. Will keep 4311.497 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4319.5133 and 4319.5134. Will keep 4319.5134 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4320.5336 and 4320.5337. Will keep 4320.5337 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4326.4714 and 4326.4715. Will keep 4326.4715 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4335.5081 and 4335.5082. Will keep 4335.5082 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4336.5286 and 4336.5287. Will keep 4336.5287 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4337.5489 and 4337.549. Will keep 4337.549 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4353.5438 and 4353.5439. Will keep 4353.5439 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4368.5184 and 4368.5185. Will keep 4368.5185 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4384.5133 and 4384.5134. Will keep 4384.5134 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4393.55 and 4393.5501. Will keep 4393.55 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4395.5908 and 4395.5909. Will keep 4395.5909 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4411.5857 and 4411.5858. Will keep 4411.5858 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4465.5712 and 4465.5713. Will keep 4465.5713 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4481.566 and 4481.5661. Will keep 4481.566 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4514.5763 and 4514.5764. Will keep 4514.5764 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4530.5712 and 4530.5713. Will keep 4530.5713 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4539.6079 and 4539.608. Will keep 4539.608 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4555.6028 and 4555.6029. Will keep 4555.6029 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4571.5977 and 4571.5978. Will keep 4571.5978 2024-01-26 21:39:14 [WARNING] - There are closed modifications: 4685.6658 and 4685.6659. Will keep 4685.6659 2024-01-26 21:39:14 [INFO] - Collecting variable modifications from all psm.tsv files... 2024-01-26 21:39:15 [INFO] - Loading and indexing all psm.tsv files... 2024-01-26 21:39:15 [INFO] - Collecting all compensation voltages if applicable... 2024-01-26 21:39:26 [INFO] - Parameters: 2024-01-26 21:39:26 [INFO] - perform-ms1quant = 1 2024-01-26 21:39:26 [INFO] - perform-isoquant = 0 2024-01-26 21:39:26 [INFO] - isotol = 20.0 2024-01-26 21:39:26 [INFO] - isolevel = 2 2024-01-26 21:39:26 [INFO] - isotype = tmt10 2024-01-26 21:39:26 [INFO] - site-reports = 1 2024-01-26 21:39:26 [INFO] - threads = 7 2024-01-26 21:39:26 [INFO] - mztol = 10.0 2024-01-26 21:39:26 [INFO] - rttol = 0.4 2024-01-26 21:39:26 [INFO] - imtol = 0.05 2024-01-26 21:39:26 [INFO] - minisotopes = 2 2024-01-26 21:39:26 [INFO] - minscans = 3 2024-01-26 21:39:26 [INFO] - psm = U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_1\psm.tsv 2024-01-26 21:39:26 [INFO] - psm = U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_2\psm.tsv 2024-01-26 21:39:26 [INFO] - psm = U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\EV_3\psm.tsv 2024-01-26 21:39:26 [INFO] - psm = U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_1\psm.tsv 2024-01-26 21:39:26 [INFO] - psm = U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_2\psm.tsv 2024-01-26 21:39:26 [INFO] - psm = U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\RNF220_3\psm.tsv 2024-01-26 21:39:26 [INFO] - psm = U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_1\psm.tsv 2024-01-26 21:39:26 [INFO] - psm = U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_2\psm.tsv 2024-01-26 21:39:26 [INFO] - psm = U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\TOPORS_3\psm.tsv 2024-01-26 21:39:26 [INFO] - multidir = U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\.\ 2024-01-26 21:39:26 [INFO] - excludemods = 2024-01-26 21:39:26 [INFO] - minions = 1 2024-01-26 21:39:26 [INFO] - maxlfq = 1 2024-01-26 21:39:26 [INFO] - ibaq = 0 2024-01-26 21:39:26 [INFO] - normalization = 1 2024-01-26 21:39:26 [INFO] - minexps = 1 2024-01-26 21:39:26 [INFO] - minfreq = 0.0 2024-01-26 21:39:26 [INFO] - tp = 0 2024-01-26 21:39:26 [INFO] - mbr = 1 2024-01-26 21:39:26 [INFO] - mbrrttol = 1.0 2024-01-26 21:39:26 [INFO] - mbrimtol = 0.05 2024-01-26 21:39:26 [INFO] - mbrtoprun = 10 2024-01-26 21:39:26 [INFO] - mbrmincorr = 0.0 2024-01-26 21:39:26 [INFO] - ionmobility = 0 2024-01-26 21:39:26 [INFO] - ionfdr = 0.01 2024-01-26 21:39:26 [INFO] - peptidefdr = 1.0 2024-01-26 21:39:26 [INFO] - proteinfdr = 1.0 2024-01-26 21:39:26 [INFO] - light = 2024-01-26 21:39:26 [INFO] - medium = 2024-01-26 21:39:26 [INFO] - heavy = 2024-01-26 21:39:26 [INFO] - requantify = 0 2024-01-26 21:39:26 [INFO] - writeindex = 0 2024-01-26 21:39:26 [INFO] - locprob = 0.75 2024-01-26 21:39:26 [INFO] - uniqueness = 0 2024-01-26 21:39:26 [INFO] - filelist = U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\filelist_ionquant.txt 2024-01-26 21:39:26 [INFO] - specdir = U:\slyon\PC1131_APMS_raw 2024-01-26 21:39:26 [INFO] - modlist = U:\slyon\fragpipe_seaches\PC1131_testOutput_run2\modmasses_ionquant.txt 