System OS: Linux, Architecture: amd64 Java Info: 17.0.12, OpenJDK 64-Bit Server VM, Red Hat, Inc. .NET Core Info: 6.0.33 Version info: FragPipe version 22.0 MSFragger version 4.1 IonQuant version 1.10.27 diaTracer version 1.1.6 Philosopher version 5.1.1 LCMS files: Experiment/Group: (if "spectral library generation" is enabled, all files will be analyzed together) - /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mzML DDA - /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mzML DDA - /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mzML DDA - /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mzML DDA - /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mzML DDA - /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mzML DDA - /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058.d DIA-Quant - /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056.d DIA-Quant - /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055.d DIA-Quant - /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063.d DIA-Quant - /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061.d DIA-Quant - /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060.d DIA-Quant 55 commands to execute: CheckCentroid java -Xmx400G -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mzML 72 WorkspaceCleanInit [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck WorkspaceCleanInit [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/4f794129-448b-42ff-898a-44c107cfdfbd MSFragger [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -jar -Dfile.encoding=UTF-8 -Xmx400G /nfs/corexfs/proteomic/yufe/tools/fragpipe_tools/MSFragger-4.1.jar /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/fragger.params /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mzML /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mzML /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mzML /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mzML /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mzML /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mzML MSFragger move pepxml java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pepXML /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pepXML MSFragger move pin java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pin /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pin MSFragger move pepxml java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pepXML /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pepXML MSFragger move pin java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pin /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pin MSFragger move pepxml java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pepXML /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pepXML MSFragger move pin java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pin /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pin MSFragger move pepxml java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pepXML /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pepXML MSFragger move pin java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pin /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pin MSFragger move pepxml java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pepXML /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pepXML MSFragger move pin java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pin /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pin MSFragger move pepxml java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pepXML /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pepXML MSFragger move pin java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pin /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pin Percolator [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pin Percolator [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pin Percolator [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pin Percolator [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pin Percolator [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pin Percolator [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pin Percolator: Convert to pepxml [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pin 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_target_psms.tsv 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_decoy_psms.tsv interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer DDA 0.5 /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_calibrated.mzML Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_target_psms.tsv Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pin 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_target_psms.tsv 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_decoy_psms.tsv interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer DDA 0.5 /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_calibrated.mzML Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_target_psms.tsv Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pin 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_target_psms.tsv 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_decoy_psms.tsv interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer