System OS: Linux, Architecture: amd64 Java Info: 17.0.13-internal, OpenJDK 64-Bit Server VM, N/A .NET Core Info: N/A Version info: FragPipe version 22.0 MSFragger version 4.1 IonQuant version 1.10.27 diaTracer version 1.1.5 Philosopher version 5.1.1 LCMS files: Experiment/Group: CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d (if "spectral library generation" is enabled, all files will be analyzed together) - /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.d DDA Experiment/Group: CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d (if "spectral library generation" is enabled, all files will be analyzed together) - /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.d DDA Experiment/Group: CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d (if "spectral library generation" is enabled, all files will be analyzed together) - /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.d DDA Experiment/Group: CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d (if "spectral library generation" is enabled, all files will be analyzed together) - /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.d DDA Experiment/Group: CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d (if "spectral library generation" is enabled, all files will be analyzed together) - /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.d DDA Experiment/Group: CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d (if "spectral library generation" is enabled, all files will be analyzed together) - /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.d DDA 75 commands to execute: CheckCentroid java -Xmx180G -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/tools/batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.d 40 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/d163ab34-aa3d-4640-88c0-fedbb3723e09 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/c46f8d19-c554-47ad-bab8-35f9fea7884c WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/cbad8113-b068-46f7-9e79-e27f93a2c314 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/24a05531-96bb-43a5-af89-bdd04774c968 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/65ab2336-abc5-4ef6-be43-40086b935d21 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/f7b9b820-4da6-49ac-bf4f-bf73ea3a4b60 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/beb601ad-f839-4edf-97e6-79f000739e24 MSFragger [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] java -jar -Dfile.encoding=UTF-8 -Xmx180G /rd1/user/lit/project/sORFs/fragpipe_tools/tools/MSFragger-4.1/MSFragger-4.1.jar /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./fragger.params /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.d /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.d /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.d /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.d /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.d /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.d MSFragger move pepxml java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pepXML /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pepXML MSFragger move pin java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pin MSFragger move pepxml java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pepXML /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pepXML MSFragger move pin java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pin MSFragger move pepxml java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pepXML /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pepXML MSFragger move pin java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pin MSFragger move pepxml java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pepXML /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pepXML MSFragger move pin java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pin MSFragger move pepxml java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pepXML /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pepXML MSFragger move pin java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pin MSFragger move pepxml java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pepXML /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pepXML MSFragger move pin java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pin MSBooster [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] java -Djava.awt.headless=true -Xmx180G -cp /rd1/user/lit/software/fragpipe/tools/MSBooster-1.2.31.jar:/rd1/user/lit/software/fragpipe/tools/batmass-io-1.33.4.jar Features.MainClass --paramsList /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./msbooster_params.txt Percolator [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_edited.pin Percolator [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_edited.pin Percolator [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_edited.pin Percolator [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_edited.pin Percolator [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_edited.pin Percolator [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_edited.pin Percolator: Convert to pepxml [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] java -cp /rd1/user/lit/software/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pin CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552 CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_target_psms.tsv CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_decoy_psms.tsv interact-CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552 DDA 0.5 /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_uncalibrated.mzML Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_target_psms.tsv Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] java -cp /rd1/user/lit/software/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pin CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559 CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_target_psms.tsv CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_decoy_psms.tsv interact-CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559 DDA 0.5 /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_uncalibrated.mzML Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_target_psms.tsv Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] java -cp /rd1/user/lit/software/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pin CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557 CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_target_psms.tsv CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_decoy_psms.tsv interact-CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557 DDA 0.5 /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_uncalibrated.mzML Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_target_psms.tsv Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] java -cp /rd1/user/lit/software/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pin CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564 CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_target_psms.tsv CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_decoy_psms.tsv interact-CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564 DDA 0.5 /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_uncalibrated.mzML Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_target_psms.tsv Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] java -cp /rd1/user/lit/software/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pin CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554 CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_target_psms.tsv CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_decoy_psms.tsv interact-CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554 DDA 0.5 /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_uncalibrated.mzML Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_target_psms.tsv Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] java -cp /rd1/user/lit/software/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pin CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562 CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_target_psms.tsv CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_decoy_psms.tsv interact-CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562 DDA 0.5 /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_uncalibrated.mzML Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_target_psms.tsv Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_decoy_psms.tsv ProteinProphet [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 proteinprophet --maxppmdiff 2000000 --output combined /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 database --annotate /rd1/user/lit/project/sORFs/custom_database/2024-11-06-decoys-contam-uniprotkb_Mus_musculus_reviewed_canonical_isoform_2024_10_25.nonCano.sorf.filtered.fa.fas --prefix rev_ PhilosopherFilter [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --sequential --prot 1 --picked --tag rev_ --pepxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --protxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./combined.prot.xml --razor PhilosopherFilter [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --sequential --prot 1 --picked --tag rev_ --pepxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d --dbbin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --protxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./combined.prot.xml --probin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --razor PhilosopherFilter [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --sequential --prot 1 --picked --tag rev_ --pepxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d --dbbin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --protxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./combined.prot.xml --probin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --razor PhilosopherFilter [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --sequential --prot 1 --picked --tag rev_ --pepxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d --dbbin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --protxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./combined.prot.xml --probin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --razor PhilosopherFilter [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --sequential --prot 1 --picked --tag rev_ --pepxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d --dbbin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --protxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./combined.prot.xml --probin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --razor PhilosopherFilter [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --sequential --prot 1 --picked --tag rev_ --pepxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d --dbbin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --protxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./combined.prot.xml --probin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --razor PhilosopherReport [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 report PhilosopherReport [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 report PhilosopherReport [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 report PhilosopherReport [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 report PhilosopherReport [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 report PhilosopherReport [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 report WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck IonQuant [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] java -Djava.awt.headless=true -Xmx180G -Dlibs.bruker.dir=/rd1/user/lit/project/sORFs/fragpipe_tools/tools/MSFragger-4.1/ext/bruker -Dlibs.thermo.dir=/rd1/user/lit/project/sORFs/fragpipe_tools/tools/MSFragger-4.1/ext/thermo -cp /rd1/user/lit/software/fragpipe/tools/jfreechart-1.5.3.jar:/rd1/user/lit/software/fragpipe/tools/batmass-io-1.33.4.jar:/rd1/user/lit/project/sORFs/fragpipe_tools/tools/IonQuant-1.10.27.jar ionquant.IonQuant --threads 40 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 1 --site-reports 1 --msstats 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 /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./filelist_ionquant.txt --modlist /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./modmasses_ionquant.txt ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] Cmd: [CheckCentroid], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] Cmd: [WorkspaceCleanInit], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] Cmd: [WorkspaceCleanInit], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] Cmd: [WorkspaceCleanInit], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] Cmd: [WorkspaceCleanInit], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] Cmd: [WorkspaceCleanInit], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] Cmd: [WorkspaceCleanInit], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] Cmd: [WorkspaceCleanInit], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] Cmd: [MSFragger], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] Cmd: [MSBooster], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] Cmd: [Percolator], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] Cmd: [ProteinProphet], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] Cmd: [PhilosopherDbAnnotate], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] Cmd: [PhilosopherFilter], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] Cmd: [PhilosopherReport], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] Cmd: [WorkspaceClean], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] Cmd: [WorkspaceClean], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] Cmd: [WorkspaceClean], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] Cmd: [WorkspaceClean], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] Cmd: [WorkspaceClean], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] Cmd: [WorkspaceClean], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] Cmd: [WorkspaceClean], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] Cmd: [IonQuant], Work dir: [/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of /rd1/user/lit/project/sORFs/custom_database/2024-11-06-decoys-contam-uniprotkb_Mus_musculus_reviewed_canonical_isoform_2024_10_25.nonCano.sorf.filtered.fa.fas~~~~~~~ >ENSMUST00000000033.12-chr7:142206195-142206339 >ENSMUST00000059794.4-chr1:171881462-171881861 >ENSMUST00000122070.2-chr2:164854867-164854981 >ENSMUST00000139992.2-chr6:39782300-39782429 >ENSMUST00000160667.8-chr13:74485644-74487807 >ENSMUST00000196850.2+chr3:34730097-34730268 >ENSMUST00000227533.2-chr15:77016990-77017062 >rev_ENSMUST00000037127.15+chr4:117439827-117439881 >rev_ENSMUST00000106008.3-chr7:140988192-140988591 >rev_ENSMUST00000133421.2+chr2:30233491-30233890 >rev_ENSMUST00000151186.8-chr6:25794584-25800307 >rev_ENSMUST00000182075.8+chr15:62130339-62130426 >rev_ENSMUST00000215155.2-chr9:114469187-114469238 >rev_sp|O09051|GUC2B_MOUSE Guanylate cyclase activator 2B OS=Mus musculus OX=10090 GN=Guca2b PE=1 SV=2 >rev_sp|Q3UW31-2|PATE2_MOUSE Isoform 2 of Prostate and testis expressed protein 2 OS=Mus musculus OX=10090 GN=Pate2 >rev_sp|Q8C078|KKCC2_MOUSE Calcium/calmodulin-dependent protein kinase kinase 2 OS=Mus musculus OX=10090 GN=Camkk2 PE=1 SV=2 >rev_sp|Q9DCC3|CC107_MOUSE Coiled-coil domain-containing protein 107 OS=Mus musculus OX=10090 GN=Ccdc107 PE=2 SV=1 >sp|P29595|NEDD8_MOUSE NEDD8 OS=Mus musculus OX=10090 GN=Nedd8 PE=1 SV=2 >sp|Q6IEE6|T132E_MOUSE Transmembrane protein 132E OS=Mus musculus OX=10090 GN=Tmem132e PE=1 SV=2 >sp|Q8VCP8|KAD6_MOUSE Adenylate kinase isoenzyme 6 OS=Mus musculus OX=10090 GN=Ak6 PE=1 SV=1 >sp|Q9Z351|KCNQ2_MOUSE Potassium voltage-gated channel subfamily KQT member 2 OS=Mus musculus OX=10090 GN=Kcnq2 PE=1 SV=1 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v22.0ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=/rd1/user/lit/project/sORFs/custom_database/2024-11-06-decoys-contam-uniprotkb_Mus_musculus_reviewed_canonical_isoform_2024_10_25.nonCano.sorf.filtered.fa.fas crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.medium= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=QuantUMS (high accuracy) diann.run-dia-nn=false diann.run-dia-plex=false diann.run-specific-protein-q-value=false diann.unrelated-runs=false diann.use-predicted-spectra=false diatracer.corr-threshold=0.3 diatracer.delta-apex-im=0.01 diatracer.delta-apex-rt=3 diatracer.mass-defect-filter=true diatracer.mass-defect-offset=0.1 diatracer.rf-max=500 diatracer.run-diatracer=false diatracer.write-intermediate-files=false 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=/rd1/user/lit/software/fragpipe/tools/diann/1.8.2_beta_8/linux/diann-1.8.1.8 fragpipe-config.bin-python=/home/lit/rd1/anaconda3/envs/py3/bin/python fragpipe-config.tools-folder=/rd1/user/lit/project/sORFs/fragpipe_tools 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.find-best-rt-model=false msbooster.find-best-spectra-model=false msbooster.koina-url= msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.rt-model=DIA-NN msbooster.run-msbooster=true msbooster.spectra-model=DIA-NN msfragger.Y_type_masses= msfragger.activation_types=all msfragger.allowed_missed_cleavage_1=2 msfragger.allowed_missed_cleavage_2=2 msfragger.analyzer_types=all 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=6 msfragger.fragment_ion_series=b,y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.group_variable=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.mass_offsets_detailed= msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.01 msfragger.misc.fragger.clear-mz-hi=0 msfragger.misc.fragger.clear-mz-lo=0 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=500 msfragger.misc.fragger.enzyme-dropdown-1=trypsin msfragger.misc.fragger.enzyme-dropdown-2=lysc msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=2 msfragger.output_format=pepXML_pin msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.output_report_topN_dda_plus=5 msfragger.output_report_topN_dia1=5 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2=K msfragger.search_enzyme_name_1=trypsin msfragger.search_enzyme_name_2=lysc msfragger.search_enzyme_nocut_1=P msfragger.search_enzyme_nocut_2=P msfragger.search_enzyme_sense_1=C msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 msfragger.track_zero_topN=0 msfragger.use_all_mods_in_first_search=false msfragger.use_detailed_offsets=false msfragger.use_topN_peaks=150 msfragger.write_calibrated_mzml=false msfragger.write_uncalibrated_mgf=false msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 opair.activation1=HCD opair.activation2=ETD opair.filterOxonium=true opair.glyco_db= opair.max_glycans=4 opair.max_isotope_error=2 opair.min_isotope_error=0 opair.ms1_tol=20 opair.ms2_tol=20 opair.oxonium_filtering_file= opair.oxonium_minimum_intensity=0.05 opair.reverse_scan_order=false opair.run-opair=false opair.single_scan_type=false peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore peptide-prophet.combine-pepxml=false peptide-prophet.run-peptide-prophet=false percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc percolator.keep-tsv-files=false percolator.min-prob=0.5 percolator.run-percolator=true phi-report.dont-use-prot-proph-file=false phi-report.filter=--sequential --prot 1 --picked phi-report.pep-level-summary=false phi-report.print-decoys=false phi-report.prot-level-summary=false phi-report.remove-contaminants=false phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 protein-prophet.run-protein-prophet=true ptmprophet.cmdline=NOSTACK KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5 ptmprophet.run-ptmprophet=false ptmshepherd.adv_params=false ptmshepherd.annotation-common=false ptmshepherd.annotation-custom=false ptmshepherd.annotation-glyco=false ptmshepherd.annotation-unimod=true ptmshepherd.annotation_file= ptmshepherd.annotation_tol=0.01 ptmshepherd.cap_y_ions= ptmshepherd.decoy_type=1 ptmshepherd.diag_ions= ptmshepherd.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=00.2 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=00.1 ptmshepherd.diagmine_fragMinSpecDiff=00.1 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=00.2 ptmshepherd.glyco_fdr=1.00 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_ppm_tol=50 ptmshepherd.glycodatabase= ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=false ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=false ptmshepherd.iterloc_maxEpoch=100 ptmshepherd.iterloc_mode=false ptmshepherd.localization_allowed_res= 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.print_full_glyco_params=false ptmshepherd.prob_mass=0.5 ptmshepherd.remainder_masses= ptmshepherd.remove_glycan_delta_mass=true ptmshepherd.run-shepherd=false ptmshepherd.run_diagextract_mode=false ptmshepherd.run_diagmine_mode=false ptmshepherd.run_glyco_mode=false ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses= quantitation.run-label-free-quant=true run-psm-validation=true run-validation-tab=true saintexpress.fragpipe.cmd-opts= saintexpress.max-replicates=10 saintexpress.run-saint-express=false saintexpress.virtual-controls=100 skyline.run-skyline=false skyline.skyline=true skyline.skyline-custom=false skyline.skyline-custom-path= skyline.skyline-daily=false skyline.skyline-mode=0 skyline.skyline-mods-mode=Default speclibgen.convert-pepxml=true speclibgen.convert-psm=false speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.max_glycan_qval=1 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.ignore_unannotated=false speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.labile_mode=Regular (not glyco) speclibgen.easypqp.neutral_loss=false speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=false tab-run.delete_calibrated_mzml=false tab-run.delete_temp_files=false tab-run.sub_mzml_prob_threshold=0.5 tab-run.write_sub_mzml=false tmtintegrator.add_Ref=-1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=true tmtintegrator.best_psm=true tmtintegrator.channel_num=TMT-6 tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=-1 tmtintegrator.groupby=0 tmtintegrator.log2transformed=true tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.philosopher-msstats=false 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=/rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/. workflow.input.data-type.im-ms=true workflow.input.data-type.regular-ms=false workflow.misc.save-sdrf=true workflow.ram=180 workflow.threads=40 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid java -Xmx180G -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/tools/batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.d 40 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="11:51:13" level=info msg="Executing Workspace v5.1.1" time="11:51:13" level=info msg="Removing workspace" time="11:51:13" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/d163ab34-aa3d-4640-88c0-fedbb3723e09 time="11:51:14" level=info msg="Executing Workspace v5.1.1" time="11:51:14" level=info msg="Creating workspace" time="11:51:14" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="11:51:14" level=info msg="Executing Workspace v5.1.1" time="11:51:14" level=info msg="Removing workspace" time="11:51:14" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/c46f8d19-c554-47ad-bab8-35f9fea7884c time="11:51:14" level=info msg="Executing Workspace v5.1.1" time="11:51:14" level=info msg="Creating workspace" time="11:51:14" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="11:51:14" level=info msg="Executing Workspace v5.1.1" time="11:51:14" level=info msg="Removing workspace" time="11:51:14" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/cbad8113-b068-46f7-9e79-e27f93a2c314 time="11:51:14" level=info msg="Executing Workspace v5.1.1" time="11:51:14" level=info msg="Creating workspace" time="11:51:14" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="11:51:15" level=info msg="Executing Workspace v5.1.1" time="11:51:15" level=info msg="Removing workspace" time="11:51:15" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/24a05531-96bb-43a5-af89-bdd04774c968 time="11:51:15" level=info msg="Executing Workspace v5.1.1" time="11:51:15" level=info msg="Creating workspace" time="11:51:15" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="11:51:15" level=info msg="Executing Workspace v5.1.1" time="11:51:15" level=info msg="Removing workspace" time="11:51:15" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/65ab2336-abc5-4ef6-be43-40086b935d21 time="11:51:15" level=info msg="Executing Workspace v5.1.1" time="11:51:15" level=info msg="Creating workspace" time="11:51:15" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="11:51:15" level=info msg="Executing Workspace v5.1.1" time="11:51:15" level=info msg="Removing workspace" time="11:51:15" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/f7b9b820-4da6-49ac-bf4f-bf73ea3a4b60 time="11:51:16" level=info msg="Executing Workspace v5.1.1" time="11:51:16" level=info msg="Creating workspace" time="11:51:16" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="11:51:16" level=info msg="Executing Workspace v5.1.1" time="11:51:16" level=info msg="Removing workspace" time="11:51:16" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/beb601ad-f839-4edf-97e6-79f000739e24 time="11:51:16" level=info msg="Executing Workspace v5.1.1" time="11:51:16" level=info msg="Creating workspace" time="11:51:16" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] java -jar -Dfile.encoding=UTF-8 -Xmx180G /rd1/user/lit/project/sORFs/fragpipe_tools/tools/MSFragger-4.1/MSFragger-4.1.jar /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./fragger.params /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.d /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.d /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.d /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.d /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.d /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.d MSFragger version MSFragger-4.1 Batmass-IO version 1.33.4 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: Linux, Architecture: amd64 Java Info: 17.0.13-internal, OpenJDK 64-Bit Server VM, Oracle Corporation JVM started with 180 GB memory Checking database... Checking spectral files... /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.d: Scans = 30270; ITMS: false; FTMS: false; Isolation sizes = [] /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.d: Scans = 30715; ITMS: false; FTMS: false; Isolation sizes = [] /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.d: Scans = 30531; ITMS: false; FTMS: false; Isolation sizes = [] /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.d: Scans = 30357; ITMS: false; FTMS: false; Isolation sizes = [] /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.d: Scans = 30525; ITMS: false; FTMS: false; Isolation sizes = [] /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.d: Scans = 30704; ITMS: false; FTMS: false; Isolation sizes = [] There is a mzBIN file from /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.d converted with timsdata-2-21-0-4. Will use this mzBIN file. There is a mzBIN file from /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.d converted with timsdata-2-21-0-4. Will use this mzBIN file. There is a mzBIN file from /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.d converted with timsdata-2-21-0-4. Will use this mzBIN file. There is a mzBIN file from /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.d converted with timsdata-2-21-0-4. Will use this mzBIN file. There is a mzBIN file from /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.d converted with timsdata-2-21-0-4. Will use this mzBIN file. There is a mzBIN file from /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.d converted with timsdata-2-21-0-4. Will use this mzBIN file. ***********************************FIRST SEARCH************************************ Parameters: num_threads = 40 database_name = /rd1/user/lit/project/sORFs/custom_database/2024-11-06-decoys-contam-uniprotkb_Mus_musculus_reviewed_canonical_isoform_2024_10_25.nonCano.sorf.filtered.fa.