2024-01-26 21:39:26 [INFO] - mod masses: 2024-01-26 21:39:26 [INFO] - 15.9949 2024-01-26 21:39:26 [INFO] - 42.0106 2024-01-26 21:39:26 [INFO] - 203.0794 2024-01-26 21:39:26 [INFO] - 349.1373 2024-01-26 21:39:26 [INFO] - 406.1588 2024-01-26 21:39:26 [INFO] - 511.1901 2024-01-26 21:39:26 [INFO] - 552.2167 2024-01-26 21:39:26 [INFO] - 568.2116 2024-01-26 21:39:26 [INFO] - 656.2276 2024-01-26 21:39:26 [INFO] - 672.2225 2024-01-26 21:39:26 [INFO] - 714.2695 2024-01-26 21:39:26 [INFO] - 730.2644 2024-01-26 21:39:26 [INFO] - 771.291 2024-01-26 21:39:26 [INFO] - 802.2855 2024-01-26 21:39:26 [INFO] - 876.3223 2024-01-26 21:39:26 [INFO] - 892.3172 2024-01-26 21:39:26 [INFO] - 917.3489 2024-01-26 21:39:26 [INFO] - 933.3438 2024-01-26 21:39:26 [INFO] - 972.2836 2024-01-26 21:39:26 [INFO] - 1005.3649 2024-01-26 21:39:26 [INFO] - 1038.3751 2024-01-26 21:39:26 [INFO] - 1052.2499 2024-01-26 21:39:26 [INFO] - 1054.3701 2024-01-26 21:39:26 [INFO] - 1079.4017 2024-01-26 21:39:26 [INFO] - 1095.3966 2024-01-26 21:39:26 [INFO] - 1134.3364 2024-01-26 21:39:26 [INFO] - 1136.4232 2024-01-26 21:39:26 [INFO] - 1175.3963 2024-01-26 21:39:26 [INFO] - 1184.433 2024-01-26 21:39:26 [INFO] - 1200.428 2024-01-26 21:39:26 [INFO] - 1214.3027 2024-01-26 21:39:26 [INFO] - 1216.4229 2024-01-26 21:39:26 [INFO] - 1225.4596 2024-01-26 21:39:26 [INFO] - 1241.4545 2024-01-26 21:39:26 [INFO] - 1257.4495 2024-01-26 21:39:26 [INFO] - 1282.4811 2024-01-26 21:39:26 [INFO] - 1296.3892 2024-01-26 21:39:26 [INFO] - 1298.476 2024-01-26 21:39:26 [INFO] - 1337.4491 2024-01-26 21:39:26 [INFO] - 1339.5025 2024-01-26 21:39:26 [INFO] - 1362.4808 2024-01-26 21:39:26 [INFO] - 1376.3556 2024-01-26 21:39:26 [INFO] - 1378.4757 2024-01-26 21:39:26 [INFO] - 1380.5291 2024-01-26 21:39:26 [INFO] - 1385.4968 2024-01-26 21:39:26 [INFO] - 1386.4921 2024-01-26 21:39:26 [INFO] - 1387.5125 2024-01-26 21:39:26 [INFO] - 1402.487 2024-01-26 21:39:26 [INFO] - 1403.5074 2024-01-26 21:39:26 [INFO] - 1419.5023 2024-01-26 21:39:26 [INFO] - 1428.539 2024-01-26 21:39:26 [INFO] - 1444.5339 2024-01-26 21:39:26 [INFO] - 1458.442 2024-01-26 21:39:26 [INFO] - 1460.5288 2024-01-26 21:39:26 [INFO] - 1483.507 2024-01-26 21:39:26 [INFO] - 1485.5604 2024-01-26 21:39:26 [INFO] - 1501.5553 2024-01-26 21:39:26 [INFO] - 1508.5387 2024-01-26 21:39:26 [INFO] - 1524.5336 2024-01-26 21:39:26 [INFO] - 1526.5871 2024-01-26 21:39:26 [INFO] - 1532.55 2024-01-26 21:39:26 [INFO] - 1532.575 2024-01-26 21:39:26 [INFO] - 1533.5703 2024-01-26 21:39:26 [INFO] - 1538.4084 2024-01-26 21:39:26 [INFO] - 1540.5285 2024-01-26 21:39:26 [INFO] - 1548.5449 2024-01-26 21:39:26 [INFO] - 1548.5699 2024-01-26 21:39:26 [INFO] - 1549.5653 2024-01-26 21:39:26 [INFO] - 1564.5398 2024-01-26 21:39:26 [INFO] - 1565.5602 2024-01-26 21:39:26 [INFO] - 1574.5969 2024-01-26 21:39:26 [INFO] - 1581.5551 2024-01-26 21:39:26 [INFO] - 1583.6085 2024-01-26 21:39:26 [INFO] - 1589.5714 2024-01-26 21:39:26 [INFO] - 1590.5918 2024-01-26 21:39:26 [INFO] - 1605.5663 2024-01-26 21:39:26 [INFO] - 1606.5867 2024-01-26 21:39:26 [INFO] - 1620.4948 2024-01-26 21:39:26 [INFO] - 1622.5817 2024-01-26 21:39:26 [INFO] - 1631.6183 2024-01-26 21:39:26 [INFO] - 1647.6132 2024-01-26 21:39:26 [INFO] - 1661.5214 2024-01-26 21:39:26 [INFO] - 1663.6082 2024-01-26 21:39:26 [INFO] - 1671.6246 2024-01-26 21:39:26 [INFO] - 1672.645 2024-01-26 21:39:26 [INFO] - 1677.6126 2024-01-26 21:39:26 [INFO] - 1678.6079 2024-01-26 21:39:26 [INFO] - 1686.5864 2024-01-26 21:39:26 [INFO] - 1687.6195 2024-01-26 21:39:26 [INFO] - 1693.6075 2024-01-26 21:39:26 [INFO] - 1694.6028 2024-01-26 21:39:26 [INFO] - 1695.6232 2024-01-26 21:39:26 [INFO] - 1700.4612 2024-01-26 21:39:26 [INFO] - 1702.5814 2024-01-26 21:39:26 [INFO] - 1704.6348 2024-01-26 21:39:26 [INFO] - 1709.6024 2024-01-26 21:39:26 [INFO] - 1710.5977 2024-01-26 21:39:26 [INFO] - 1711.6181 2024-01-26 21:39:26 [INFO] - 1726.5927 2024-01-26 21:39:26 [INFO] - 1727.613 2024-01-26 21:39:26 [INFO] - 1729.6664 2024-01-26 21:39:26 [INFO] - 1735.6293 2024-01-26 21:39:26 [INFO] - 1736.6497 2024-01-26 21:39:26 [INFO] - 1743.6079 2024-01-26 21:39:26 [INFO] - 1751.6242 2024-01-26 21:39:26 [INFO] - 1752.6446 2024-01-26 21:39:26 [INFO] - 1767.6191 2024-01-26 21:39:26 [INFO] - 1768.6396 2024-01-26 21:39:26 [INFO] - 1777.6762 2024-01-26 21:39:26 [INFO] - 1782.5477 2024-01-26 21:39:26 [INFO] - 1784.6345 2024-01-26 21:39:26 [INFO] - 1786.6878 2024-01-26 21:39:26 [INFO] - 1792.6508 2024-01-26 21:39:26 [INFO] - 1793.6711 2024-01-26 21:39:26 [INFO] - 1807.6127 2024-01-26 21:39:26 [INFO] - 1808.6457 2024-01-26 21:39:26 [INFO] - 1809.6661 2024-01-26 21:39:26 [INFO] - 1817.6825 2024-01-26 21:39:26 [INFO] - 1818.7029 2024-01-26 21:39:26 [INFO] - 1823.5742 2024-01-26 21:39:26 [INFO] - 1823.6705 2024-01-26 21:39:26 [INFO] - 1825.661 2024-01-26 21:39:26 [INFO] - 1833.6774 2024-01-26 21:39:26 [INFO] - 1839.6403 2024-01-26 21:39:26 [INFO] - 1839.6654 2024-01-26 21:39:26 [INFO] - 1840.6607 2024-01-26 21:39:26 [INFO] - 1848.6393 2024-01-26 21:39:26 [INFO] - 1850.6927 2024-01-26 21:39:26 [INFO] - 1855.6352 2024-01-26 