DDA 0.5 /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_calibrated.mzML Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_target_psms.tsv Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pin 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_target_psms.tsv 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_decoy_psms.tsv interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer DDA 0.5 /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_calibrated.mzML Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_target_psms.tsv Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pin 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_target_psms.tsv 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_decoy_psms.tsv interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer DDA 0.5 /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_calibrated.mzML Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_target_psms.tsv Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pin 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_target_psms.tsv 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_decoy_psms.tsv interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer DDA 0.5 /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_calibrated.mzML Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_target_psms.tsv Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_decoy_psms.tsv PTMProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/PTMProphet/PTMProphetParser KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,DE:43.0422,DE:87.03203 MINPROB=0.5 MAXTHREADS=1 interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pep.xml interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mod.pep.xml PTMProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/PTMProphet/PTMProphetParser KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,DE:43.0422,DE:87.03203 MINPROB=0.5 MAXTHREADS=1 interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pep.xml interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mod.pep.xml PTMProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/PTMProphet/PTMProphetParser KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,DE:43.0422,DE:87.03203 MINPROB=0.5 MAXTHREADS=1 interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pep.xml interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mod.pep.xml PTMProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/PTMProphet/PTMProphetParser KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,DE:43.0422,DE:87.03203 MINPROB=0.5 MAXTHREADS=1 interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pep.xml interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mod.pep.xml PTMProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/PTMProphet/PTMProphetParser KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,DE:43.0422,DE:87.03203 MINPROB=0.5 MAXTHREADS=1 interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pep.xml interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mod.pep.xml PTMProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/PTMProphet/PTMProphetParser KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,DE:43.0422,DE:87.03203 MINPROB=0.5 MAXTHREADS=1 interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pep.xml interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mod.pep.xml ProteinProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 proteinprophet --maxppmdiff 2000000 --output combined /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 database --annotate /storage/yufe/2021-03-23-decoys-reviewed-contam-UP000005640.fas --prefix rev_ PhilosopherFilter [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --picked --prot 0.01 --tag rev_ --pepxml /storage/yufe/github_issues/github_fragpipe_1815/yufe_3 --protxml /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/combined.prot.xml --razor PhilosopherReport [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 report --removecontam WorkspaceClean [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck SpecLibGen [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] python -u /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/speclib/gen_con_spec_lib.py /storage/yufe/2021-03-23-decoys-reviewed-contam-UP000005640.fas /storage/yufe/github_issues/github_fragpipe_1815/yufe_3 unused /storage/yufe/github_issues/github_fragpipe_1815/yufe_3 True unused use_easypqp noiRT:noIM 72 "--unimod /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.0" delete_intermediate_files /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/filelist_speclibgen.txt DIA-NN [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/diann/1.8.2_beta_8/linux/diann-1.8.1.8 --lib library.tsv --threads 72 --verbose 1 --out diann-output/report.tsv --qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --cfg /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/filelist_diann.txt-- DIA-NN: Propagate information [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/diann-output] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/batmass-io-1.33.4.