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 = nonspecific search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = P allowed_missed_cleavage_1 = 2 search_enzyme_sense_2 = C search_enzyme_cut_2 = K search_enzyme_nocut_2 = P allowed_missed_cleavage_2 = 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 = 6 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 analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.10 Da. 358409658 fragments to be searched in 1 slices (5.34 GB total) Operating on slice 1 of 1: Fragment index slice generated in 3.76 s 001. CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.mzBIN 32.2 s | deisotoping 3.5 s [progress: 176271/176271 (100%) - 23721 spectra/s] 7.4s | postprocessing 0.9 s 002. CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.mzBIN 30.8 s | deisotoping 2.8 s [progress: 174642/174642 (100%) - 52210 spectra/s] 3.3s | postprocessing 0.7 s 003. CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.mzBIN 31.0 s | deisotoping 2.8 s [progress: 175512/175512 (100%) - 52314 spectra/s] 3.4s | postprocessing 0.7 s 004. CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.mzBIN 31.1 s | deisotoping 3.0 s [progress: 175353/175353 (100%) - 52548 spectra/s] 3.3s | postprocessing 0.9 s 005. CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.mzBIN 29.0 s | deisotoping 2.7 s [progress: 172513/172513 (100%) - 52213 spectra/s] 3.3s | postprocessing 1.1 s 006. CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.mzBIN 29.1 s | deisotoping 2.7 s [progress: 170233/170233 (100%) - 54808 spectra/s] 3.1s | postprocessing 1.2 s ***************************FIRST SEARCH DONE IN 4.051 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | 1.81 2.82 | 0.15 2.32 | -0.38 4.67 | -0.03 4.65 002 | 1.77 2.98 | 0.16 2.39 | -0.42 4.68 | -0.05 4.64 003 | 1.93 3.03 | 0.15 2.36 | -0.24 4.74 | -0.03 4.70 004 | 1.43 3.01 | 0.13 2.38 | -0.76 4.73 | -0.07 4.69 005 | 1.96 2.91 | 0.17 2.39 | -0.34 4.66 | -0.02 4.63 006 | 1.65 2.87 | 0.12 2.37 | -0.60 4.64 | -0.05 4.62 -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|-------|-------|------- MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 -------|-------|-------|-------|-------|-------|-------|-------|------- Count | skip | skip | 73114| 74268| 74425| 73964| skip rest -------|-------|-------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 -------|-------|-------|-------|-------|-------|------- Count | 75043| 74911| skip rest -------|-------|-------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 75057 -------|------- -------|------- Rm P. | 0 -------|------- Count | 74466 -------|------- New fragment_mass_tolerance = 20.000000 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 2.846 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 40 database_name = /rd1/user/lit/project/sORFs/custom_database/2024-11-06-decoys-contam-uniprotkb_Mus_musculus_reviewed_canonical_isoform_2024_10_25.nonCano.sorf.filtered.fa.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 = 0/1/2 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 = nonspecific search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = P allowed_missed_cleavage_1 = 2 search_enzyme_sense_2 = C search_enzyme_cut_2 = K search_enzyme_nocut_2 = P allowed_missed_cleavage_2 = 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 = 6 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 analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.10 Da. 358409658 fragments to be searched in 1 slices (5.34 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.26 s 001. CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.mzBIN_calibrated 2.8 s [progress: 176271/176271 (100%) - 29354 spectra/s] 6.0s | remapping alternative proteins and postprocessing 18.1 s 002. CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.mzBIN_calibrated 2.1 s [progress: 174642/174642 (100%) - 29083 spectra/s] 6.0s | remapping alternative proteins and postprocessing 15.0 s 003. CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.mzBIN_calibrated 2.0 s [progress: 175512/175512 (100%) - 29713 spectra/s] 5.9s | remapping alternative proteins and postprocessing 15.2 s 004. CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.mzBIN_calibrated 2.0 s [progress: 175353/175353 (100%) - 29676 spectra/s] 5.9s | remapping alternative proteins and postprocessing 15.6 s 005. CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.mzBIN_calibrated 1.9 s [progress: 172513/172513 (100%) - 29961 spectra/s] 5.8s | remapping alternative proteins and postprocessing 14.2 s 006. CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.mzBIN_calibrated 2.1 s [progress: 170233/170233 (100%) - 30923 spectra/s] 5.5s | remapping alternative proteins and postprocessing 13.3 s ***************************MAIN SEARCH DONE IN 2.462 MIN*************************** *******************************TOTAL TIME 9.359 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pepXML /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pepXML /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pepXML /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pepXML /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pepXML /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pepXML /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar:/rd1/user/lit/software/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] java -Djava.awt.headless=true -Xmx180G -cp /rd1/user/lit/software/fragpipe/tools/MSBooster-1.2.31.jar:/rd1/user/lit/software/fragpipe/tools/batmass-io-1.33.4.jar Features.MainClass --paramsList /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./msbooster_params.txt 2024-11-18 12:00:45 [INFO] - MSBooster v1.2.31 2024-11-18 12:00:45 [INFO] - Using 40 threads 2024-11-18 12:00:45 [INFO] - Initializing /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_uncalibrated.mzML 2024-11-18 12:00:49 [INFO] - Instrument detected: timsTOF 2024-11-18 12:00:49 [INFO] - Initializing /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_uncalibrated.mzML 2024-11-18 12:00:51 [INFO] - Initializing /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_uncalibrated.mzML 2024-11-18 12:00:53 [INFO] - Initializing /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_uncalibrated.mzML 2024-11-18 12:00:55 [INFO] - Initializing /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_uncalibrated.mzML 2024-11-18 12:00:58 [INFO] - Initializing /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_uncalibrated.mzML 2024-11-18 12:01:00 [INFO] - No fragmentation type detected. Setting fragmentation type to HCD. You can specify this with '--FragmentationType' via the command line or 'FragmentationType=' in the param file. 2024-11-18 12:01:00 [INFO] - No NCE detected. Setting NCE to 25. You can specify this with '--NCE' via the command line or 'NCE=' in the param file. 2024-11-18 12:01:00 [INFO] - Creating input file for createFull 2024-11-18 12:01:02 [INFO] - 453542 PSMs for prediction 2024-11-18 12:01:02 [INFO] - createFull input file generation took 1846 milliseconds 2024-11-18 12:01:02 [INFO] - Input file at /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/spectraRT_full.tsv 2024-11-18 12:01:02 [INFO] - Generating input file for DIA-NN 2024-11-18 12:01:02 [INFO] - Creating input file for Diann 2024-11-18 12:01:03 [INFO] - 453542 PSMs for prediction 2024-11-18 12:01:03 [INFO] - Writing DIA-NN input file 2024-11-18 12:01:03 [INFO] - Diann input file generation took 1204 milliseconds 2024-11-18 12:01:03 [INFO] - Input file at /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/spectraRT.tsv 2024-11-18 12:01:03 [INFO] - Generating DIA-NN predictions 2024-11-18 12:01:03 [INFO] - /rd1/user/lit/software/fragpipe/tools/diann/1.8.2_beta_8/linux/diann-1.8.1.8 --lib /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/spectraRT.tsv --predict --threads 40 --strip-unknown-mods --predict-n-frag 100 2024-11-18 12:01:03 [INFO] - DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks) 2024-11-18 12:01:03 [INFO] - Compiled on Dec 1 2022 14:47:06 2024-11-18 12:01:03 [INFO] - Current date and time: Mon Nov 18 12:01:03 2024 2024-11-18 12:01:03 [INFO] - Logical CPU cores: 48 2024-11-18 12:01:03 [INFO] - Predicted spectra will be saved in a binary format 2024-11-18 12:01:03 [INFO] - Thread number set to 40 2024-11-18 12:01:03 [INFO] - 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 2024-11-18 12:01:03 [INFO] - Deep learning predictor will predict 100 fragments 2024-11-18 12:01:03 [INFO] - 2024-11-18 12:01:03 [INFO] - 0 files will be processed 2024-11-18 12:01:03 [INFO] - [0:00] Loading spectral library /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/spectraRT.tsv 2024-11-18 12:01:06 [INFO] - [0:02] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) 2024-11-18 12:01:06 [INFO] - [0:03] Spectral library loaded: 0 protein isoforms, 0 protein groups and 453542 precursors in 420337 elution groups. 2024-11-18 12:01:10 [INFO] - [0:06] Encoding peptides for spectra and RTs prediction 2024-11-18 12:01:11 [INFO] - [0:07] Predicting spectra and IMs 2024-11-18 12:01:52 [INFO] - [0:48] Predicting RTs 2024-11-18 12:02:02 [INFO] - [0:58] Decoding predicted spectra and IMs 2024-11-18 12:02:29 [INFO] - [1:25] Decoding RTs 2024-11-18 12:02:29 [INFO] - [1:25] Saving the list of predictions to /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/spectraRT.predicted.bin 2024-11-18 12:02:31 [INFO] - Finished 2024-11-18 12:02:32 [INFO] - Done generating DIA-NN predictions 2024-11-18 12:02:32 [INFO] - Model running took 88561 milliseconds 2024-11-18 12:02:32 [INFO] - Generating edited pin with following features: [predRTrealUnits, unweightedSpectralEntropy, deltaRTLOESS] 2024-11-18 12:02:32 [INFO] - Loading predicted library 2024-11-18 12:02:42 [INFO] - Processing pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pin 2024-11-18 12:02:43 [INFO] - /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pin has 156697 PSMs 2024-11-18 12:02:43 [INFO] - Processing /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_uncalibrated.mzML ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:02:59 [INFO] - RT regression using 5000 PSMs Iteration 1...2...3...4...5... 2024-11-18 12:03:06 [INFO] - Best average bandwidth for mass from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.034 2024-11-18 12:03:10 [INFO] - Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:03:12 [INFO] - Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:03:14 [INFO] - Edited pin file at /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_edited.pin 2024-11-18 12:03:15 [INFO] - Processing pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pin 2024-11-18 12:03:16 [INFO] - /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pin has 154792 PSMs 2024-11-18 12:03:16 [INFO] - Processing /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_uncalibrated.mzML ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:03:32 [INFO] - RT regression using 5000 PSMs Iteration 1...2...3...4...5... 2024-11-18 12:03:37 [INFO] - Best average bandwidth for mass from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.026 2024-11-18 12:03:41 [INFO] - Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:03:44 [INFO] - Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:03:46 [INFO] - Edited pin file at /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_edited.pin 2024-11-18 12:03:47 [INFO] - Processing pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pin 2024-11-18 12:03:47 [INFO] - /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pin has 155573 PSMs 2024-11-18 12:03:47 [INFO] - Processing /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_uncalibrated.mzML ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:04:05 [INFO] - RT regression using 5000 PSMs Iteration 1...2...3...4...5... 2024-11-18 12:04:10 [INFO] - Best average bandwidth for mass from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.034 2024-11-18 12:04:12 [INFO] - Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:04:17 [INFO] - Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:04:19 [INFO] - Edited pin file at /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_edited.pin 2024-11-18 12:04:20 [INFO] - Processing pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pin 2024-11-18 12:04:20 [INFO] - /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pin has 155222 PSMs 2024-11-18 12:04:20 [INFO] - Processing /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_uncalibrated.mzML ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:04:40 [INFO] - RT regression using 5000 PSMs Iteration 1...2...3...4...5... 2024-11-18 12:04:46 [INFO] - Best average bandwidth for mass from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.018 2024-11-18 12:04:48 [INFO] - Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:04:53 [INFO] - Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:04:56 [INFO] - Edited pin file at /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_edited.pin 2024-11-18 12:04:56 [INFO] - Processing pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pin 2024-11-18 12:04:57 [INFO] - /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pin has 150618 PSMs 2024-11-18 12:04:57 [INFO] - Processing /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_uncalibrated.mzML ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:05:17 [INFO] - RT regression using 5000 PSMs Iteration 1...2...3...4...5... 2024-11-18 12:05:22 [INFO] - Best average bandwidth for mass from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.034 2024-11-18 12:05:25 [INFO] - Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:05:28 [INFO] - Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:05:31 [INFO] - Edited pin file at /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_edited.pin 2024-11-18 12:05:31 [INFO] - Processing pin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pin 2024-11-18 12:05:32 [INFO] - /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pin has 148399 PSMs 2024-11-18 12:05:32 [INFO] - Processing /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_uncalibrated.mzML ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:05:49 [INFO] - RT regression using 5000 PSMs Iteration 1...2...3...4...5... 