21:39:26 [INFO] - 1855.6603 2024-01-26 21:39:26 [INFO] - 1856.6557 2024-01-26 21:39:26 [INFO] - 1857.676 2024-01-26 21:39:26 [INFO] - 1862.514 2024-01-26 21:39:26 [INFO] - 1864.6008 2024-01-26 21:39:27 [INFO] - 1864.6342 2024-01-26 21:39:27 [INFO] - 1866.6876 2024-01-26 21:39:27 [INFO] - 1871.6301 2024-01-26 21:39:27 [INFO] - 1872.6506 2024-01-26 21:39:27 [INFO] - 1873.6709 2024-01-26 21:39:27 [INFO] - 1874.7039 2024-01-26 21:39:27 [INFO] - 1875.7243 2024-01-26 21:39:27 [INFO] - 1880.6668 2024-01-26 21:39:27 [INFO] - 1881.6872 2024-01-26 21:39:27 [INFO] - 1888.6454 2024-01-26 21:39:27 [INFO] - 1889.6658 2024-01-26 21:39:27 [INFO] - 1890.6988 2024-01-26 21:39:27 [INFO] - 1896.6617 2024-01-26 21:39:27 [INFO] - 1897.6821 2024-01-26 21:39:27 [INFO] - 1898.7025 2024-01-26 21:39:27 [INFO] - 1905.6608 2024-01-26 21:39:27 [INFO] - 1907.7141 2024-01-26 21:39:27 [INFO] - 1912.6566 2024-01-26 21:39:27 [INFO] - 1913.677 2024-01-26 21:39:27 [INFO] - 1914.6975 2024-01-26 21:39:27 [INFO] - 1929.672 2024-01-26 21:39:27 [INFO] - 1930.6924 2024-01-26 21:39:27 [INFO] - 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3769.3123 2024-01-26 21:39:28 [INFO] - 3770.3327 2024-01-26 21:39:28 [INFO] - 3771.3531 2024-01-26 21:39:28 [INFO] - 3784.2867 2024-01-26 21:39:28 [INFO] - 3785.3072 2024-01-26 21:39:28 [INFO] - 3786.3276 2024-01-26 21:39:28 [INFO] - 3794.3439 2024-01-26 21:39:28 [INFO] - 3794.3691 2024-01-26 21:39:28 [INFO] - 3795.3643 2024-01-26 21:39:28 [INFO] - 3796.3847 2024-01-26 21:39:28 [INFO] - 3801.3021 2024-01-26 21:39:28 [INFO] - 3808.3232 2024-01-26 21:39:28 [INFO] - 3809.3436 2024-01-26 21:39:28 [INFO] - 3810.3388 2024-01-26 21:39:28 [INFO] - 3810.364 2024-01-26 21:39:28 [INFO] - 3811.3592 2024-01-26 21:39:28 [INFO] - 3812.3796 2024-01-26 21:39:28 [INFO] - 3824.3181 2024-01-26 21:39:28 [INFO] - 3825.3385 2024-01-26 21:39:28 [INFO] - 3826.3337 2024-01-26 21:39:28 [INFO] - 3826.3589 2024-01-26 21:39:28 [INFO] - 3827.3541 2024-01-26 21:39:28 [INFO] - 3827.3793 2024-01-26 21:39:28 [INFO] - 3828.3745 2024-01-26 21:39:28 [INFO] - 3840.313 2024-01-26 21:39:28 [INFO] - 3841.3334 2024-01-26 21:39:28 [INFO] - 3842.3286 2024-01-26 21:39:28 [INFO] - 3842.3539 2024-01-26 21:39:28 [INFO] - 3843.349 2024-01-26 21:39:28 [INFO] - 3843.3743 2024-01-26 21:39:28 [INFO] - 3851.3905 2024-01-26 21:39:28 [INFO] - 3856.3079 2024-01-26 21:39:28 [INFO] - 3857.3283 2024-01-26 21:39:28 [INFO] - 3858.3488 2024-01-26 21:39:28 [INFO] - 3859.3692 2024-01-26 21:39:28 [INFO] - 3866.365 2024-01-26 21:39:28 [INFO] - 3867.3854 2024-01-26 21:39:28 [INFO] - 3868.4058 2024-01-26 21:39:28 [INFO] - 3872.3028 2024-01-26 21:39:28 [INFO] - 3873.3232 2024-01-26 21:39:28 [INFO] - 3874.3437 2024-01-26 21:39:28 [INFO] - 3875.3641 2024-01-26 21:39:28 [INFO] - 3882.36 2024-01-26 21:39:28 [INFO] - 3883.3803 2024-01-26 21:39:28 [INFO] - 3884.4008 2024-01-26 21:39:28 [INFO] - 3885.4211 2024-01-26 21:39:28 [INFO] - 3888.2977 2024-01-26 21:39:28 [INFO] - 3890.3386 2024-01-26 21:39:28 [INFO] - 3898.3549 2024-01-26 21:39:28 [INFO] - 3899.3753 2024-01-26 21:39:28 [INFO] - 3900.3957 2024-01-26 21:39:28 [INFO] - 3901.416 2024-01-26 21:39:28 [INFO] - 3914.3498 2024-01-26 21:39:28 [INFO] - 3915.3702 2024-01-26 21:39:28 [INFO] - 3916.3906 2024-01-26 21:39:28 [INFO] - 3917.411 2024-01-26 21:39:28 [INFO] - 3930.3447 2024-01-26 21:39:28 [INFO] - 3931.3651 2024-01-26 21:39:28 [INFO] - 3932.3855 2024-01-26 21:39:28 [INFO] - 3940.4018 2024-01-26 21:39:28 [INFO] - 3941.4222 2024-01-26 21:39:28 [INFO] - 3942.4426 2024-01-26 21:39:28 [INFO] - 3946.3396 2024-01-26 21:39:28 [INFO] - 3947.36 2024-01-26 21:39:28 [INFO] - 3954.3811 2024-01-26 21:39:28 [INFO] - 3955.4015 2024-01-26 21:39:28 [INFO] - 3956.3967 2024-01-26 21:39:28 [INFO] - 3956.4219 2024-01-26 21:39:28 [INFO] - 3957.4171 2024-01-26 21:39:28 [INFO] - 3958.4375 2024-01-26 21:39:28 [INFO] - 3970.376 2024-01-26 21:39:28 [INFO] - 3971.3965 2024-01-26 21:39:28 [INFO] - 3972.3917 2024-01-26 21:39:28 [INFO] - 3972.4168 2024-01-26 21:39:28 [INFO] - 3973.412 2024-01-26 21:39:28 [INFO] - 3974.4324 2024-01-26 21:39:28 [INFO] - 3986.3709 2024-01-26 21:39:28 [INFO] - 3987.3913 2024-01-26 21:39:28 [INFO] - 3988.3866 2024-01-26 21:39:28 [INFO] - 3988.4117 2024-01-26 21:39:28 [INFO] - 3989.407 2024-01-26 21:39:28 [INFO] - 3989.4322 2024-01-26 21:39:28 [INFO] - 3997.4484 2024-01-26 21:39:28 [INFO] - 4002.3658 2024-01-26 21:39:28 [INFO] - 4003.3863 2024-01-26 21:39:28 [INFO] - 4004.3815 2024-01-26 21:39:28 [INFO] - 4004.4067 2024-01-26 21:39:28 [INFO] - 4005.4271 2024-01-26 21:39:28 [INFO] - 4011.4026 2024-01-26 21:39:28 [INFO] - 4012.4229 2024-01-26 21:39:28 [INFO] - 4013.4434 2024-01-26 21:39:28 [INFO] - 4018.3607 2024-01-26 21:39:28 [INFO] - 4019.3812 2024-01-26 21:39:28 [INFO] - 4020.4016 2024-01-26 21:39:28 [INFO] - 4021.422 2024-01-26 21:39:28 [INFO] - 4027.3975 2024-01-26 21:39:28 [INFO] - 4028.4179 2024-01-26 21:39:28 [INFO] - 4029.4383 2024-01-26 21:39:28 [INFO] - 4030.4587 2024-01-26 21:39:28 [INFO] - 4034.3556 2024-01-26 21:39:28 [INFO] - 4035.3761 2024-01-26 21:39:28 [INFO] - 4036.3965 2024-01-26 21:39:28 [INFO] - 4043.3923 2024-01-26 21:39:28 [INFO] - 4044.4128 2024-01-26 21:39:28 [INFO] - 4045.4332 2024-01-26 21:39:28 [INFO] - 4046.4536 2024-01-26 21:39:28 [INFO] - 4059.3873 2024-01-26 21:39:28 [INFO] - 4060.4077 2024-01-26 21:39:28 [INFO] - 4061.428 2024-01-26 21:39:28 [INFO] - 4062.4485 2024-01-26 21:39:28 [INFO] - 4075.3822 2024-01-26 21:39:28 [INFO] - 4076.4026 2024-01-26 21:39:28 [INFO] - 4077.423 2024-01-26 21:39:28 [INFO] - 4078.4434 2024-01-26 21:39:28 [INFO] - 4085.4393 2024-01-26 21:39:28 [INFO] - 4086.4597 2024-01-26 21:39:28 [INFO] - 4088.5005 2024-01-26 21:39:28 [INFO] - 4091.3771 2024-01-26 21:39:28 [INFO] - 4092.3976 2024-01-26 21:39:28 [INFO] - 4093.4179 2024-01-26 21:39:28 [INFO] - 4100.4391 2024-01-26 21:39:28 [INFO] - 4101.4342 2024-01-26 21:39:28 [INFO] - 4101.4594 2024-01-26 21:39:28 [INFO] - 4102.4546 2024-01-26 21:39:28 [INFO] - 4102.4797 2024-01-26 21:39:28 [INFO] - 4103.475 2024-01-26 21:39:28 [INFO] - 4104.4955 2024-01-26 21:39:28 [INFO] - 4108.3925 2024-01-26 21:39:28 [INFO] - 4116.434 2024-01-26 21:39:28 [INFO] - 4117.4291 2024-01-26 21:39:28 [INFO] - 4117.4543 2024-01-26 21:39:28 [INFO] - 4118.4496 2024-01-26 21:39:28 [INFO] - 4118.4747 2024-01-26 21:39:28 [INFO] - 4120.4904 2024-01-26 21:39:28 [INFO] - 4132.4289 2024-01-26 21:39:28 [INFO] - 4133.424 2024-01-26 21:39:28 [INFO] - 4133.4492 2024-01-26 21:39:28 [INFO] - 4134.4445 2024-01-26 21:39:28 [INFO] - 4134.4697 2024-01-26 21:39:28 [INFO] - 4148.4238 2024-01-26 21:39:28 [INFO] - 4149.4189 2024-01-26 21:39:28 [INFO] - 4149.4442 2024-01-26 21:39:28 [INFO] - 4150.4394 2024-01-26 21:39:28 [INFO] - 4150.4646 2024-01-26 21:39:28 [INFO] - 4157.4605 2024-01-26 21:39:28 [INFO] - 4158.4808 2024-01-26 21:39:28 [INFO] - 4159.5012 2024-01-26 21:39:28 [INFO] - 4164.4187 2024-01-26 21:39:28 [INFO] - 4165.439 2024-01-26 21:39:28 [INFO] - 4166.4595 2024-01-26 21:39:28 [INFO] - 4173.4554 2024-01-26 21:39:28 [INFO] - 4174.4758 2024-01-26 21:39:28 [INFO] - 4175.4962 2024-01-26 21:39:28 [INFO] - 4176.5165 2024-01-26 21:39:28 [INFO] - 4180.4136 2024-01-26 21:39:28 [INFO] - 4181.434 2024-01-26 21:39:28 [INFO] - 4182.4544 2024-01-26 21:39:28 [INFO] - 4189.4503 2024-01-26 21:39:28 [INFO] - 4190.4707 2024-01-26 21:39:28 [INFO] - 4191.4911 2024-01-26 21:39:28 [INFO] - 4192.5115 2024-01-26 21:39:28 [INFO] - 4196.4085 2024-01-26 21:39:28 [INFO] - 4205.4452 2024-01-26 21:39:28 [INFO] - 4206.4656 2024-01-26 21:39:28 [INFO] - 4207.486 2024-01-26 21:39:28 [INFO] - 4208.5064 2024-01-26 21:39:28 [INFO] - 4221.4401 2024-01-26 21:39:28 [INFO] - 4222.4606 2024-01-26 21:39:28 [INFO] - 4223.4809 2024-01-26 21:39:28 [INFO] - 4224.5013 2024-01-26 21:39:28 [INFO] - 4231.4972 2024-01-26 21:39:28 [INFO] - 4232.5176 2024-01-26 21:39:28 [INFO] - 4233.538 2024-01-26 21:39:28 [INFO] - 4237.435 2024-01-26 21:39:28 [INFO] - 4238.4555 2024-01-26 21:39:28 [INFO] - 4239.4758 2024-01-26 21:39:28 [INFO] - 4246.4969 2024-01-26 21:39:28 [INFO] - 4247.4922 2024-01-26 21:39:28 [INFO] - 4247.5173 2024-01-26 21:39:28 [INFO] - 4248.5125 2024-01-26 21:39:28 [INFO] - 4249.533 2024-01-26 21:39:28 [INFO] - 4253.4299 2024-01-26 21:39:28 [INFO] - 4254.4504 2024-01-26 21:39:28 [INFO] - 4262.4919 2024-01-26 21:39:28 [INFO] - 4263.487 2024-01-26 21:39:28 [INFO] - 4263.5123 2024-01-26 21:39:29 [INFO] - 4264.5074 2024-01-26 21:39:29 [INFO] - 4265.5279 2024-01-26 21:39:29 [INFO] - 4272.5237 2024-01-26 21:39:29 [INFO] - 4278.4868 2024-01-26 21:39:29 [INFO] - 4279.482 2024-01-26 21:39:29 [INFO] - 4279.5071 2024-01-26 21:39:29 [INFO] - 4280.5023 2024-01-26 21:39:29 [INFO] - 4281.5228 2024-01-26 21:39:29 [INFO] - 4294.4817 2024-01-26 21:39:29 [INFO] - 4295.4769 2024-01-26 21:39:29 [INFO] - 4295.502 2024-01-26 21:39:29 [INFO] - 4303.5184 2024-01-26 21:39:29 [INFO] - 4304.5388 2024-01-26 21:39:29 [INFO] - 4305.5591 2024-01-26 21:39:29 [INFO] - 4310.4766 2024-01-26 21:39:29 [INFO] - 4311.4718 2024-01-26 21:39:29 [INFO] - 4311.497 2024-01-26 21:39:29 [INFO] - 4319.5134 2024-01-26 21:39:29 [INFO] - 4320.5337 2024-01-26 21:39:29 [INFO] - 4321.554 2024-01-26 21:39:29 [INFO] - 4326.4715 2024-01-26 21:39:29 [INFO] - 4327.4919 2024-01-26 21:39:29 [INFO] - 4335.5082 2024-01-26 21:39:29 [INFO] - 4336.5287 2024-01-26 21:39:29 [INFO] - 4337.549 2024-01-26 21:39:29 [INFO] - 4342.4664 2024-01-26 21:39:29 [INFO] - 4351.5031 2024-01-26 21:39:29 [INFO] - 4352.5235 2024-01-26 21:39:29 [INFO] - 4353.5439 2024-01-26 21:39:29 [INFO] - 4367.498 2024-01-26 21:39:29 [INFO] - 4368.5185 2024-01-26 21:39:29 [INFO] - 4369.5388 2024-01-26 21:39:29 [INFO] - 4376.5348 2024-01-26 21:39:29 [INFO] - 4377.5551 2024-01-26 21:39:29 [INFO] - 4378.5755 2024-01-26 21:39:29 [INFO] - 4379.5959 2024-01-26 21:39:29 [INFO] - 4383.4929 2024-01-26 21:39:29 [INFO] - 4384.5134 2024-01-26 21:39:29 [INFO] - 4385.5338 2024-01-26 21:39:29 [INFO] - 4392.5297 2024-01-26 21:39:29 [INFO] - 4393.55 2024-01-26 21:39:29 [INFO] - 4394.5704 2024-01-26 21:39:29 [INFO] - 4395.5909 2024-01-26 21:39:29 [INFO] - 4399.4878 2024-01-26 21:39:29 [INFO] - 4400.5083 2024-01-26 21:39:29 [INFO] - 4408.5245 2024-01-26 21:39:29 [INFO] - 4409.545 2024-01-26 