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.Propagation /storage/yufe/github_issues/github_fragpipe_1815/yufe_3 DIA-NN: Convert DIA-NN output to MSstats.csv [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/diann-output] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.DiannToMsstats report.tsv ./ /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/psm.tsv 0.01 1 0.01 0.01 /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/fragpipe-files.fp-manifest ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [CheckCentroid], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [WorkspaceCleanInit], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [diaTracer], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [MSFragger], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [Percolator], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [PTMProphet], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [ProteinProphet], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [PhilosopherDbAnnotate], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [PhilosopherFilter], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [PhilosopherReport], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [WorkspaceClean], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [SpecLibGen], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] Cmd: [DIA-NN], Work dir: [/storage/yufe/github_issues/github_fragpipe_1815/yufe_3] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of /storage/yufe/2021-03-23-decoys-reviewed-contam-UP000005640.fas~~~~~~~ >Biognosys|iRT-Kit_WR_fusion >rev_sp|O60231|DHX16_HUMAN Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 OS=Homo sapiens OX=9606 GN=DHX16 PE=1 SV=2 >rev_sp|P0DSO3|GAGE4_HUMAN G antigen 4 OS=Homo sapiens OX=9606 GN=GAGE4 PE=5 SV=1 >rev_sp|P50993|AT1A2_HUMAN Sodium/potassium-transporting ATPase subunit alpha-2 OS=Homo sapiens OX=9606 GN=ATP1A2 PE=1 SV=1 >rev_sp|Q14573|ITPR3_HUMAN Inositol 1,4,5-trisphosphate receptor type 3 OS=Homo sapiens OX=9606 GN=ITPR3 PE=1 SV=2 >rev_sp|Q6GQQ9|OTU7B_HUMAN OTU domain-containing protein 7B OS=Homo sapiens OX=9606 GN=OTUD7B PE=1 SV=1 >rev_sp|Q8IXL9|IQCF2_HUMAN IQ domain-containing protein F2 OS=Homo sapiens OX=9606 GN=IQCF2 PE=1 SV=1 >rev_sp|Q8WWQ2|HPSE2_HUMAN Inactive heparanase-2 OS=Homo sapiens OX=9606 GN=HPSE2 PE=1 SV=3 >rev_sp|Q9BSC4|NOL10_HUMAN Nucleolar protein 10 OS=Homo sapiens OX=9606 GN=NOL10 PE=1 SV=1 >rev_sp|Q9NVM1|EVA1B_HUMAN Protein eva-1 homolog B OS=Homo sapiens OX=9606 GN=EVA1B PE=1 SV=1 >rev_sp|W6CW81|PYDC5_HUMAN Pyrin domain-containing protein 5 OS=Homo sapiens OX=9606 GN=PYDC5 PE=1 SV=1 >sp|O60231|DHX16_HUMAN Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 OS=Homo sapiens OX=9606 GN=DHX16 PE=1 SV=2 >sp|P0DSO3|GAGE4_HUMAN G antigen 4 OS=Homo sapiens OX=9606 GN=GAGE4 PE=5 SV=1 >sp|P50993|AT1A2_HUMAN Sodium/potassium-transporting ATPase subunit alpha-2 OS=Homo sapiens OX=9606 GN=ATP1A2 PE=1 SV=1 >sp|Q14573|ITPR3_HUMAN Inositol 1,4,5-trisphosphate receptor type 3 OS=Homo sapiens OX=9606 GN=ITPR3 PE=1 SV=2 >sp|Q6GQQ9|OTU7B_HUMAN OTU domain-containing protein 7B OS=Homo sapiens OX=9606 GN=OTUD7B PE=1 SV=1 >sp|Q8IXL9|IQCF2_HUMAN IQ domain-containing protein F2 OS=Homo sapiens OX=9606 GN=IQCF2 PE=1 SV=1 >sp|Q8WWQ2|HPSE2_HUMAN Inactive heparanase-2 OS=Homo sapiens OX=9606 GN=HPSE2 PE=1 SV=3 >sp|Q9BSC4|NOL10_HUMAN Nucleolar protein 10 OS=Homo sapiens OX=9606 GN=NOL10 PE=1 SV=1 >sp|Q9NVM1|EVA1B_HUMAN Protein eva-1 homolog B OS=Homo sapiens OX=9606 GN=EVA1B PE=1 SV=1 >sp|W6CW81|PYDC5_HUMAN Pyrin domain-containing protein 5 OS=Homo sapiens OX=9606 GN=PYDC5 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=/storage/yufe/2021-03-23-decoys-reviewed-contam-UP000005640.fas crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.medium= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=QuantUMS (high accuracy) diann.run-dia-nn=true 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=false diatracer.mass-defect-offset=0.1 diatracer.rf-max=500 diatracer.run-diatracer=true 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=/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/diann/1.8.2_beta_8/linux/diann-1.8.1.8 fragpipe-config.bin-python=python fragpipe-config.tools-folder=/nfs/corexfs/proteomic/yufe/tools/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=false 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=false msfragger.clip_nTerm_M=true msfragger.deisotope=1 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) msfragger.deneutralloss=1 msfragger.diagnostic_fragments= msfragger.diagnostic_intensity_filter=0 msfragger.digest_max_length=50 msfragger.digest_min_length=7 msfragger.fragment_ion_series=b,y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.group_variable=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.mass_offsets_detailed= msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=10000 msfragger.max_variable_mods_per_peptide=4 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.00 msfragger.misc.fragger.clear-mz-hi=0 msfragger.misc.fragger.clear-mz-lo=0 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=500 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin msfragger.misc.fragger.enzyme-dropdown-2=null msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=2 msfragger.output_format=pepXML_pin msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.output_report_topN_dda_plus=5 