2024-11-18 12:05:54 [INFO] - Best average bandwidth for mass from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.026 2024-11-18 12:05:56 [INFO] - Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:06:00 [INFO] - Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-11-18 12:06:02 [INFO] - Edited pin file at /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_edited.pin 2024-11-18 12:06:03 [INFO] - Feature calculation, edited pin writing, and QC plot generation done in 211328 ms Process 'MSBooster' finished, exit code: 0 Percolator [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_edited.pin Percolator version 3.06.5, Build Date Feb 8 2024 10:00:35 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: /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_edited.pin Started Mon Nov 18 12:06:07 2024 on galaxy Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_edited.pin Features: rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more 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 pred_RT_real_units unweighted_spectral_entropy delta_RT_loess Found 155573 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 116203 positives and 39370 negatives, size ratio=2.95156 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 8 as initial direction. Could separate 46563 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 46803 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 46751 training set positives with q<0.01 in that direction. Found 70047 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 35.1200 cpu seconds or 2 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 75085 PSMs with q<0.01 Iteration 2: Estimated 75588 PSMs with q<0.01 Iteration 3: Estimated 75656 PSMs with q<0.01 Iteration 4: Estimated 75672 PSMs with q<0.01 Iteration 5: Estimated 75660 PSMs with q<0.01 Iteration 6: Estimated 75649 PSMs with q<0.01 Iteration 7: Estimated 75644 PSMs with q<0.01 Iteration 8: Estimated 75650 PSMs with q<0.01 Iteration 9: Estimated 75655 PSMs with q<0.01 Iteration 10: Estimated 75656 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 -0.2774 -0.2858 -0.2628 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0675 0.0446 0.0568 isotope_error_0 0.0333 0.0509 0.0397 isotope_error_1 -0.1273 -0.1163 -0.1201 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -2.3712 -2.2301 -2.3037 log10_evalue 1.7259 1.7040 1.2904 hyperscore 1.2182 1.1531 1.1818 delta_hyperscore -0.6161 -0.1098 0.0069 matched_ion_num -1.1376 -1.3866 -1.2770 complementary_ions -0.5271 -0.7009 -0.4608 ion_series -0.3032 -0.2801 -0.3002 weighted_average_abs_fragment_ppm -0.1271 -0.1046 -0.1297 length_7 -0.0841 -0.0672 -0.0902 length_8 -0.0119 -0.0208 -0.0281 length_9_30 0.1281 0.1177 0.1530 length_31 0.0000 0.0000 0.0000 ntt 0.0398 0.0253 0.0177 nmc 0.0210 0.0122 0.0122 charge_1 0.0936 0.0935 0.1084 charge_2 0.0196 0.0414 0.0307 charge_3 -0.0893 -0.1149 -0.1250 charge_4 -0.1827 -0.1942 -0.1899 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.2840 -0.2216 -0.2712 15.9949M 0.1970 0.1476 0.1971 pred_RT_real_units 1.5151 1.5357 1.4842 unweighted_spectral_entropy -0.7894 -0.7269 -0.7761 delta_RT_loess 1.3174 1.2769 1.3366 m0 Found 75587 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 116203 target PSMs and 39370 decoy PSMs. Calculating q values. Final list yields 75587 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 172.1800 cpu seconds or 15 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_edited.pin Percolator version 3.06.5, Build Date Feb 8 2024 10:00:35 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: /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_edited.pin Started Mon Nov 18 12:06:25 2024 on galaxy Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_edited.pin Features: rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more 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 pred_RT_real_units unweighted_spectral_entropy delta_RT_loess Found 148399 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 111934 positives and 36465 negatives, size ratio=3.06963 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 8 as initial direction. Could separate 47441 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 47226 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 47059 training set positives with q<0.01 in that direction. Found 70863 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 34.4800 cpu seconds or 2 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 74464 PSMs with q<0.01 Iteration 2: Estimated 74780 PSMs with q<0.01 Iteration 3: Estimated 74840 PSMs with q<0.01 Iteration 4: Estimated 74868 PSMs with q<0.01 Iteration 5: Estimated 74884 PSMs with q<0.01 Iteration 6: Estimated 74881 PSMs with q<0.01 Iteration 7: Estimated 74877 PSMs with q<0.01 Iteration 8: Estimated 74887 PSMs with q<0.01 Iteration 9: Estimated 74886 PSMs with q<0.01 Iteration 10: Estimated 74884 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 -0.2105 -0.2514 -0.2544 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0556 0.0596 0.0569 isotope_error_0 0.0146 0.0232 0.0456 isotope_error_1 -0.0911 -0.1061 -0.1273 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -1.9633 -1.8469 -1.9848 log10_evalue 1.4577 1.3017 2.3293 hyperscore 1.1115 1.2369 1.2722 delta_hyperscore -0.0586 0.0312 -0.2812 matched_ion_num -1.1089 -1.0941 -1.3892 complementary_ions -0.3620 -0.2001 -0.4331 ion_series -0.1772 -0.1979 -0.2059 weighted_average_abs_fragment_ppm -0.1097 -0.1304 -0.1079 length_7 -0.0755 -0.1030 -0.0978 length_8 -0.0327 -0.0109 -0.0398 length_9_30 0.1362 0.1357 0.1569 length_31 0.0000 0.0000 0.0000 ntt -0.0982 -0.1033 -0.1158 nmc -0.0031 0.0068 -0.0124 charge_1 0.0710 0.0644 0.0608 charge_2 0.0365 0.0216 0.0394 charge_3 -0.0927 -0.0833 -0.0672 charge_4 -0.1576 -0.1119 -0.1815 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.2196 -0.2320 -0.2239 15.9949M 0.1457 0.1608 0.1467 pred_RT_real_units 1.2645 1.3679 1.5120 unweighted_spectral_entropy -0.5856 -0.5963 -0.6212 delta_RT_loess 1.2269 1.6140 1.7979 m0 Found 74819 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 111934 target PSMs and 36465 decoy PSMs. Calculating q values. Final list yields 74829 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 169.5000 cpu seconds or 14 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_edited.pin Percolator version 3.06.5, Build Date Feb 8 2024 10:00:35 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: /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_edited.pin Started Mon Nov 18 12:06:42 2024 on galaxy Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_edited.pin Features: rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more 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 pred_RT_real_units unweighted_spectral_entropy delta_RT_loess Found 150618 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 112929 positives and 37689 negatives, size ratio=2.99634 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 8 as initial direction. Could separate 46722 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 46525 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 46826 training set positives with q<0.01 in that direction. Found 70035 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 35.1200 cpu seconds or 2 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 74239 PSMs with q<0.01 Iteration 2: Estimated 74727 PSMs with q<0.01 Iteration 3: Estimated 74774 PSMs with q<0.01 Iteration 4: Estimated 74778 PSMs with q<0.01 Iteration 5: Estimated 74778 PSMs with q<0.01 Iteration 6: Estimated 74764 PSMs with q<0.01 Iteration 7: Estimated 74766 PSMs with q<0.01 Iteration 8: Estimated 74763 PSMs with q<0.01 Iteration 9: Estimated 74765 PSMs with q<0.01 Iteration 10: Estimated 74767 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 -0.3409 -0.2728 -0.3608 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0547 0.0602 0.0798 isotope_error_0 0.0292 0.0282 0.0112 isotope_error_1 -0.1063 -0.1125 -0.1200 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -1.9258 -2.0959 -1.8785 log10_evalue 1.3260 1.3340 1.1798 hyperscore 1.1870 1.2406 1.3817 delta_hyperscore 0.0540 -0.0406 0.3259 matched_ion_num -1.2559 -1.1776 -1.3906 complementary_ions -0.1494 -0.1155 -0.1996 ion_series -0.2440 -0.2490 -0.2475 weighted_average_abs_fragment_ppm -0.1247 -0.1157 -0.1209 length_7 -0.0897 -0.0779 -0.0999 length_8 -0.0218 -0.0234 -0.0271 length_9_30 0.1303 0.1218 0.1402 length_31 0.0000 0.0000 0.0000 ntt -0.0635 -0.0401 -0.0768 nmc -0.0332 -0.0238 -0.0500 charge_1 0.0662 0.0766 0.0716 charge_2 0.0612 0.0421 0.0530 charge_3 -0.0819 -0.0788 -0.1155 charge_4 -0.1982 -0.1851 -0.1235 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.2846 -0.2134 -0.2696 15.9949M 0.1349 0.1112 0.1594 pred_RT_real_units 1.3015 1.1908 1.3988 unweighted_spectral_entropy -0.6167 -0.5881 -0.6082 delta_RT_loess 1.4649 1.3434 1.5589 m0 Found 74711 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 112929 target PSMs and 37689 decoy PSMs. Calculating q values. Final list yields 74716 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 164.3500 cpu seconds or 14 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_edited.pin Percolator version 3.06.5, Build Date Feb 8 2024 10:00:35 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: /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_edited.pin Started Mon Nov 18 12:06:59 2024 on galaxy Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_edited.pin Features: rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more 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 pred_RT_real_units unweighted_spectral_entropy delta_RT_loess Found 154792 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 118187 positives and 36605 negatives, size ratio=3.22871 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 8 as initial direction. Could separate 50490 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 50593 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 50540 training set positives with q<0.01 in that direction. Found 75819 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 35.3900 cpu seconds or 2 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 79951 PSMs with q<0.01 Iteration 2: Estimated 80425 PSMs with q<0.01 Iteration 3: Estimated 80466 PSMs with q<0.01 Iteration 4: Estimated 80474 PSMs with q<0.01 Iteration 5: Estimated 80473 PSMs with q<0.01 Iteration 6: Estimated 80481 PSMs with q<0.01 Iteration 7: Estimated 80485 PSMs with q<0.01 Iteration 8: Estimated 80484 PSMs with q<0.01 Iteration 9: Estimated 80480 PSMs with q<0.01 Iteration 10: Estimated 80484 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 -0.2125 -0.2386 -0.2555 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0512 0.0717 0.0572 isotope_error_0 0.0205 0.0270 0.0150 isotope_error_1 -0.0918 -0.1266 -0.0937 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -1.4436 -1.5147 -1.4387 log10_evalue 2.3215 1.8808 1.2655 hyperscore 1.3552 1.3281 1.1682 delta_hyperscore -0.0073 0.2888 0.6288 matched_ion_num -1.5002 -1.4223 -1.2016 complementary_ions -0.2870 -0.4410 -0.1964 ion_series -0.2220 -0.2444 -0.2408 weighted_average_abs_fragment_ppm -0.1258 -0.1267 -0.1400 length_7 -0.0857 -0.0808 -0.0898 length_8 0.0059 0.0094 0.0028 length_9_30 0.1089 0.1019 0.1224 length_31 0.0000 0.0000 0.0000 ntt -0.0841 -0.1090 -0.1388 nmc -0.0258 0.0106 -0.0358 charge_1 0.1131 0.1047 0.1017 charge_2 -0.0104 -0.0107 -0.0087 charge_3 -0.0871 -0.0728 -0.0755 charge_4 -0.1574 -0.1694 -0.1451 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.2574 -0.2823 -0.2692 15.9949M 0.1213 0.1730 0.1239 pred_RT_real_units 1.4028 1.4306 1.2914 unweighted_spectral_entropy -0.7731 -0.7419 -0.6827 delta_RT_loess 1.8258 1.7044 1.6907 m0 Found 80427 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 118187 target PSMs and 36605 decoy PSMs. Calculating q values. Final list yields 80429 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 176.1000 cpu seconds or 15 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_edited.pin Percolator version 3.06.5, Build Date Feb 8 2024 10:00:35 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: /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_edited.pin Started Mon Nov 18 12:07:17 2024 on galaxy Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_edited.pin Features: rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more 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 pred_RT_real_units unweighted_spectral_entropy delta_RT_loess Found 155222 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 116250 positives and 38972 negatives, size ratio=2.98291 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 8 as initial direction. Could separate 47763 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 47562 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 47772 training set positives with q<0.01 in that direction. Found 71553 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 36.7500 cpu seconds or 2 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 76323 PSMs with q<0.01 Iteration 2: Estimated 76669 PSMs with q<0.01 Iteration 3: Estimated 76673 PSMs with q<0.01 Iteration 4: Estimated 76682 PSMs with q<0.01 Iteration 5: Estimated 76691 PSMs with q<0.01 Iteration 6: Estimated 76695 PSMs with q<0.01 Iteration 7: Estimated 76697 PSMs with q<0.01 Iteration 8: Estimated 76699 PSMs with q<0.01 Iteration 9: Estimated 76701 PSMs with q<0.01 Iteration 10: Estimated 76700 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 -0.2732 -0.2658 -0.3107 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0853 0.0868 0.0875 isotope_error_0 0.0244 -0.0002 0.0136 isotope_error_1 -0.1422 -0.1167 -0.1331 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -2.2017 -2.1938 -2.0623 log10_evalue 1.0751 2.1755 1.5100 hyperscore 1.4017 1.3395 1.2101 delta_hyperscore 0.1616 -0.8271 -0.0208 matched_ion_num -1.2227 -1.2060 -1.1881 complementary_ions -0.2930 -0.3194 -0.4039 ion_series -0.3296 -0.2809 -0.2642 weighted_average_abs_fragment_ppm -0.1177 -0.1297 -0.1104 length_7 -0.0815 -0.0903 -0.0780 length_8 -0.0199 -0.0237 -0.0283 length_9_30 0.1244 0.1395 0.1291 length_31 0.0000 0.0000 0.0000 ntt 0.0148 -0.0339 -0.0164 nmc 0.0223 0.0063 -0.0056 charge_1 0.0908 0.1051 0.1084 charge_2 0.0242 0.0108 -0.0117 charge_3 -0.0816 -0.0718 -0.0423 charge_4 -0.1798 -0.1976 -0.1974 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.3201 -0.2753 -0.3038 15.9949M 0.1850 0.2126 0.2075 pred_RT_real_units 1.4268 1.5267 1.4635 unweighted_spectral_entropy -0.7002 -0.6470 -0.6246 delta_RT_loess 1.5680 1.5495 1.4778 m0 Found 76642 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 116250 target PSMs and 38972 decoy PSMs. Calculating q values. Final list yields 76644 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 177.7400 cpu seconds or 14 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_edited.pin Percolator version 3.06.5, Build Date Feb 8 2024 10:00:35 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: /rd1/user/lit/software/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 40 --results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_target_psms.tsv --decoy-results-psms CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_edited.pin Started Mon Nov 18 12:07:34 2024 on galaxy Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_edited.pin Features: rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more 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 