21:39:29 [INFO] - 4410.5653 2024-01-26 21:39:29 [INFO] - 4411.5858 2024-01-26 21:39:29 [INFO] - 4424.5195 2024-01-26 21:39:29 [INFO] - 4425.5399 2024-01-26 21:39:29 [INFO] - 4426.5602 2024-01-26 21:39:29 [INFO] - 4427.5807 2024-01-26 21:39:29 [INFO] - 4440.5144 2024-01-26 21:39:29 [INFO] - 4441.5348 2024-01-26 21:39:29 [INFO] - 4449.5763 2024-01-26 21:39:29 [INFO] - 4450.5967 2024-01-26 21:39:29 [INFO] - 4456.5093 2024-01-26 21:39:29 [INFO] - 4457.5297 2024-01-26 21:39:29 [INFO] - 4465.5713 2024-01-26 21:39:29 [INFO] - 4466.5916 2024-01-26 21:39:29 [INFO] - 4481.566 2024-01-26 21:39:29 [INFO] - 4482.5865 2024-01-26 21:39:29 [INFO] - 4497.561 2024-01-26 21:39:29 [INFO] - 4498.5814 2024-01-26 21:39:29 [INFO] - 4513.5559 2024-01-26 21:39:29 [INFO] - 4514.5764 2024-01-26 21:39:29 [INFO] - 4522.5927 2024-01-26 21:39:29 [INFO] - 4523.613 2024-01-26 21:39:29 [INFO] - 4529.5508 2024-01-26 21:39:29 [INFO] - 4530.5713 2024-01-26 21:39:29 [INFO] - 4538.5876 2024-01-26 21:39:29 [INFO] - 4539.608 2024-01-26 21:39:29 [INFO] - 4545.5457 2024-01-26 21:39:29 [INFO] - 4546.5662 2024-01-26 21:39:29 [INFO] - 4554.5824 2024-01-26 21:39:29 [INFO] - 4555.6029 2024-01-26 21:39:29 [INFO] - 4570.5774 2024-01-26 21:39:29 [INFO] - 4571.5978 2024-01-26 21:39:29 [INFO] - 4586.5723 2024-01-26 21:39:29 [INFO] - 4587.5927 2024-01-26 21:39:29 [INFO] - 4602.5672 2024-01-26 21:39:29 [INFO] - 4603.5876 2024-01-26 21:39:29 [INFO] - 4669.671 2024-01-26 21:39:29 [INFO] - 4685.6659 2024-01-26 21:39:29 [INFO] - 4701.6608 2024-01-26 21:39:29 [INFO] - 4717.6557 2024-01-26 21:39:29 [INFO] - 4733.6506 2024-01-26 21:39:29 [INFO] - 4749.6455 2024-01-26 21:39:29 [INFO] - 4757.6871 2024-01-26 21:39:29 [INFO] - 4773.6819 2024-01-26 21:39:29 [INFO] - 4789.6768 2024-01-26 21:39:29 [INFO] - 4805.6718 2024-01-26 21:39:29 [INFO] - 4821.6667 2024-01-26 21:39:29 [INFO] - 4837.6616 2024-01-26 21:39:29 [INFO] - 4903.745 2024-01-26 21:39:29 [INFO] - 4919.7399 2024-01-26 21:39:29 [INFO] - 4935.7347 2024-01-26 21:39:29 [INFO] - 4951.7297 2024-01-26 21:39:29 [INFO] - 4960.7664 2024-01-26 21:39:29 [INFO] - 4967.7246 2024-01-26 21:39:29 [INFO] - 4976.7613 2024-01-26 21:39:29 [INFO] - 4983.7195 2024-01-26 21:39:29 [INFO] - 4992.7562 2024-01-26 21:39:29 [INFO] - 5008.7511 2024-01-26 21:39:29 [INFO] - 5024.746 2024-01-26 21:39:29 [INFO] - 5040.7409 2024-01-26 21:39:29 [INFO] - 5106.8243 2024-01-26 21:39:29 [INFO] - 5122.8192 2024-01-26 21:39:29 [INFO] - 5138.8141 2024-01-26 21:39:29 [INFO] - 5154.809 2024-01-26 21:39:29 [INFO] - 5170.8039 2024-01-26 21:39:29 [INFO] - 5186.7988 2024-01-26 21:39:29 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2024-01-26 21:39:29 [INFO] - Loading U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.raw... 2024-01-26 21:41:30 [INFO] - Building index... 2024-01-26 21:41:30 [INFO] - Writing index to U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.quantindex 2024-01-26 21:41:31 [INFO] - Quantifying... 2024-01-26 21:41:32 [INFO] - Loading U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2.raw... 2024-01-26 21:42:20 [INFO] - Building index... 2024-01-26 21:42:20 [INFO] - Writing index to U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2.quantindex 2024-01-26 21:42:22 [INFO] - Quantifying... 2024-01-26 21:42:23 [INFO] - Loading U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3.raw... 2024-01-26 21:44:27 [INFO] - Building index... 2024-01-26 21:44:28 [INFO] - Writing index to U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3.quantindex 2024-01-26 21:44:29 [INFO] - Quantifying... 2024-01-26 21:44:29 [INFO] - Loading U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4.raw... 2024-01-26 21:46:33 [INFO] - Building index... 2024-01-26 21:46:33 [INFO] - Writing index to U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4.quantindex 2024-01-26 21:46:34 [INFO] - Quantifying... 2024-01-26 21:46:35 [INFO] - Loading U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5.raw... 2024-01-26 21:49:06 [INFO] - Building index... 2024-01-26 21:49:06 [INFO] - Writing index to U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5.quantindex 2024-01-26 21:49:07 [INFO] - Quantifying... 2024-01-26 21:49:07 [INFO] - Loading U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6.raw... 2024-01-26 21:50:56 [INFO] - Building index... 2024-01-26 21:50:56 [INFO] - Writing index to U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6.quantindex 2024-01-26 21:50:57 [INFO] - Quantifying... 2024-01-26 21:50:57 [INFO] - Loading U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7.raw... 2024-01-26 21:53:05 [INFO] - Building index... 2024-01-26 21:53:06 [INFO] - Writing index to U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7.quantindex 2024-01-26 21:53:07 [INFO] - Quantifying... 2024-01-26 21:53:07 [INFO] - Loading U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8.raw... 2024-01-26 21:55:02 [INFO] - Building index... 2024-01-26 21:55:02 [INFO] - Writing index to U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8.quantindex 2024-01-26 21:55:04 [INFO] - Quantifying... 