msfragger.output_report_topN_dia1=5 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=true msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2= msfragger.search_enzyme_name_1=stricttrypsin msfragger.search_enzyme_name_2=null msfragger.search_enzyme_nocut_1= msfragger.search_enzyme_nocut_2= msfragger.search_enzyme_sense_1=C msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 msfragger.table.var-mods=15.9949,M,true,2; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 43.0422,]^,false,1; 43.0422,DE,true,2; 87.03203,]^,false,1; 87.03203,DE,true,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=300 msfragger.write_calibrated_mzml=true 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=--picked --prot 0.01 phi-report.pep-level-summary=true phi-report.print-decoys=false phi-report.prot-level-summary=true phi-report.remove-contaminants=true phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 protein-prophet.run-protein-prophet=true ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106,DE\:43.0422,DE\:87.03203 MINPROB\=0.5 ptmprophet.run-ptmprophet=true 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=true ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=true 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=false 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=true 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=/storage/yufe/github_issues/github_fragpipe_1815/yufe_3 workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.ram=400 workflow.threads=72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid java -Xmx400G -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mzML 72 Done in 18.5 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="11:05:46" level=info msg="Executing Workspace v5.1.1" time="11:05:46" level=info msg="Removing workspace" time="11:05:46" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --init --nocheck --temp /tmp/4f794129-448b-42ff-898a-44c107cfdfbd time="11:05:46" level=info msg="Executing Workspace v5.1.1" time="11:05:46" level=info msg="Creating workspace" time="11:05:46" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -jar -Dfile.encoding=UTF-8 -Xmx400G /nfs/corexfs/proteomic/yufe/tools/fragpipe_tools/MSFragger-4.1.jar /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/fragger.params /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mzML /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mzML /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mzML /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mzML /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mzML /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mzML 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: 17.0.12, OpenJDK 64-Bit Server VM, Red Hat, Inc. JVM started with 400 GB memory Checking database... ***********************************FIRST SEARCH************************************ Parameters: num_threads = 72 database_name = /storage/yufe/2021-03-23-decoys-reviewed-contam-UP000005640.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 1 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 0 override_charge = 0 precursor_charge_low = 2 precursor_charge_high = 3 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 1 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 = 0 variable_mod_01 = 15.9949 M 2 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. 309669348 fragments to be searched in 1 slices (4.61 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.27 s 001. 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mzML 58.0 s | deisotoping 6.7 s [progress: 1129827/1129827 (100%) - 54692 spectra/s] 20.7s | postprocessing 4.3 s 002. 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mzML 55.3 s | deisotoping 5.0 s [progress: 1051796/1051796 (100%) - 91389 spectra/s] 11.5s | postprocessing 3.5 s 003. 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mzML 44.0 s | deisotoping 4.3 s [progress: 1075730/1075730 (100%) - 93672 spectra/s] 11.5s | postprocessing 5.3 s 004. 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mzML 30.6 s | deisotoping 3.2 s [progress: 740940/740940 (100%) - 97262 spectra/s] 7.6s | postprocessing 3.7 s 005. 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mzML 44.8 s | deisotoping 4.4 s [progress: 1078793/1078793 (100%) - 89408 spectra/s] 12.1s | postprocessing 6.0 s 006. 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mzML 45.4 s | deisotoping 4.6 s [progress: 1109612/1109612 (100%) - 92138 spectra/s] 12.0s | postprocessing 6.2 s ***************************FIRST SEARCH DONE IN 7.209 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | -3.58 3.91 | 0.15 3.25 | -4.66 5.33 | -0.61 4.42 002 | -3.36 3.82 | 0.14 3.19 | -4.07 4.96 | -0.40 4.46 003 | -3.91 3.82 | 0.15 3.15 | -4.64 5.19 | -0.55 4.31 004 | -4.74 3.97 | 0.19 3.40 | -5.48 5.79 | -0.81 4.65 005 | -3.90 3.82 | 0.00 3.11 | -4.51 5.04 | -0.47 4.22 006 | -4.49 3.85 | 0.11 3.12 | -5.05 5.23 | -0.61 4.27 -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|-------|-------|------- MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 -------|-------|-------|-------|-------|-------|-------|-------|------- Count | skip | skip | 106407| 104452| skip rest -------|-------|-------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 -------|-------|-------|-------|-------|-------|------- Count | 106407| 102892| skip rest -------|-------|-------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 109148 -------|------- -------|------- Rm P. | 0 -------|------- Count | 109165 -------|------- New fragment_mass_tolerance = 10.000000 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 0 ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 20.350 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 72 database_name = /storage/yufe/2021-03-23-decoys-reviewed-contam-UP000005640.