pred_RT_real_units unweighted_spectral_entropy delta_RT_loess Found 156697 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 117723 positives and 38974 negatives, size ratio=3.02055 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 8 as initial direction. Could separate 48977 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 49196 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 49276 training set positives with q<0.01 in that direction. Found 73730 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 37.3700 cpu seconds or 2 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 77709 PSMs with q<0.01 Iteration 2: Estimated 78256 PSMs with q<0.01 Iteration 3: Estimated 78331 PSMs with q<0.01 Iteration 4: Estimated 78338 PSMs with q<0.01 Iteration 5: Estimated 78324 PSMs with q<0.01 Iteration 6: Estimated 78326 PSMs with q<0.01 Iteration 7: Estimated 78330 PSMs with q<0.01 Iteration 8: Estimated 78325 PSMs with q<0.01 Iteration 9: Estimated 78328 PSMs with q<0.01 Iteration 10: Estimated 78327 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 -0.2113 -0.2202 -0.2028 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0425 0.0515 0.0520 isotope_error_0 0.0173 0.0302 0.0115 isotope_error_1 -0.0762 -0.1026 -0.0824 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -1.6758 -2.0253 -1.6714 log10_evalue 2.5092 2.0031 1.6461 hyperscore 1.1668 1.2624 0.9728 delta_hyperscore -0.6050 -0.5657 -0.2627 matched_ion_num -1.2212 -1.1929 -1.0285 complementary_ions -0.2835 -0.1859 -0.2179 ion_series -0.2045 -0.2317 -0.1861 weighted_average_abs_fragment_ppm -0.1011 -0.1140 -0.0949 length_7 -0.0981 -0.1097 -0.0727 length_8 -0.0020 -0.0255 -0.0093 length_9_30 0.1172 0.1608 0.1072 length_31 0.0000 0.0000 0.0000 ntt -0.1051 -0.1465 -0.1158 nmc -0.0104 0.0249 0.0161 charge_1 0.1032 0.1020 0.0664 charge_2 -0.0037 0.0079 0.0089 charge_3 -0.0895 -0.0991 -0.0697 charge_4 -0.1555 -0.1821 -0.1196 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.2294 -0.2452 -0.2308 15.9949M 0.1515 0.1744 0.1372 pred_RT_real_units 1.3619 1.3212 1.0905 unweighted_spectral_entropy -0.7615 -0.6903 -0.6163 delta_RT_loess 1.5628 1.6790 1.0580 m0 Found 78250 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 117723 target PSMs and 38974 decoy PSMs. Calculating q values. Final list yields 78252 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 175.1500 cpu seconds or 14 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] java -cp /rd1/user/lit/software/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pin CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552 CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_target_psms.tsv CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_decoy_psms.tsv interact-CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552 DDA 0.5 /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] java -cp /rd1/user/lit/software/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pin CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559 CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_target_psms.tsv CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_decoy_psms.tsv interact-CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559 DDA 0.5 /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] java -cp /rd1/user/lit/software/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pin CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557 CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_target_psms.tsv CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_decoy_psms.tsv interact-CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557 DDA 0.5 /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] java -cp /rd1/user/lit/software/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pin CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564 CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_target_psms.tsv CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_decoy_psms.tsv interact-CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564 DDA 0.5 /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] java -cp /rd1/user/lit/software/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pin CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554 CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_target_psms.tsv CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_decoy_psms.tsv interact-CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554 DDA 0.5 /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] java -cp /rd1/user/lit/software/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pin CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562 CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_target_psms.tsv CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_decoy_psms.tsv interact-CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562 DDA 0.5 /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /rd1/user/lit/software/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 proteinprophet --maxppmdiff 2000000 --output combined /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./filelist_proteinprophet.txt time="12:08:20" level=info msg="Executing ProteinProphet v5.1.1" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105021430-exported (Linux-x86_64)) (no FPKM) (no groups) (using degen pep info) Reading in /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pep.xml... ...read in 50 1+, 46361 2+, 25490 3+, 6279 4+, 900 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pep.xml... ...read in 37 1+, 46658 2+, 26741 3+, 6792 4+, 977 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pep.xml... ...read in 65 1+, 42395 2+, 25895 3+, 7159 4+, 1323 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pep.xml... ...read in 45 1+, 42000 2+, 26108 3+, 7822 4+, 1591 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pep.xml... ...read in 57 1+, 40095 2+, 25969 3+, 7908 4+, 1433 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pep.xml... ...read in 42 1+, 42074 2+, 25699 3+, 6770 4+, 985 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 81532 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database /rd1/user/lit/project/sORFs/custom_database/2024-11-06-decoys-contam-uniprotkb_Mus_musculus_reviewed_canonical_isoform_2024_10_25.nonCano.sorf.filtered.fa.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........43000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........44000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........45000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........46000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........47000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........48000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........49000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........50000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........51000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........52000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........53000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........54000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........55000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........56000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........57000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........58000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........59000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........60000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........61000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........62000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........63000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........64000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........65000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........66000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........67000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........68000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........78000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........82000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........85000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........86000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........87000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........88000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........89000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........90000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........91000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........92000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........93000 .........:.........:.........WARNING: Found the following zero-mass residues in protein entry rev_sp|O70325-2|GPX4_MOUSE : U MLYCPLDKEIVQPEEMPGYRKVVCGNKDILFKTFNWKIANGLMGRGKPQVKMWKWLPHADDGNVCIKSYMDFKVNYGAAFEKIEQNSGPEQRGFQNCPFALIRLGCEAYRAHLDVLQTYNVDTKGUQSAVNTVICVFGRYKDLCVMHGDIDKASFEHMSRACRWDDRSAC WARNING: Found the following zero-mass residues in protein entry rev_sp|O70325-3|GPX4_MOUSE : U MLYCPLDKEIVQPEEMPGYRKVVCGNKDILFKTFNWKIANGLMGRGKPQVKMWKWLPHADDGNVCIKSYMDFKVNYGAAFEKIEQNSGPEQRGFQNCPFALIRLGCEAYRAHLDVLQTYNVDTKGUSQAVNTVICVFGRYKDLCVMHGDIDKASFEHMSRACRWDDRSACLGLFESSNCYQPPEQLLPGPNFPEPIPEMRRPRARRRRRARAKRRRPGPRKRPSQRGPGRRRRGRPSGGRQRCRGRKRAAARG :.........:.........:.........:.........:.........:.........:.........94000 .........:.........:.........:.........:.........WARNING: Found the following zero-mass residues in protein entry rev_sp|P11352|GPX1_MOUSE : U MSNGSQQSLLTEIDPEIDITRFRRSYRRVPVGDPGVLFKEFNWAIDNRCVPSWIIYKPDTMLATPDDSPTPLANRLFTFLPHAKEGNVECKEFLTFNPEFGGGPRVYKLSNLIEENKGNEQHGFQNCPFGLVVLGRPGLRKQLDNMETYDRITTGULSAVNEILLVKGRLSGLSVPEGGTLPRASFAYVTSQAAASLRAAC :.........:.........:.........:.........:.........95000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........96000 .........:.........:.........:.........:.........:.........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry rev_sp|P62342|SELT_MOUSE : U MSRHHPISDMHVNLKMENDLIQVLQQMSPLHGSELKSWVPVDNLTIEFAGTSMCQNEIMNSLFFVMMCAYVKNEQGWQWISPAQMGFFAFPDKGVIIGLILVLKFVSLFSAIHRYIPQPLYNEGEIRIDPYRQSIVRMYEEFVRRYGUSVCIQFKLLPGTAYQMKLRKSPVGGLNASAESRVVASAAVLLLLLLR .......97000 .........:.........WARNING: Found the following zero-mass residues in protein entry rev_sp|P70274|SEPP1_MOUSE : UUUUUUUUUU MNSHUKUKRTQNDUSUNPNAEMPNMPQNQUAAPPSRCQCSETVKEEAFLGQUSCLSPLNEACQUAIASGSKEFILHRCHCCCSSPAAESEKSLKCLLQNICGRRULKRQALSLHLGESATTDUSELHGQRHQGRHRHHHHLGSPPLTTESPGPQQNESPKSSGLHEQGHKNHHKHHSHAESPEATKNATASTVTKCFDEDELSTLNCNGCREECYAIKIAEEVYPFTLFSYPLGLHYVLRGCRDYILFDDKNGNLLTWVDIGDEEQRYVAIHESVQKKLHSHKLQSPSGQHNVVIYSINFYGQSELKIRLDELRSAQLLCLYUSAQLLAVVTVKGESNLMPNQDGIYWEPAKYCASSQGQSEAGGYPLLCLALALGLSRW :.........:.........:.........:.........:.........:.........:.........:.........98000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........99000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........100000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........101000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........102000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........103000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........104000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........105000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........106000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........107000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........108000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........109000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........110000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........111000 .........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry rev_sp|Q99MD6|TRXR3_MOUSE : U MGUCGKQTIDLGSSKTIELTTFVEGCTPHIGITDDLLQKTLGCKMAAAFGQTIEGANPGLLHFGVVRENDFKNCIIKAYCTNNDRGAVTWELPWFLTHYVELNEKKYMEIAKEESLGCCGYELPTFVTTPINIYDCKELSVGFLRRALLKGAQIAVPTLEPKGDLIDGIAYVHPVNTQEVDNVPIKGNKENIKVGIKELGIKRTCSDRGIALLVTNYIGEVTEPGETSKAVVKLKGPLGKELQQVLIPTFKRQFKVGQQELYSGVKEAMEQDFGRLLVSRVMVTVDLGLGALFGACELGVYSAGVVLTCGPCYPLSFLDDSTICYEKDGQIGLYRPREGTAIVFKSATYFTEQGKKNTAKIKHLDVFEGFSNVYTVGKERLTVRYGWNLSGIHSQIAETMAEWNHKVQQNYEWGYKKADQLAHGLLAAQHMLKKPICGVNVCTGGLGWTTGQPSPVVFDLVMVKKGLNAAEKACSLGGSGGGIIILDYDHASDDQLLKQLLGNQHAQFTRDCGGVHVKNVFINPVTKQNSIETLVEQVSAGDDVQDLELINYVVGLSSFLEKVRTSHPCYSKSFIMVRNGEILDRLRRRLEERAESSPRSTGPSALRARRGPPSSMLGGRVAGLRRNPLVGVKGLGPSTQARPPPPPSPPKE ..:.........:.........:.........:.........:.........112000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........113000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........114000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........115000 .........:.........WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9JMH6-2|TRXR1_MOUSE : U MGUCGSQLIDGGSRKTVSLTTFIEACVPHIGITSDLQQKTLGCKLAAAFGQTVEGANPGLVHFGVVREDDKLNCIIKAYCKNNDRSPVTWELPWFFSHYVEINEEGFKEVAKEESLGCCGYELPTFVTTPVNDYDCKVNSGGYLRQALLRGAQIAVPTLELKGELIDGIAYIYPVNTQEEDTVPIKGTKENIKVGVTELGITRTCSDRGVALLVTNFEGEITEESNTSQATVRLRGPTGAEIQEIKTPVQFRIFKIGHEEMHEGIKNAMDQDFGRLLISRVMVTVDLGIGALFGACELAVYSAGVVLTKGPCYPLSFLDDSSICYEKDGPIGLYRPREGTAILFREASYIKEKGKNNTAVIRHPGIFRGYANEYVVKKERLAVRYGWNLSGIHSQVSETMKEWDHKVTDEVKWGYNRSDKLAQGLLAAQHMLKKPICGVNVCTGGLGWRTGLPTPTVFDLVLVKKDFKAAEKAAALGGSGGGIIILDFDYSGPPDKSGN WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9JMH6|TRXR1_MOUSE : U MGUCGSQLIDGGSRKTVSLTTFIEACVPHIGITSDLQQKTLGCKLAAAFGQTVEGANPGLVHFGVVREDDKLNCIIKAYCKNNDRSPVTWELPWFFSHYVEINEEGFKEVAKEESLGCCGYELPTFVTTPVNDYDCKVNSGGYLRQALLRGAQIAVPTLELKGELIDGIAYIYPVNTQEEDTVPIKGTKENIKVGVTELGITRTCSDRGVALLVTNFEGEITEESNTSQATVRLRGPTGAEIQEIKTPVFQRIFKIGHEEMHEGIKNAMDQDFGRLLISRVMVTVDLGIGALFGACELAVYSAGVVTLKGPCYPLSFLDDSSICYEKDGPIGLYRPREGTAILFREASYIKEKGKNNTAVIRHPGIFRGYANEYVVKKERLAVRYGWNLSGIHSQVSETMKEWDHKVTDEVKWGYNRSDKLAQGLLAAQHMLKKPICGVNVCTGGLGWRTGLPTPTVFDLVLVKKDFKAAEKAAALGGSGGGIIILDFDYSGPPDKSGNMTPLKQLQGKKNPLESQTNKEQRSDPTSPPPCICPDTPCPTQSSSPLTKSPRSAPLVAGRPGRLLVRPVHPPRPVPPLFGPFWCCNPCTPAVWVTQVFTRGRSAPFYLWCDDVP :.........:.........:.........:.........:.........:.........:.........:.........116000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........117000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........118000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........119000 ..WARNING: Found the following zero-mass residues in protein entry sp|O70325-2|GPX4_MOUSE : U MCASRDDWRCARSMHEFSAKDIDGHMVCLDKYRGFVCIVTNVASQUGKTDVNYTQLVDLHARYAECGLRILAFPCNQFGRQEPGSNQEIKEFAAGYNVKFDMYSKICVNGDDAHPLWKWMKVQPKGRGMLGNAIKWNFTKFLIDKNGCVVKRYGPMEEPQVIEKDLPCYL WARNING: Found the following zero-mass residues in protein entry sp|O70325-3|GPX4_MOUSE : U MGRAAARKRGRCRQRGGSPRGRRRRGPGRQSPRKRPGPRRRKARARRRRRARPRRMEPIPEPFNPGPLLQEPPQYCNSSEFLGLCASRDDWRCARSMHEFSAKDIDGHMVCLDKYRGFVCIVTNVASQUGKTDVNYTQLVDLHARYAECGLRILAFPCNQFGRQEPGSNQEIKEFAAGYNVKFDMYSKICVNGDDAHPLWKWMKVQPKGRGMLGNAIKWNFTKFLIDKNGCVVKRYGPMEEPQVIEKDLPCYL WARNING: Found the following zero-mass residues in protein entry sp|O70325|GPX4_MOUSE : U MSWGRLSRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVCLDKYRGFVCIVTNVASQUGKTDVNYTQLVDLHARYAECGLRILAFPCNQFGRQEPGSNQEIKEFAAGYNVKFDMYSKICVNGDDAHPLWKWMKVQPKGRGMLGNAIKWNFTKFLIDKNGCVVKRYGPMEEPQVIEKDLPCYL .......:.........:.........:.........:.........:.........:.........:.........:.........:.........120000 .........