2024-01-26 21:55:04 [INFO] - Loading U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9.raw... 2024-01-26 21:57:17 [INFO] - Building index... 2024-01-26 21:57:17 [INFO] - Writing index to U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9.quantindex 2024-01-26 21:57:19 [INFO] - Quantifying... 2024-01-26 21:57:19 [INFO] - Updating Philosopher's tables... 2024-01-26 21:57:38 [INFO] - Matching-between-runs: 20230602_PHCOQEHF_PC1131-Emanuele_1... 2024-01-26 21:57:39 [INFO] - Calculating correlations between all other runs... 2024-01-26 21:57:39 [INFO] - Reading index from U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_1.quantindex 2024-01-26 21:57:41 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_2... 2024-01-26 21:57:41 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_3... 2024-01-26 21:57:41 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_4... 2024-01-26 21:57:42 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_5... 2024-01-26 21:57:42 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_6... 2024-01-26 21:57:42 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_7... 2024-01-26 21:57:42 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_8... 2024-01-26 21:57:43 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_9... 2024-01-26 21:57:43 [INFO] - Training LDA models for all matched features. 2024-01-26 21:57:43 [INFO] - #{+1} = 8104, #{-1} = 802, #{+2} = 7137, #{-2} = 546 2024-01-26 21:57:43 [INFO] - Standardized coefficients: 2024-01-26 21:57:43 [INFO] - log10(intensity): 0.6341425739479999 2024-01-26 21:57:43 [INFO] - log10(KL): -0.16021135602444736 2024-01-26 21:57:43 [INFO] - abs(ppm): -0.7433341120753877 2024-01-26 21:57:43 [INFO] - RT diff: -0.16456589392224732 2024-01-26 21:57:43 [INFO] - Fitting a mixture model... 2024-01-26 21:57:49 [INFO] - Matching-between-runs: 20230602_PHCOQEHF_PC1131-Emanuele_2... 2024-01-26 21:57:49 [INFO] - Calculating correlations between all other runs... 2024-01-26 21:57:49 [INFO] - Reading index from U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_2.quantindex 2024-01-26 21:57:51 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_1... 2024-01-26 21:57:51 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_3... 2024-01-26 21:57:51 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_4... 2024-01-26 21:57:51 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_5... 2024-01-26 21:57:52 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_6... 2024-01-26 21:57:52 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_7... 2024-01-26 21:57:52 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_8... 2024-01-26 21:57:52 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_9... 2024-01-26 21:57:52 [INFO] - Training LDA models for all matched features. 2024-01-26 21:57:52 [INFO] - #{+1} = 7312, #{-1} = 687, #{+2} = 4587, #{-2} = 368 2024-01-26 21:57:52 [INFO] - Standardized coefficients: 2024-01-26 21:57:52 [INFO] - log10(intensity): 0.7025013551215714 2024-01-26 21:57:52 [INFO] - log10(KL): -0.12147800017399228 2024-01-26 21:57:52 [INFO] - abs(ppm): -0.7091911936526092 2024-01-26 21:57:52 [INFO] - RT diff: -0.043181724271123635 2024-01-26 21:57:52 [INFO] - Fitting a mixture model... 2024-01-26 21:57:53 [INFO] - Matching-between-runs: 20230602_PHCOQEHF_PC1131-Emanuele_3... 2024-01-26 21:57:53 [INFO] - Calculating correlations between all other runs... 2024-01-26 21:57:53 [INFO] - Reading index from U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_3.quantindex 2024-01-26 21:57:55 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_1... 2024-01-26 21:57:55 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_2... 2024-01-26 21:57:55 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_4... 2024-01-26 21:57:55 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_5... 2024-01-26 21:57:55 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_6... 2024-01-26 21:57:55 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_7... 2024-01-26 21:57:56 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_8... 2024-01-26 21:57:56 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_9... 2024-01-26 21:57:56 [INFO] - Training LDA models for all matched features. 2024-01-26 21:57:56 [INFO] - #{+1} = 8584, #{-1} = 856, #{+2} = 9002, #{-2} = 639 2024-01-26 21:57:56 [INFO] - Standardized coefficients: 2024-01-26 21:57:56 [INFO] - log10(intensity): 0.7334856830670801 2024-01-26 21:57:56 [INFO] - log10(KL): -0.1820164801783993 2024-01-26 21:57:56 [INFO] - abs(ppm): -0.6599076079752845 2024-01-26 21:57:56 [INFO] - RT diff: -0.1304068869134057 2024-01-26 21:57:56 [INFO] - Fitting a mixture model... 2024-01-26 21:57:57 [INFO] - Matching-between-runs: 20230602_PHCOQEHF_PC1131-Emanuele_4... 2024-01-26 21:57:57 [INFO] - Calculating correlations between all other runs... 2024-01-26 21:57:57 [INFO] - Reading index from U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_4.quantindex 2024-01-26 21:57:58 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_1... 2024-01-26 21:57:58 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_2... 