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 10.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 1 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1/2 mass_offsets = 0.0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 4 max_variable_mods_combinations = 10000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 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 = 1 remove_precursor_peak = 0 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 = 0 variable_mod_01 = 15.9949 M 2 variable_mod_02 = 42.0106 [^ 1 variable_mod_07 = 43.0422 DE 2 variable_mod_09 = 87.03203 DE 2 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 Number of unique peptides of length 7: 287296 of length 8: 278637 of length 9: 277812 of length 10: 262335 of length 11: 248956 of length 12: 238303 of length 13: 232040 of length 14: 217527 of length 15: 206290 of length 16: 192767 of length 17: 180346 of length 18: 173187 of length 19: 170252 of length 20: 152272 of length 21: 145743 of length 22: 136727 of length 23: 127469 of length 24: 120858 of length 25: 113769 of length 26: 105799 of length 27: 100956 of length 28: 96313 of length 29: 87595 of length 30: 83137 of length 31: 77970 of length 32: 73923 of length 33: 69017 of length 34: 64617 of length 35: 58638 of length 36: 56927 of length 37: 51925 of length 38: 48853 of length 39: 43985 of length 40: 41908 of length 41: 39027 of length 42: 35991 of length 43: 30203 of length 44: 24468 of length 45: 18758 of length 46: 12288 of length 47: 7723 of length 48: 4464 of length 49: 2419 of length 50: 1474 In total 5000964 peptides. Generated 616059732 modified peptides. Number of peptides with more than 10000 modification patterns: 5721 Selected fragment index width 0.05 Da. 38181559520 fragments to be searched in 2 slices (568.95 GB total) Operating on slice 1 of 2: Fragment index slice generated in 47.94 s 001. 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mzBIN_calibrated 16.1 s [progress: 1129827/1129827 (100%) - 21128 spectra/s] 53.5s 002. 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mzBIN_calibrated 12.7 s [progress: 1051796/1051796 (100%) - 21562 spectra/s] 48.8s 003. 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mzBIN_calibrated 12.8 s [progress: 1075730/1075730 (100%) - 21437 spectra/s] 50.2s 004. 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mzBIN_calibrated 9.6 s [progress: 740940/740940 (100%) - 24399 spectra/s] 30.4s 005. 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mzBIN_calibrated 12.7 s [progress: 1078793/1078793 (100%) - 21034 spectra/s] 51.3s 006. 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mzBIN_calibrated 7.6 s [progress: 1109612/1109612 (100%) - 20808 spectra/s] 53.3s Operating on slice 2 of 2: Fragment index slice generated in 40.08 s 001. 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mzBIN_calibrated 7.7 s [progress: 1129827/1129827 (100%) - 86810 spectra/s] 13.0s | remapping alternative proteins and postprocessing 37.5 s 002. 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mzBIN_calibrated 7.0 s [progress: 1051796/1051796 (100%) - 101918 spectra/s] 10.3s | remapping alternative proteins and postprocessing 39.3 s 003. 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mzBIN_calibrated 7.1 s [progress: 1075730/1075730 (100%) - 96374 spectra/s] 11.2s | remapping alternative proteins and postprocessing 35.8 s 004. 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mzBIN_calibrated 5.1 s [progress: 740940/740940 (100%) - 105128 spectra/s] 7.0s | remapping alternative proteins and postprocessing 22.1 s 005. 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mzBIN_calibrated 7.6 s [progress: 1078793/1078793 (100%) - 101524 spectra/s] 10.6s | remapping alternative proteins and postprocessing 42.8 s 006. 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mzBIN_calibrated 7.8 s [progress: 1109612/1109612 (100%) - 103896 spectra/s] 10.7s | remapping alternative proteins and postprocessing 39.2 s ***************************MAIN SEARCH DONE IN 14.119 MIN*************************** *******************************TOTAL TIME 41.678 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pepXML /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pin /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pepXML /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pin /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pepXML /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pin /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pepXML /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pin /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pepXML /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pin /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pepXML /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pin /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pin Process 'MSFragger move pin' finished, exit code: 0 Percolator [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.