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|P11352|GPX1_MOUSE : U MCAARLSAAAQSTVYAFSARPLTGGEPVSLGSLRGKVLLIENVASLUGTTIRDYTEMNDLQKRLGPRGLVVLGFPCNQFGHQENGKNEEILNSLKYVRPGGGFEPNFTLFEKCEVNGEKAHPLFTFLRNALPTPSDDPTALMTDPKYIIWSPVCRNDIAWNFEKFLVGPDGVPVRRYSRRFRTIDIEPDIETLLSQQSGNS ......:.........:.........:.........:.........:.........:.........:.........121000 .........:.........:.........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|P46412|GPX3_MOUSE : U MARILRASCLLSLLLAGFVPPGRGQEKSKTDCHGGMSGTIYEYGALTIDGEEYIPFKQYAGKYILFVNVASYUGLTDQYLELNALQEELGPFGLVILGFPSNQFGKQEPGENSEILPSLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTAELLGSPGRLFWEPMKIHDIRWNFEKFLVGPDGIPVMRWYHRTTVSNVKMDILSYMRRQAALSARGK ..:.........:.........:.........122000 .........:.........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|P62342|SELT_MOUSE : U MRLLLLLLVAASAVVRSEASANLGGVPSKRLKMQYATGPLLKFQICVSUGYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKVYACMMVFFLSNMIENQCMSTGAFEITLNDVPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPHHRS ...:.........:.........:.........123000 .........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|P97364|SPS2_MOUSE : U MAEAAAAGASGETMAALVAAEGSLGPAGWSAGRSFSNYRPFEPQTLGFSPSWRLTSFSGMKGUGCKVPQETLLKLLEGLTRPALQPPLTSGLVGGQEETVQEGGLSTRPGPGSAFPSLSIGMDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQSMSEKEREKVTPLMIKGFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQQNEFIMPDSAVVGDVLVLTKPLGTQVAANAHQWLDNPEKWNKIKMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFGILGHSQNLAKQQKNEVSFVIHNLPIIAKMAAISKASGRFGLLQGTSAETSGGLLICLPREQAARFCSEIKSSKYGEGHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGASAAAAAAPDNSNAASEPSS ...:.........:.........:.........:.........:.........:.........:.........124000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........125000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........126000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........127000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........128000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........129000 .........:.........:.........:.........:.........:.........:.........:.........:.........WARNING: Found the following zero-mass residues in protein entry sp|Q80TA1|EPT1_MOUSE : U MAGYEYVSPEQLSGFDKYKYSALDTNPLSLYIMHPFWNTIVKVFPTWLAPNLITFSGFMLLVFNFLLLTYFDPDFYASAPGHKHVPDWVWIVVGILNFAAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGPTGVSVFVLYLLLWVVLFSFILSHWEKYNTGVLFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKSNTLKHKSVYEAMVPFFSPCLLFTLCTVWILWSPSDILEIHPRIFYFMVGTAFANITCQLIVCQMSSTRCPTLNWLLLPLLLVVAAVIVGAATSRLESALLYTLTAAFTLAHIHYGVQVVKQLSRHFQIYPFSLRKPNSDULGMEEQNIGL :.........130000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........131000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........132000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........133000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........134000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........135000 .........:.........:.........:.........:.........:.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|Q8VHC3|SELM_MOUSE : U MSILLSPPSLLLLLAALVAPATSTTNYRPDWNRLRGLARGRVETCGGUQLNRLKEVKAFVTEDIQLYHNLVMKHLPGADPELVLLSRNYQELERIPLSQMTRDEINALVQELGFYRKSAPEAQVPPEYLWAPAKPPEEASEHDDL .........:.........:.........136000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........137000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........138000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........139000 .........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|Q9DBC0|SELO_MOUSE : U MASVRAAVGASLAVARTRPRCVGLALPSSAPRSAWAAAMEPTPRWLAGLRFDNRALRELPVETPPPGPEDSLATPRPVPGACFSRARPAPLRRPRLVALSEPALALLGLEASEEAEVEAEAALFFSGNALLPGTEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTAAGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGIPTTRAGACVTSESTVMRDVFYDGNPKYEKCTVVLRIAPTFIRFGSFEIFKPPDEHTGRAGPSVGRDDIRVQLLDYVISSFYPEIQAAHTCDTDNIQRNAAFFREVTQRTARMVAEWQCVGFCHGVLNTDNMSIVGLTIDYGPFGFLDRYDPDHICNASDNAGRYTYSKQPQVCKWNLQKLAEALEPELPLALAEAILKEEFDTEFQRHYLQKMRKKLGLIRVEKEEDGTLVAKLLETMHLTGADFTNTFCVLSSFPADLSDSAEFLSRLTSQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALIGTQANVTKELERVEHQSRLEQLSPSDLQRKNRDHWEAWLQEYRDRLDKEKEGVGDTAAWQAERVRVMRANNPKYVLRNYIAQKAIEAAENGDFSEVRRVLKLLESPYHSEEEATGPEAVARSTEEQSSYSNRPPLWAAELCVTUSS ...:.........:.........:.........:.........140000 .........:.WARNING: Found the following zero-mass residues in protein entry sp|Q9ERR7|SEP15_MOUSE : U MAAGQGGWLRPALGLRLLLATAFQAVSALGAEFASEACRELGFSSNLLCSSCDLLGQFNLLPLDPVCRGCCQEEAQFETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEELSILKWNTDSVEEFLSEKLERI ........:.........:.........:.........:.........:.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|Q9JLJ1|SELK_MOUSE : U MVYISNGQVLDSRNQSPWRVSFLTDFFWGIAEFVVFFFKTLLQQDVKKRRGYGSSSDSRYDDGRGPPGNPPRRMGRISHLRGPSPPPMAGGUGR ....WARNING: Found the following zero-mass residues in protein entry sp|Q9JLT4-2|TRXR2_MOUSE : U MEGQQSFDLLVIGGGSGGLACAKEAAQLGKKVAVADYVEPSPRGTKWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAHHYGWEVAQPVQHNWKTMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVRGVDKGGKATLLSAEHIVIATGGRPRYPTQVKGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTVMMRSIPLRGFDQQMSSLVTEHMESHGTQFLKGCVPSHIKKLPTNQLQVTWEDHASGKEDTGTFDTVLWAIGRVPETRTLNLEKAGISTNPKNQKIIVDAQEATSVPHIYAIGDVAEGRPELTPTAIKAGKLLAQRLFGKSSTLMDYSNVPTTVFTPLEYGCVGLSEEEAVALHGQEHVEVYHAYYKPLEFTVADRDASQCYIKMVCMREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMQTVGIHPTCSEEVVKLHISKRSGLEPTVTGCUG WARNING: Found the following zero-mass residues in protein entry sp|Q9JLT4-4|TRXR2_MOUSE : U MVAAMVAALRGPSRRFRPRTRALTRGTRGAASAAGGQQSFDLLVIGGGSGGLACAKEAAQLGKKVAVADYVEPSPRGTKWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAHHYGWEVAQPVQHNWKTMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVRGVDKGGKATLLSAEHIVIATGGRPRYPTQVKGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTVMMRSIPLRGFDQQMSSLVTEHMESHGTQFLKGCVPSHIKKLPTNQLQVTWEDHASGKEDTGTFDTVLWAIGRVPETRTLNLEKAGISTNPKNQKIIVDAQEATSVPHIYAIGDVAEGRPELTPTAIKAGKLLAQRLFGKSSTLMDYSNVYHAYYKPLEFTVADRDASQCYIKMVCMREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMQTVGIHPTCSEEVVKLHISKRSGLEPTVTGCUG WARNING: Found the following zero-mass residues in protein entry sp|Q9JLT4|TRXR2_MOUSE : U MVAAMVAALRGPSRRFRPRTRALTRGTRGAASAAGGQQSFDLLVIGGGSGGLACAKEAAQLGKKVAVADYVEPSPRGTKWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAHHYGWEVAQPVQHNWKTMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVRGVDKGGKATLLSAEHIVIATGGRPRYPTQVKGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTVMMRSIPLRGFDQQMSSLVTEHMESHGTQFLKGCVPSHIKKLPTNQLQVTWEDHASGKEDTGTFDTVLWAIGRVPETRTLNLEKAGISTNPKNQKIIVDAQEATSVPHIYAIGDVAEGRPELTPTAIKAGKLLAQRLFGKSSTLMDYSNVPTTVFTPLEYGCVGLSEEEAVALHGQEHVEVYHAYYKPLEFTVADRDASQCYIKMVCMREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMQTVGIHPTCSEEVVKLHISKRSGLEPTVTGCUG .....:...WARNING: Found the following zero-mass residues in protein entry sp|Q9JMH6-2|TRXR1_MOUSE : U MNGSKDPPGSYDFDLIIIGGGSGGLAAAKEAAKFDKKVLVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALKDSRNYGWKVEDTVKHDWEKMTESVQSHIGSLNWGYRVALREKKVVYENAYGRFIGPHRIVATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPTKIEQIEAGTPGRLRVTAQSTNSEETIEGEFNTVLLAVGRDSCTRTIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSNVKCDYDNVPTTVFTPLEYGCCGLSEEKAVEKFGEENIEVYHSFFWPLEWTVPSRDNNKCYAKIICNLKDDERVVGFHVLGPNAGEVTQGFAAALKCGLTKQQLDSTIGIHPVCAEIFTTLSVTKRSGGDILQSGCUG WARNING: Found the following zero-mass residues in protein entry sp|Q9JMH6|TRXR1_MOUSE : U MPVDDCWLYFPASRGRTFVQTVWVAPTCPNCCWFPGFLPPVPRPPHVPRVLLRGPRGAVLPASRPSKTLPSSSQTPCPTDPCICPPPSTPDSRQEKNTQSELPNKKGQLQKLPTMNGSKDPPGSYDFDLIIIGGGSGGLAAAKEAAKFDKKVLVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALKDSRNYGWKVEDTVKHDWEKMTESVQSHIGSLNWGYRVALREKKVVYENAYGRFIGPHRIVATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPTKIEQIEAGTPGRLRVTAQSTNSEETIEGEFNTVLLAVGRDSCTRTIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSNVKCDYDNVPTTVFTPLEYGCCGLSEEKAVEKFGEENIEVYHSFFWPLEWTVPSRDNNKCYAKIICNLKDDERVVGFHVLGPNAGEVTQGFAAALKCGLTKQQLDSTIGIHPVCAEIFTTLSVTKRSGGDILQSGCUG ......141000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........142000 .........:.........:.........:.........:.........:. Total: 142510 Computing degenerate peptides for 23571 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 27582 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 27582 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 27582 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 27582 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 27582 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 27582 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=4.20124e-05, db_size=71140851 Computing MU for 27582 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% time="12:08:55" level=info msg=Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 database --annotate /rd1/user/lit/project/sORFs/custom_database/2024-11-06-decoys-contam-uniprotkb_Mus_musculus_reviewed_canonical_isoform_2024_10_25.nonCano.sorf.filtered.fa.fas --prefix rev_ time="12:08:55" level=info msg="Executing Database v5.1.1" time="12:08:55" level=info msg="Annotating the database" time="12:08:56" level=info msg=Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --sequential --prot 1 --picked --tag rev_ --pepxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --protxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./combined.prot.xml --razor time="12:08:56" level=info msg="Executing Filter v5.1.1" time="12:08:56" level=info msg="Processing peptide identification files" time="12:08:56" level=info msg="Parsing /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pep.xml" time="12:09:04" level=info msg="1+ Charge profile" decoy=3 target=47 time="12:09:04" level=info msg="2+ Charge profile" decoy=511 target=45850 time="12:09:04" level=info msg="3+ Charge profile" decoy=224 target=25266 time="12:09:04" level=info msg="4+ Charge profile" decoy=52 target=6227 time="12:09:04" level=info msg="5+ Charge profile" decoy=5 target=895 time="12:09:04" level=info msg="6+ Charge profile" decoy=0 target=0 time="12:09:05" level=info msg="Database search results" ions=41691 peptides=33241 psms=79080 time="12:09:05" level=info msg="Converged to 1.00 % FDR with 78255 PSMs" decoy=782 threshold=0.506956 total=79037 time="12:09:05" level=info msg="Converged to 1.00 % FDR with 31900 Peptides" decoy=319 threshold=0.747708 total=32219 time="12:09:05" level=info msg="Converged to 1.00 % FDR with 40425 Ions" decoy=404 threshold=0.693221 total=40829 time="12:09:05" level=info msg="Protein inference results" decoy=3429 target=13842 time="12:09:05" level=info msg="Converged to 24.06 % FDR with 8420 Proteins" decoy=2026 threshold=0 total=10446 time="12:09:06" level=info msg="Applying sequential FDR estimation" ions=41342 peptides=32893 psms=78705 time="12:09:06" level=info msg="Converged to 0.62 % FDR with 78218 PSMs" decoy=487 threshold=0.506956 total=78705 time="12:09:06" level=info msg="Converged to 1.00 % FDR with 32220 Peptides" decoy=322 threshold=0.617813 total=32542 time="12:09:06" level=info msg="Converged to 1.00 % FDR with 40844 Ions" decoy=408 threshold=0.532126 total=41252 time="12:09:06" level=info msg="Post processing identifications" time="12:09:07" level=info msg="Assigning protein identifications to layers" time="12:09:23" level=info msg="Processing protein inference" time="12:09:24" level=info msg="Synchronizing PSMs and proteins" time="12:09:25" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=40844 peptides=32220 proteins=5713 psms=78218 time="12:09:25" level=info msg=Saving time="12:09:25" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --sequential --prot 1 --picked --tag rev_ --pepxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d --dbbin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --protxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./combined.prot.xml --probin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --razor time="12:09:25" level=info msg="Executing Filter v5.1.1" time="12:09:25" level=info msg="Fetching protein inference from /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d" time="12:09:25" level=info msg="Processing peptide identification files" time="12:09:25" level=info msg="Parsing /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.pep.xml" time="12:09:34" level=info msg="1+ Charge profile" decoy=1 target=36 time="12:09:34" level=info msg="2+ Charge profile" decoy=495 target=46163 time="12:09:34" level=info msg="3+ Charge profile" decoy=226 target=26515 time="12:09:34" level=info msg="4+ Charge profile" decoy=60 target=6732 time="12:09:34" level=info msg="5+ Charge profile" decoy=8 target=969 time="12:09:34" level=info msg="6+ Charge profile" decoy=0 target=0 time="12:09:34" level=info msg="Database search results" ions=43557 peptides=34695 psms=81205 time="12:09:35" level=info msg="Converged to 0.98 % FDR with 80415 PSMs" decoy=790 threshold=0.500129 total=81205 time="12:09:35" level=info msg="Converged to 1.00 % FDR with 33419 Peptides" decoy=334 threshold=0.714125 total=33753 time="12:09:35" level=info msg="Converged to 1.00 % FDR with 42377 Ions" decoy=423 threshold=0.651591 total=42800 time="12:09:35" level=info msg="Protein inference results" decoy=3429 target=13842 time="12:09:35" level=info msg="Converged to 24.06 % FDR with 8420 Proteins" decoy=2026 threshold=0 total=10446 time="12:09:36" level=info msg="Applying sequential FDR estimation" ions=43269 peptides=34408 psms=80906 time="12:09:36" level=info msg="Converged to 0.64 % FDR with 80391 PSMs" decoy=515 threshold=0.500129 total=80906 time="12:09:36" level=info msg="Converged to 1.00 % FDR with 33656 