2024-01-26 21:57:58 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_3... 2024-01-26 21:57:58 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_5... 2024-01-26 21:57:59 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_6... 2024-01-26 21:57:59 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_7... 2024-01-26 21:57:59 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_8... 2024-01-26 21:57:59 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_9... 2024-01-26 21:57:59 [INFO] - Training LDA models for all matched features. 2024-01-26 21:57:59 [INFO] - #{+1} = 8776, #{-1} = 969, #{+2} = 12018, #{-2} = 981 2024-01-26 21:57:59 [INFO] - Standardized coefficients: 2024-01-26 21:57:59 [INFO] - log10(intensity): 0.6493842010317266 2024-01-26 21:57:59 [INFO] - log10(KL): -0.2296217745195752 2024-01-26 21:57:59 [INFO] - abs(ppm): -0.7050042313781828 2024-01-26 21:57:59 [INFO] - RT diff: -0.18019415692872864 2024-01-26 21:57:59 [INFO] - Fitting a mixture model... 2024-01-26 21:58:00 [INFO] - Matching-between-runs: 20230602_PHCOQEHF_PC1131-Emanuele_5... 2024-01-26 21:58:00 [INFO] - Calculating correlations between all other runs... 2024-01-26 21:58:00 [INFO] - Reading index from U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_5.quantindex 2024-01-26 21:58:02 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_1... 2024-01-26 21:58:02 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_2... 2024-01-26 21:58:02 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_3... 2024-01-26 21:58:02 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_4... 2024-01-26 21:58:02 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_6... 2024-01-26 21:58:02 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_7... 2024-01-26 21:58:02 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_8... 2024-01-26 21:58:03 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_9... 2024-01-26 21:58:03 [INFO] - Training LDA models for all matched features. 2024-01-26 21:58:03 [INFO] - #{+1} = 8180, #{-1} = 1025, #{+2} = 10752, #{-2} = 919 2024-01-26 21:58:03 [INFO] - Standardized coefficients: 2024-01-26 21:58:03 [INFO] - log10(intensity): 0.6895474558217216 2024-01-26 21:58:03 [INFO] - log10(KL): -0.28238537248250006 2024-01-26 21:58:03 [INFO] - abs(ppm): -0.6606264998902035 2024-01-26 21:58:03 [INFO] - RT diff: -0.09140806977794569 2024-01-26 21:58:03 [INFO] - Fitting a mixture model... 2024-01-26 21:58:03 [INFO] - Matching-between-runs: 20230602_PHCOQEHF_PC1131-Emanuele_6... 2024-01-26 21:58:03 [INFO] - Calculating correlations between all other runs... 2024-01-26 21:58:03 [INFO] - Reading index from U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_6.quantindex 2024-01-26 21:58:05 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_1... 2024-01-26 21:58:05 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_2... 2024-01-26 21:58:05 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_3... 2024-01-26 21:58:05 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_4... 2024-01-26 21:58:06 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_5... 2024-01-26 21:58:06 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_7... 2024-01-26 21:58:06 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_8... 2024-01-26 21:58:06 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_9... 2024-01-26 21:58:06 [INFO] - Training LDA models for all matched features. 2024-01-26 21:58:06 [INFO] - #{+1} = 9913, #{-1} = 1071, #{+2} = 11499, #{-2} = 908 2024-01-26 21:58:06 [INFO] - Standardized coefficients: 2024-01-26 21:58:06 [INFO] - log10(intensity): 0.675793462184857 2024-01-26 21:58:06 [INFO] - log10(KL): -0.1949043499585675 2024-01-26 21:58:06 [INFO] - abs(ppm): -0.6922256584722931 2024-01-26 21:58:06 [INFO] - RT diff: -0.18120969290874597 2024-01-26 21:58:06 [INFO] - Fitting a mixture model... 2024-01-26 21:58:07 [INFO] - Matching-between-runs: 20230602_PHCOQEHF_PC1131-Emanuele_7... 2024-01-26 21:58:07 [INFO] - Calculating correlations between all other runs... 2024-01-26 21:58:07 [INFO] - Reading index from U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_7.quantindex 2024-01-26 21:58:09 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_1... 2024-01-26 21:58:09 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_2... 2024-01-26 21:58:09 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_3... 2024-01-26 21:58:09 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_4... 2024-01-26 21:58:09 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_5... 2024-01-26 21:58:09 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_6... 2024-01-26 21:58:10 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_8... 2024-01-26 21:58:10 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_9... 2024-01-26 21:58:10 [INFO] - Training LDA models for all matched features. 