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: /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pin Started Sat Oct 5 11:47:47 2024 on nesvilab-ap-ps2a.med.umich.edu Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.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 43.0422DE 87.03203DE Found 720254 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 403070 positives and 317184 negatives, size ratio=1.27078 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 8 as initial direction. Could separate 35128 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 35279 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 35442 training set positives with q<0.01 in that direction. Found 52915 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 823.1292 cpu seconds or 17 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 61035 PSMs with q<0.01 Iteration 2: Estimated 62735 PSMs with q<0.01 Iteration 3: Estimated 63071 PSMs with q<0.01 Iteration 4: Estimated 63210 PSMs with q<0.01 Iteration 5: Estimated 63315 PSMs with q<0.01 Iteration 6: Estimated 63365 PSMs with q<0.01 Iteration 7: Estimated 63421 PSMs with q<0.01 Iteration 8: Estimated 63417 PSMs with q<0.01 Iteration 9: Estimated 63409 PSMs with q<0.01 Iteration 10: Estimated 63401 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 -0.4302 -0.5263 -0.6212 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0174 0.0572 0.0710 isotope_error_0 0.0249 0.0107 0.0277 isotope_error_1 -0.0433 -0.0698 -0.1013 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -0.8602 -1.2577 -1.3016 log10_evalue 1.1000 1.1696 1.2426 hyperscore 0.3248 0.3914 0.4075 delta_hyperscore -0.1410 0.0330 0.1446 matched_ion_num -0.1841 -0.1898 -0.2200 complementary_ions 0.1544 0.1928 0.2818 ion_series -0.1110 -0.1521 -0.1950 weighted_average_abs_fragment_ppm -0.0248 -0.1048 -0.1022 length_7 -0.0292 -0.0110 0.0208 length_8 0.0361 0.0866 0.0681 length_9_30 0.0085 -0.0524 -0.0844 length_31 0.0000 0.0000 0.0000 ntt -0.3212 -0.4256 -0.5192 nmc -0.3360 -0.3783 -0.4920 charge_1 -0.0609 -0.0655 -0.1054 charge_2 0.1741 0.1885 0.2517 charge_3 0.0899 0.1088 0.1701 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.0552 0.0793 0.1164 15.9949M -1.0440 -1.1371 -1.5698 43.0422DE -1.4163 -1.4047 -1.5912 87.03203DE -4.2128 -4.0651 -4.9015 m0 Found 63073 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 403070 target PSMs and 317184 decoy PSMs. Calculating q values. Final list yields 63076 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 670.0365 cpu seconds or 47 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.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: /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pin Started Sat Oct 5 11:48:54 2024 on nesvilab-ap-ps2a.med.umich.edu Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.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 43.0422DE 87.03203DE Found 704929 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 445098 positives and 259831 negatives, size ratio=1.71303 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 8 as initial direction. Could separate 87166 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 87623 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 87146 training set positives with q<0.01 in that direction. Found 131001 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 188.8305 cpu seconds or 8 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 146912 PSMs with q<0.01 Iteration 2: Estimated 151068 PSMs with q<0.01 Iteration 3: Estimated 152472 PSMs with q<0.01 Iteration 4: Estimated 153179 PSMs with q<0.01 Iteration 5: Estimated 153406 PSMs with q<0.01 Iteration 6: Estimated 153610 PSMs with q<0.01 Iteration 7: Estimated 153650 PSMs with q<0.01 Iteration 8: Estimated 153754 PSMs with q<0.01 Iteration 9: Estimated 153783 PSMs with q<0.01 Iteration 10: Estimated 153726 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 -0.7356 -0.6071 -0.6312 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0640 0.0295 0.0398 isotope_error_0 0.0328 0.0308 0.0335 isotope_error_1 -0.0998 -0.0621 -0.0755 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -1.4427 -1.3513 -1.3590 log10_evalue 0.9072 0.5875 0.4950 hyperscore 0.8544 0.7130 0.7301 delta_hyperscore 1.0231 0.9635 1.0407 matched_ion_num -0.0035 -0.0724 -0.0112 complementary_ions 0.3193 0.2336 0.2497 ion_series -0.3186 -0.2826 -0.2522 weighted_average_abs_fragment_ppm -0.1743 -0.1311 -0.1562 length_7 -0.0532 -0.0489 -0.0469 length_8 0.1265 0.1067 0.1168 length_9_30 0.1043 0.0587 0.0769 length_31 0.0000 0.0000 0.0000 ntt -0.3972 -0.3393 -0.3409 nmc -0.4794 -0.5756 -0.6170 charge_1 -0.0863 -0.0447 -0.0424 charge_2 0.1825 0.1627 0.1653 charge_3 0.1041 0.1160 0.1296 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.2573 -0.2409 -0.2021 15.9949M -1.4694 -1.1700 -1.3118 43.0422DE -1.6046 -1.5717 -1.5212 87.03203DE -2.6958 -2.7126 -2.7902 m0 Found 153494 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 445098 target PSMs and 259831 decoy PSMs. Calculating q values. Final list yields 153507 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 556.5701 cpu seconds or 48 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.