Peptides" decoy=336 threshold=0.606468 total=33992 time="12:09:36" level=info msg="Converged to 1.00 % FDR with 42690 Ions" decoy=426 threshold=0.537526 total=43116 time="12:09:36" level=info msg="Post processing identifications" time="12:09:37" level=info msg="Assigning protein identifications to layers" time="12:09:53" level=info msg="Processing protein inference" time="12:09:53" level=info msg="Synchronizing PSMs and proteins" time="12:09:54" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=42690 peptides=33656 proteins=5745 psms=80391 time="12:09:54" level=info msg=Saving time="12:09:55" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --sequential --prot 1 --picked --tag rev_ --pepxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d --dbbin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --protxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./combined.prot.xml --probin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --razor time="12:09:55" level=info msg="Executing Filter v5.1.1" time="12:09:55" level=info msg="Fetching protein inference from /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d" time="12:09:55" level=info msg="Processing peptide identification files" time="12:09:55" level=info msg="Parsing /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.pep.xml" time="12:10:03" level=info msg="1+ Charge profile" decoy=2 target=63 time="12:10:03" level=info msg="2+ Charge profile" decoy=544 target=41851 time="12:10:03" level=info msg="3+ Charge profile" decoy=287 target=25608 time="12:10:03" level=info msg="4+ Charge profile" decoy=66 target=7093 time="12:10:03" level=info msg="5+ Charge profile" decoy=14 target=1309 time="12:10:03" level=info msg="6+ Charge profile" decoy=0 target=0 time="12:10:04" level=info msg="Database search results" ions=40417 peptides=32388 psms=76837 time="12:10:04" level=info msg="Converged to 1.00 % FDR with 75590 PSMs" decoy=755 threshold=0.561735 total=76345 time="12:10:04" level=info msg="Converged to 1.00 % FDR with 30751 Peptides" decoy=307 threshold=0.757507 total=31058 time="12:10:04" level=info msg="Converged to 1.00 % FDR with 38843 Ions" decoy=388 threshold=0.709776 total=39231 time="12:10:04" level=info msg="Protein inference results" decoy=3429 target=13842 time="12:10:04" level=info msg="Converged to 24.06 % FDR with 8420 Proteins" decoy=2026 threshold=0 total=10446 time="12:10:05" level=info msg="Applying sequential FDR estimation" ions=39751 peptides=31748 psms=76002 time="12:10:05" level=info msg="Converged to 0.59 % FDR with 75557 PSMs" decoy=445 threshold=0.561735 total=76002 time="12:10:05" level=info msg="Converged to 1.00 % FDR with 31115 Peptides" decoy=311 threshold=0.636454 total=31426 time="12:10:05" level=info msg="Converged to 1.00 % FDR with 39311 Ions" decoy=393 threshold=0.570446 total=39704 time="12:10:05" level=info msg="Post processing identifications" time="12:10:06" level=info msg="Assigning protein identifications to layers" time="12:10:20" level=info msg="Processing protein inference" time="12:10:21" level=info msg="Synchronizing PSMs and proteins" time="12:10:22" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=39309 peptides=31113 proteins=5276 psms=75555 time="12:10:22" level=info msg=Saving time="12:10:23" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --sequential --prot 1 --picked --tag rev_ --pepxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d --dbbin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --protxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./combined.prot.xml --probin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --razor time="12:10:23" level=info msg="Executing Filter v5.1.1" time="12:10:23" level=info msg="Fetching protein inference from /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d" time="12:10:23" level=info msg="Processing peptide identification files" time="12:10:23" level=info msg="Parsing /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.pep.xml" time="12:10:31" level=info msg="1+ Charge profile" decoy=2 target=43 time="12:10:31" level=info msg="2+ Charge profile" decoy=478 target=41522 time="12:10:31" level=info msg="3+ Charge profile" decoy=245 target=25863 time="12:10:31" level=info msg="4+ Charge profile" decoy=74 target=7748 time="12:10:31" level=info msg="5+ Charge profile" decoy=14 target=1577 time="12:10:31" level=info msg="6+ Charge profile" decoy=0 target=0 time="12:10:31" level=info msg="Database search results" ions=41112 peptides=32721 psms=77566 time="12:10:32" level=info msg="Converged to 1.00 % FDR with 76644 PSMs" decoy=766 threshold=0.523315 total=77410 time="12:10:32" level=info msg="Converged to 1.00 % FDR with 31412 Peptides" decoy=314 threshold=0.753806 total=31726 time="12:10:32" level=info msg="Converged to 1.00 % FDR with 39827 Ions" decoy=398 threshold=0.699396 total=40225 time="12:10:32" level=info msg="Protein inference results" decoy=3429 target=13842 time="12:10:32" level=info msg="Converged to 24.06 % FDR with 8420 Proteins" decoy=2026 threshold=0 total=10446 time="12:10:33" level=info msg="Applying sequential FDR estimation" ions=40697 peptides=32319 psms=77084 time="12:10:33" level=info msg="Converged to 0.61 % FDR with 76618 PSMs" decoy=466 threshold=0.523315 total=77084 time="12:10:33" level=info msg="Converged to 1.00 % FDR with 31676 Peptides" decoy=316 threshold=0.617565 total=31992 time="12:10:33" level=info msg="Converged to 1.00 % FDR with 40214 Ions" decoy=402 threshold=0.53787 total=40616 time="12:10:33" level=info msg="Post processing identifications" time="12:10:34" level=info msg="Assigning protein identifications to layers" time="12:10:49" level=info msg="Processing protein inference" time="12:10:50" level=info msg="Synchronizing PSMs and proteins" time="12:10:51" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=40214 peptides=31676 proteins=5217 psms=76618 time="12:10:51" level=info msg=Saving time="12:10:51" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --sequential --prot 1 --picked --tag rev_ --pepxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d --dbbin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --protxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./combined.prot.xml --probin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --razor time="12:10:52" level=info msg="Executing Filter v5.1.1" time="12:10:52" level=info msg="Fetching protein inference from /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d" time="12:10:52" level=info msg="Processing peptide identification files" time="12:10:52" level=info msg="Parsing /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.pep.xml" time="12:11:00" level=info msg="1+ Charge profile" decoy=2 target=55 time="12:11:00" level=info msg="2+ Charge profile" decoy=438 target=39657 time="12:11:00" level=info msg="3+ Charge profile" decoy=227 target=25742 time="12:11:00" level=info msg="4+ Charge profile" decoy=64 target=7844 time="12:11:00" level=info msg="5+ Charge profile" decoy=15 target=1418 time="12:11:00" level=info msg="6+ Charge profile" decoy=0 target=0 time="12:11:00" level=info msg="Database search results" ions=37054 peptides=29240 psms=75462 time="12:11:00" level=info msg="Converged to 1.00 % FDR with 74716 PSMs" decoy=746 threshold=0.500028 total=75462 time="12:11:00" level=info msg="Converged to 1.00 % FDR with 28013 Peptides" decoy=280 threshold=0.765216 total=28293 time="12:11:00" level=info msg="Converged to 1.00 % FDR with 35885 Ions" decoy=358 threshold=0.701212 total=36243 time="12:11:00" level=info msg="Protein inference results" decoy=3429 target=13842 time="12:11:01" level=info msg="Converged to 24.06 % FDR with 8420 Proteins" decoy=2026 threshold=0 total=10446 time="12:11:01" level=info msg="Applying sequential FDR estimation" ions=36748 peptides=28937 psms=75138 time="12:11:01" level=info msg="Converged to 0.60 % FDR with 74691 PSMs" decoy=447 threshold=0.500028 total=75138 time="12:11:01" level=info msg="Converged to 1.00 % FDR with 28293 Peptides" decoy=282 threshold=0.614536 total=28575 time="12:11:01" level=info msg="Converged to 1.00 % FDR with 36243 Ions" decoy=362 threshold=0.532844 total=36605 time="12:11:01" level=info msg="Post processing identifications" time="12:11:03" level=info msg="Assigning protein identifications to layers" time="12:11:15" level=info msg="Processing protein inference" time="12:11:15" level=info msg="Synchronizing PSMs and proteins" time="12:11:16" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=36243 peptides=28293 proteins=4702 psms=74691 time="12:11:16" level=info msg=Saving time="12:11:17" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --sequential --prot 1 --picked --tag rev_ --pepxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d --dbbin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --protxml /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./combined.prot.xml --probin /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d --razor time="12:11:17" level=info msg="Executing Filter v5.1.1" time="12:11:17" level=info msg="Fetching protein inference from /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d" time="12:11:17" level=info msg="Processing peptide identification files" time="12:11:17" level=info msg="Parsing /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.pep.xml" time="12:11:26" level=info msg="1+ Charge profile" decoy=2 target=40 time="12:11:26" level=info msg="2+ Charge profile" decoy=443 target=41631 time="12:11:26" level=info msg="3+ Charge profile" decoy=234 target=25465 time="12:11:26" level=info msg="4+ Charge profile" decoy=61 target=6709 time="12:11:26" level=info msg="5+ Charge profile" decoy=6 target=979 time="12:11:26" level=info msg="6+ Charge profile" decoy=0 target=0 time="12:11:26" level=info msg="Database search results" ions=36692 peptides=28748 psms=75570 time="12:11:26" level=info msg="Converged to 1.00 % FDR with 74824 PSMs" decoy=746 threshold=0.500057 total=75570 time="12:11:26" level=info msg="Converged to 1.00 % FDR with 27535 Peptides" decoy=275 threshold=0.73352 total=27810 time="12:11:26" level=info msg="Converged to 1.00 % FDR with 35538 Ions" decoy=355 threshold=0.672363 total=35893 time="12:11:26" level=info msg="Protein inference results" decoy=3429 target=13842 time="12:11:26" level=info msg="Converged to 24.06 % FDR with 8420 Proteins" decoy=2026 threshold=0 total=10446 time="12:11:27" level=info msg="Applying sequential FDR estimation" ions=36402 peptides=28461 psms=75272 time="12:11:27" level=info msg="Converged to 0.64 % FDR with 74797 PSMs" decoy=475 threshold=0.500057 total=75272 time="12:11:27" level=info msg="Converged to 1.00 % FDR with 27754 Peptides" decoy=277 threshold=0.618259 total=28031 time="12:11:27" level=info msg="Converged to 1.00 % FDR with 35794 Ions" decoy=357 threshold=0.554103 total=36151 time="12:11:27" level=info msg="Post processing identifications" time="12:11:28" level=info msg="Assigning protein identifications to layers" time="12:11:41" level=info msg="Processing protein inference" time="12:11:41" level=info msg="Synchronizing PSMs and proteins" time="12:11:42" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=35793 peptides=27754 proteins=4924 psms=74796 time="12:11:42" level=info msg=Saving time="12:11:43" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 report time="12:11:43" level=info msg="Executing Report v5.1.1" time="12:11:43" level=info msg="Creating reports" time="12:11:45" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 report time="12:11:45" level=info msg="Executing Report v5.1.1" time="12:11:45" level=info msg="Creating reports" time="12:11:47" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 report time="12:11:47" level=info msg="Executing Report v5.1.1" time="12:11:47" level=info msg="Creating reports" time="12:11:49" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 report time="12:11:49" level=info msg="Executing Report v5.1.1" time="12:11:49" level=info msg="Creating reports" time="12:11:51" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 report time="12:11:51" level=info msg="Executing Report v5.1.1" time="12:11:51" level=info msg="Creating reports" time="12:11:53" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 report time="12:11:53" level=info msg="Executing Report v5.1.1" time="12:11:53" level=info msg="Creating reports" time="12:11:55" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="12:11:55" level=info msg="Executing Workspace v5.1.1" time="12:11:55" level=info msg="Removing workspace" time="12:11:55" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="12:11:55" level=info msg="Executing Workspace v5.1.1" time="12:11:55" level=info msg="Removing workspace" time="12:11:55" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="12:11:56" level=info msg="Executing Workspace v5.1.1" time="12:11:56" level=info msg="Removing workspace" time="12:11:56" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="12:11:56" level=info msg="Executing Workspace v5.1.1" time="12:11:56" level=info msg="Removing workspace" time="12:11:56" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="12:11:56" level=info msg="Executing Workspace v5.1.1" time="12:11:56" level=info msg="Removing workspace" time="12:11:56" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="12:11:56" level=info msg="Executing Workspace v5.1.1" time="12:11:56" level=info msg="Removing workspace" time="12:11:56" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d] /rd1/user/lit/software/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="12:11:56" level=info msg="Executing Workspace v5.1.1" time="12:11:56" level=info msg="Removing workspace" time="12:11:56" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 IonQuant [Work dir: /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/.] java -Djava.awt.headless=true -Xmx180G -Dlibs.bruker.dir=/rd1/user/lit/project/sORFs/fragpipe_tools/tools/MSFragger-4.1/ext/bruker -Dlibs.thermo.dir=/rd1/user/lit/project/sORFs/fragpipe_tools/tools/MSFragger-4.1/ext/thermo -cp /rd1/user/lit/software/fragpipe/tools/jfreechart-1.5.3.jar:/rd1/user/lit/software/fragpipe/tools/batmass-io-1.33.4.jar:/rd1/user/lit/project/sORFs/fragpipe_tools/tools/IonQuant-1.10.27.jar ionquant.IonQuant --threads 40 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 1 --site-reports 1 --msstats 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 /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./filelist_ionquant.txt --modlist /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./modmasses_ionquant.txt IonQuant version IonQuant-1.10.27 Batmass-IO version 1.33.4 timsdata library version timsdata-2-21-0-4 (c) University of Michigan System OS: Linux, Architecture: amd64 Java Info: 17.0.13-internal, OpenJDK 64-Bit Server VM, Oracle Corporation JVM started with 180 GB memory 2024-11-18 12:11:57 [INFO] - Collecting variable modifications from all psm.tsv files... 