2024-01-26 21:58:10 [INFO] - #{+1} = 9781, #{-1} = 1020, #{+2} = 10401, #{-2} = 876 2024-01-26 21:58:10 [INFO] - Standardized coefficients: 2024-01-26 21:58:10 [INFO] - log10(intensity): 0.7268730950366316 2024-01-26 21:58:10 [INFO] - log10(KL): -0.1335353489490534 2024-01-26 21:58:10 [INFO] - abs(ppm): -0.6256948449942954 2024-01-26 21:58:10 [INFO] - RT diff: -0.24965931835300548 2024-01-26 21:58:10 [INFO] - Fitting a mixture model... 2024-01-26 21:58:11 [INFO] - Matching-between-runs: 20230602_PHCOQEHF_PC1131-Emanuele_8... 2024-01-26 21:58:11 [INFO] - Calculating correlations between all other runs... 2024-01-26 21:58:11 [INFO] - Reading index from U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_8.quantindex 2024-01-26 21:58:12 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_1... 2024-01-26 21:58:12 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_2... 2024-01-26 21:58:13 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_3... 2024-01-26 21:58:13 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_4... 2024-01-26 21:58:13 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_5... 2024-01-26 21:58:13 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_6... 2024-01-26 21:58:13 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_7... 2024-01-26 21:58:13 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_9... 2024-01-26 21:58:14 [INFO] - Training LDA models for all matched features. 2024-01-26 21:58:14 [INFO] - #{+1} = 10456, #{-1} = 1066, #{+2} = 10588, #{-2} = 867 2024-01-26 21:58:14 [INFO] - Standardized coefficients: 2024-01-26 21:58:14 [INFO] - log10(intensity): 0.6673527001074568 2024-01-26 21:58:14 [INFO] - log10(KL): -0.14577220335355195 2024-01-26 21:58:14 [INFO] - abs(ppm): -0.7027677473643013 2024-01-26 21:58:14 [INFO] - RT diff: -0.22002889578542784 2024-01-26 21:58:14 [INFO] - Fitting a mixture model... 2024-01-26 21:58:14 [INFO] - Matching-between-runs: 20230602_PHCOQEHF_PC1131-Emanuele_9... 2024-01-26 21:58:14 [INFO] - Calculating correlations between all other runs... 2024-01-26 21:58:14 [INFO] - Reading index from U:\slyon\PC1131_APMS_raw\20230602_PHCOQEHF_PC1131-Emanuele_9.quantindex 2024-01-26 21:58:16 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_1... 2024-01-26 21:58:17 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_2... 2024-01-26 21:58:17 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_3... 2024-01-26 21:58:17 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_4... 2024-01-26 21:58:17 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_5... 2024-01-26 21:58:17 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_6... 2024-01-26 21:58:17 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_7... 2024-01-26 21:58:18 [INFO] - Transferring 20230602_PHCOQEHF_PC1131-Emanuele_8... 2024-01-26 21:58:18 [INFO] - Training LDA models for all matched features. 2024-01-26 21:58:18 [INFO] - #{+1} = 9514, #{-1} = 987, #{+2} = 8847, #{-2} = 743 2024-01-26 21:58:18 [INFO] - Standardized coefficients: 2024-01-26 21:58:18 [INFO] - log10(intensity): 0.7234519910843598 2024-01-26 21:58:18 [INFO] - log10(KL): -0.07156010279815743 2024-01-26 21:58:18 [INFO] - abs(ppm): -0.6747991342406675 2024-01-26 21:58:18 [INFO] - RT diff: -0.18201989792972154 2024-01-26 21:58:18 [INFO] - Fitting a mixture model... 2024-01-26 21:58:18 [INFO] - Estimating match-between-runs FDR... 2024-01-26 21:58:20 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.987000 2024-01-26 21:58:20 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100 2024-01-26 21:58:20 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100 2024-01-26 21:58:20 [INFO] - Updating Philosopher's tables... 2024-01-26 21:58:31 [INFO] - Combining experiments and estimating protein intensity... 2024-01-26 21:58:45 [INFO] - Done! Process 'IonQuant' finished, exit code: 0 Please cite: (Any searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017) (Any searches) Fast deisotoping algorithm and its implementation in the MSFragger search engine. J. Proteome Res. 20:498 (2021) (timsTOF PASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19:1575 (2020) (Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020) (Glyco search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125 (2020) (Labile search) MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics. Mol Cell Proteomics 22:100538 (2023) (MSBooster) MSBooster: improving peptide identification rates using deep learning-based features. Nat Commun. 14:4539 (2023) (PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923 (2007) (Protein inference with ProteinProphet)A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75:4646 (2003) (FDR filtering and reporting) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020) (Glycan identification and FDR control) Multiattribute glycan identification and FDR control for Glycoproteomics. Mol Cell Proteomics 21:100105 (2022) (Label-free/isotopic-labeling quantification) IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics 20:100077 (2021) (Visualization with FragPipe-PDV) PDV: an integrative proteomics data viewer. Bioinformatics. 35(7):1249 (2019) =============================================================ALL JOBS DONE IN 74.4 MINUTES=============================================================