2024-11-18 12:11:58 [INFO] - Loading and indexing all psm.tsv files... 2024-11-18 12:12:08 [INFO] - Parameters: 2024-11-18 12:12:08 [INFO] - perform-ms1quant = 1 2024-11-18 12:12:08 [INFO] - perform-isoquant = 0 2024-11-18 12:12:08 [INFO] - isotol = 20.0 2024-11-18 12:12:08 [INFO] - isolevel = 2 2024-11-18 12:12:08 [INFO] - isotype = tmt10 2024-11-18 12:12:08 [INFO] - site-reports = 1 2024-11-18 12:12:08 [INFO] - msstats = 1 2024-11-18 12:12:08 [INFO] - threads = 40 2024-11-18 12:12:08 [INFO] - mztol = 10.0 2024-11-18 12:12:08 [INFO] - rttol = 0.4 2024-11-18 12:12:08 [INFO] - imtol = 0.05 2024-11-18 12:12:08 [INFO] - minisotopes = 2 2024-11-18 12:12:08 [INFO] - minscans = 3 2024-11-18 12:12:08 [INFO] - psm = /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/psm.tsv 2024-11-18 12:12:08 [INFO] - psm = /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2_54_1_3564_d/psm.tsv 2024-11-18 12:12:08 [INFO] - psm = /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1_41_1_3552_d/psm.tsv 2024-11-18 12:12:08 [INFO] - psm = /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1_43_1_3554_d/psm.tsv 2024-11-18 12:12:08 [INFO] - psm = /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1_45_1_3557_d/psm.tsv 2024-11-18 12:12:08 [INFO] - psm = /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1_54_1_3559_d/psm.tsv 2024-11-18 12:12:08 [INFO] - multidir = /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./ 2024-11-18 12:12:08 [INFO] - excludemods = 2024-11-18 12:12:08 [INFO] - minions = 1 2024-11-18 12:12:08 [INFO] - maxlfq = 1 2024-11-18 12:12:08 [INFO] - ibaq = 0 2024-11-18 12:12:08 [INFO] - normalization = 1 2024-11-18 12:12:08 [INFO] - minexps = 1 2024-11-18 12:12:08 [INFO] - minfreq = 0.0 2024-11-18 12:12:08 [INFO] - tp = 0 2024-11-18 12:12:08 [INFO] - mbr = 1 2024-11-18 12:12:08 [INFO] - mbrrttol = 1.0 2024-11-18 12:12:08 [INFO] - mbrimtol = 0.05 2024-11-18 12:12:08 [INFO] - mbrtoprun = 10 2024-11-18 12:12:08 [INFO] - mbrmincorr = 0.0 2024-11-18 12:12:08 [INFO] - ionmobility = 1 2024-11-18 12:12:08 [INFO] - ionfdr = 0.01 2024-11-18 12:12:08 [INFO] - peptidefdr = 1.0 2024-11-18 12:12:08 [INFO] - proteinfdr = 1.0 2024-11-18 12:12:08 [INFO] - light = 2024-11-18 12:12:08 [INFO] - medium = 2024-11-18 12:12:08 [INFO] - heavy = 2024-11-18 12:12:08 [INFO] - requantify = 0 2024-11-18 12:12:08 [INFO] - writeindex = 0 2024-11-18 12:12:08 [INFO] - locprob = 0.75 2024-11-18 12:12:08 [INFO] - uniqueness = 0 2024-11-18 12:12:08 [INFO] - filelist = /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./filelist_ionquant.txt 2024-11-18 12:12:08 [INFO] - specdir = /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min 2024-11-18 12:12:08 [INFO] - modlist = /rd1/user/lit/project/sORFs/output/MS/Fragpipe_output/2024_11_18_batch_run_6_samples_test_overlap/Trypsin_LysC/./modmasses_ionquant.txt 2024-11-18 12:12:08 [INFO] - mod masses: 2024-11-18 12:12:08 [INFO] - 15.9949 2024-11-18 12:12:08 [INFO] - 42.0106 2024-11-18 12:12:08 [INFO] - 57.02146 2024-11-18 12:12:08 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2024-11-18 12:12:08 [INFO] - Loading /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.d... 2024-11-18 12:12:09 [INFO] - ...20%...40%...60%...80%...100% 2024-11-18 12:12:45 [INFO] - Building index... 2024-11-18 12:15:06 [INFO] - Writing index to /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.quantindex 2024-11-18 12:15:27 [INFO] - Quantifying... 2024-11-18 12:15:34 [INFO] - Loading /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.d... 2024-11-18 12:15:34 [INFO] - ...20%...40%...60%...80%...100% 2024-11-18 12:16:06 [INFO] - Building index... 2024-11-18 12:18:36 [INFO] - Writing index to /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.quantindex 2024-11-18 12:18:59 [INFO] - Quantifying... 2024-11-18 12:19:04 [INFO] - Loading /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.d... 2024-11-18 12:19:04 [INFO] - ...20%...40%...60%...80%...100% 2024-11-18 12:19:40 [INFO] - Building index... 2024-11-18 12:22:07 [INFO] - Writing index to /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.quantindex 2024-11-18 12:22:32 [INFO] - Quantifying... 2024-11-18 12:22:36 [INFO] - Loading /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.d... 2024-11-18 12:22:36 [INFO] - ...20%...40%...60%...80%...100% 2024-11-18 12:23:13 [INFO] - Building index... 2024-11-18 12:25:38 [INFO] - Writing index to /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.quantindex 2024-11-18 12:26:03 [INFO] - Quantifying... 2024-11-18 12:26:07 [INFO] - Loading /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.d... 2024-11-18 12:26:07 [INFO] - ...20%...40%...60%...80%...100% 2024-11-18 12:26:43 [INFO] - Building index... 2024-11-18 12:29:06 [INFO] - Writing index to /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.quantindex 2024-11-18 12:29:31 [INFO] - Quantifying... 2024-11-18 12:29:35 [INFO] - Loading /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.d... 2024-11-18 12:29:35 [INFO] - ...20%...40%...60%...80%...100% 2024-11-18 12:30:10 [INFO] - Building index... 2024-11-18 12:32:32 [INFO] - Writing index to /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.quantindex 2024-11-18 12:32:54 [INFO] - Quantifying... 2024-11-18 12:32:58 [INFO] - Updating Philosopher's tables... 2024-11-18 12:33:15 [INFO] - Matching-between-runs: CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562... 2024-11-18 12:33:18 [INFO] - Calculating correlations between all other runs... 2024-11-18 12:33:21 [INFO] - Reading index from /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.quantindex 2024-11-18 12:33:43 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564... 2024-11-18 12:33:49 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552... 2024-11-18 12:33:53 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554... 2024-11-18 12:33:58 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557... 2024-11-18 12:34:03 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559... 2024-11-18 12:34:08 [INFO] - Training LDA models for all matched features. 2024-11-18 12:34:08 [INFO] - #{+1} = 20345, #{-1} = 8829, #{+2} = 32493, #{-2} = 12393 2024-11-18 12:34:08 [INFO] - Standardized coefficients: 2024-11-18 12:34:08 [INFO] - log10(intensity): 0.9075805092634535 2024-11-18 12:34:08 [INFO] - log10(KL): -0.18097196975385643 2024-11-18 12:34:08 [INFO] - abs(ppm): -0.09183276900565357 2024-11-18 12:34:08 [INFO] - IM diff: -0.27823640835343694 2024-11-18 12:34:08 [INFO] - RT diff: -0.24020409857417846 2024-11-18 12:34:08 [INFO] - Fitting a mixture model... 2024-11-18 12:34:11 [INFO] - Matching-between-runs: CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564... 2024-11-18 12:34:12 [INFO] - Calculating correlations between all other runs... 2024-11-18 12:34:13 [INFO] - Reading index from /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564.quantindex 2024-11-18 12:34:36 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562... 2024-11-18 12:34:41 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552... 2024-11-18 12:34:46 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554... 2024-11-18 12:34:54 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557... 2024-11-18 12:34:59 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559... 2024-11-18 12:35:03 [INFO] - Training LDA models for all matched features. 2024-11-18 12:35:03 [INFO] - #{+1} = 19262, #{-1} = 8204, #{+2} = 33054, #{-2} = 12639 2024-11-18 12:35:03 [INFO] - Standardized coefficients: 2024-11-18 12:35:03 [INFO] - log10(intensity): 0.2545973507641611 2024-11-18 12:35:03 [INFO] - log10(KL): -0.053669098095873606 2024-11-18 12:35:03 [INFO] - abs(ppm): -0.027505729713482106 2024-11-18 12:35:03 [INFO] - IM diff: -0.07421317171402647 2024-11-18 12:35:03 [INFO] - RT diff: -0.06788416654751533 2024-11-18 12:35:03 [INFO] - Fitting a mixture model... 2024-11-18 12:35:06 [INFO] - Matching-between-runs: CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552... 2024-11-18 12:35:09 [INFO] - Calculating correlations between all other runs... 2024-11-18 12:35:11 [INFO] - Reading index from /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552.quantindex 2024-11-18 12:35:33 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562... 2024-11-18 12:35:38 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564... 2024-11-18 12:35:43 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554... 2024-11-18 12:35:48 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557... 2024-11-18 12:35:52 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559... 2024-11-18 12:35:56 [INFO] - Training LDA models for all matched features. 2024-11-18 12:35:57 [INFO] - #{+1} = 22949, #{-1} = 10092, #{+2} = 30409, #{-2} = 11685 2024-11-18 12:35:57 [INFO] - Standardized coefficients: 2024-11-18 12:35:57 [INFO] - log10(intensity): 0.9090919550720332 2024-11-18 12:35:57 [INFO] - log10(KL): -0.18313199900552948 2024-11-18 12:35:57 [INFO] - abs(ppm): -0.08813163299974504 2024-11-18 12:35:57 [INFO] - IM diff: -0.292933690062671 2024-11-18 12:35:57 [INFO] - RT diff: -0.21549282274500955 2024-11-18 12:35:57 [INFO] - Fitting a mixture model... 2024-11-18 12:35:59 [INFO] - Matching-between-runs: CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554... 2024-11-18 12:36:00 [INFO] - Calculating correlations between all other runs... 2024-11-18 12:36:02 [INFO] - Reading index from /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554.quantindex 2024-11-18 12:36:25 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562... 2024-11-18 12:36:31 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564... 2024-11-18 12:36:35 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552... 2024-11-18 12:36:40 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557... 2024-11-18 12:36:44 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559... 2024-11-18 12:36:48 [INFO] - Training LDA models for all matched features. 2024-11-18 12:36:49 [INFO] - #{+1} = 25033, #{-1} = 10226, #{+2} = 33090, #{-2} = 13023 2024-11-18 12:36:49 [INFO] - Standardized coefficients: 2024-11-18 12:36:49 [INFO] - log10(intensity): 0.2583309497604087 2024-11-18 12:36:49 [INFO] - log10(KL): -0.05143138098818366 2024-11-18 12:36:49 [INFO] - abs(ppm): -0.0240440437231681 2024-11-18 12:36:49 [INFO] - IM diff: -0.07931929644148336 2024-11-18 12:36:49 [INFO] - RT diff: -0.0645312686106694 2024-11-18 12:36:49 [INFO] - Fitting a mixture model... 2024-11-18 12:36:50 [INFO] - Matching-between-runs: CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557... 2024-11-18 12:36:51 [INFO] - Calculating correlations between all other runs... 2024-11-18 12:36:53 [INFO] - Reading index from /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557.quantindex 2024-11-18 12:37:15 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562... 2024-11-18 12:37:20 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564... 2024-11-18 12:37:25 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552... 2024-11-18 12:37:29 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554... 2024-11-18 12:37:33 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559... 2024-11-18 12:37:37 [INFO] - Training LDA models for all matched features. 2024-11-18 12:37:37 [INFO] - #{+1} = 26826, #{-1} = 11040, #{+2} = 29245, #{-2} = 11110 2024-11-18 12:37:37 [INFO] - Standardized coefficients: 2024-11-18 12:37:37 [INFO] - log10(intensity): 0.20432806714959706 2024-11-18 12:37:37 [INFO] - log10(KL): -0.041543822036894926 2024-11-18 12:37:37 [INFO] - abs(ppm): -0.02145052157076024 2024-11-18 12:37:37 [INFO] - IM diff: -0.06146277961951812 2024-11-18 12:37:37 [INFO] - RT diff: -0.0510415770293091 2024-11-18 12:37:37 [INFO] - Fitting a mixture model... 2024-11-18 12:37:39 [INFO] - Matching-between-runs: CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559... 2024-11-18 12:37:40 [INFO] - Calculating correlations between all other runs... 2024-11-18 12:37:42 [INFO] - Reading index from /rd1/user/lit/project/sORFs/raw_data/MS/Guomics_SP_MSdata/CAD20241022licq_BSEP_PreExp_DDA_60min/CAD20241022licq_BSEP_PreExp_DDA_60min_S4_Slot1-54_1_3559.quantindex 2024-11-18 12:38:00 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562... 2024-11-18 12:38:04 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_F4_Slot2-54_1_3564... 2024-11-18 12:38:09 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_P2_Slot1-41_1_3552... 2024-11-18 12:38:14 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_P4_Slot1-43_1_3554... 2024-11-18 12:38:19 [INFO] - Transferring CAD20241022licq_BSEP_PreExp_DDA_60min_S2_Slot1-45_1_3557... 2024-11-18 12:38:23 [INFO] - Training LDA models for all matched features. 2024-11-18 12:38:23 [INFO] - #{+1} = 23709, #{-1} = 9576, #{+2} = 28428, #{-2} = 10536 2024-11-18 12:38:23 [INFO] - Standardized coefficients: 2024-11-18 12:38:23 [INFO] - log10(intensity): 0.3144082877919718 2024-11-18 12:38:23 [INFO] - log10(KL): -0.06357932871268465 2024-11-18 12:38:23 [INFO] - abs(ppm): -0.035732383398989834 2024-11-18 12:38:23 [INFO] - IM diff: -0.08977924775092003 2024-11-18 12:38:23 [INFO] - RT diff: -0.08040668907107568 2024-11-18 12:38:23 [INFO] - Fitting a mixture model... 2024-11-18 12:38:26 [INFO] - Estimating match-between-runs FDR... 2024-11-18 12:38:43 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.976000 2024-11-18 12:38:43 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100 2024-11-18 12:38:43 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100 2024-11-18 12:38:43 [INFO] - Updating Philosopher's tables... 2024-11-18 12:38:58 [INFO] - Combining experiments and estimating protein intensity... 2024-11-18 12:39:10 [INFO] - Generating modification reports... 2024-11-18 12:39:11 [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 ddaPASEF) 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) (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) (Visualization with Skyline) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics. 26(7):966 (2010) =============================================================ALL JOBS DONE IN 48.2 MINUTES=============================================================