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: /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pin Started Sat Oct 5 11:49:52 2024 on nesvilab-ap-ps2a.med.umich.edu Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.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 43.0422DE 87.03203DE Found 444484 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 245429 positives and 199055 negatives, size ratio=1.23297 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 8 as initial direction. Could separate 17440 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 16848 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 17118 training set positives with q<0.01 in that direction. Found 25663 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 165.0571 cpu seconds or 5 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 30611 PSMs with q<0.01 Iteration 2: Estimated 31777 PSMs with q<0.01 Iteration 3: Estimated 32069 PSMs with q<0.01 Iteration 4: Estimated 32139 PSMs with q<0.01 Iteration 5: Estimated 32201 PSMs with q<0.01 Iteration 6: Estimated 32275 PSMs with q<0.01 Iteration 7: Estimated 32275 PSMs with q<0.01 Iteration 8: Estimated 32322 PSMs with q<0.01 Iteration 9: Estimated 32340 PSMs with q<0.01 Iteration 10: Estimated 32346 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 -0.4941 -0.5158 -0.6641 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0663 0.0599 0.0568 isotope_error_0 0.0321 0.0330 0.0554 isotope_error_1 -0.1013 -0.0956 -0.1153 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -1.2932 -1.0165 -1.4092 log10_evalue 0.9807 0.9494 1.0954 hyperscore 0.3252 0.2608 0.3778 delta_hyperscore -0.1600 -0.2095 -0.0198 matched_ion_num -0.2086 -0.2259 -0.2361 complementary_ions 0.1995 0.2252 0.2431 ion_series -0.1329 -0.0951 -0.1774 weighted_average_abs_fragment_ppm -0.0317 -0.0166 -0.0277 length_7 -0.0224 -0.0373 -0.0125 length_8 0.0349 0.0372 0.0196 length_9_30 0.0140 0.0146 0.0403 length_31 0.0000 0.0000 0.0000 ntt -0.5241 -0.5045 -0.6209 nmc -0.3943 -0.3166 -0.3813 charge_1 -0.0568 -0.0665 -0.1071 charge_2 0.1873 0.1682 0.2411 charge_3 0.0626 0.0602 0.0569 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.0555 0.0796 0.0342 15.9949M -1.2069 -1.0041 -1.3653 43.0422DE -2.2297 -1.1560 -2.2907 87.03203DE -5.5998 -4.4182 -5.9376 m0 Found 32101 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 245429 target PSMs and 199055 decoy PSMs. Calculating q values. Final list yields 32125 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 326.3787 cpu seconds or 26 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.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: /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pin Started Sat Oct 5 11:50:25 2024 on nesvilab-ap-ps2a.med.umich.edu Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.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 43.0422DE 87.03203DE Found 747894 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 472864 positives and 275030 negatives, size ratio=1.71932 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 8 as initial direction. Could separate 93539 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 93101 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 93563 training set positives with q<0.01 in that direction. Found 140086 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 183.4428 cpu seconds or 8 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 157252 PSMs with q<0.01 Iteration 2: Estimated 162251 PSMs with q<0.01 Iteration 3: Estimated 163741 PSMs with q<0.01 Iteration 4: Estimated 164581 PSMs with q<0.01 Iteration 5: Estimated 165073 PSMs with q<0.01 Iteration 6: Estimated 165310 PSMs with q<0.01 Iteration 7: Estimated 165405 PSMs with q<0.01 Iteration 8: Estimated 165377 PSMs with q<0.01 Iteration 9: Estimated 165382 PSMs with q<0.01 Iteration 10: Estimated 165490 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 -0.7109 -0.7295 -0.7390 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0330 0.0384 0.0442 isotope_error_0 0.0261 0.0325 0.0409 isotope_error_1 -0.0607 -0.0728 -0.0874 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -1.3188 -1.3407 -1.3646 log10_evalue 0.7800 0.8874 0.9079 hyperscore 0.9285 0.8936 0.9213 delta_hyperscore 1.1481 1.1264 1.0844 matched_ion_num 0.0677 0.0540 0.0533 complementary_ions 0.2499 0.2567 0.2571 ion_series -0.2976 -0.3121 -0.2719 weighted_average_abs_fragment_ppm -0.1341 -0.1153 -0.1574 length_7 -0.0500 -0.0552 -0.0392 length_8 0.1074 0.0959 0.1038 length_9_30 0.0609 0.0761 0.1006 length_31 0.0000 0.0000 0.0000 ntt -0.4299 -0.4183 -0.4466 nmc -0.4453 -0.4640 -0.6307 charge_1 -0.1082 -0.1025 -0.0675 charge_2 0.1651 0.1807 0.2095 charge_3 0.1644 0.1390 0.1242 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.2951 -0.3192 -0.3029 15.9949M -1.5153 -1.5358 -1.5619 43.0422DE -1.8365 -1.6281 -1.8516 87.03203DE -2.9005 -2.7326 -2.9577 m0 Found 165187 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 472864 target PSMs and 275030 decoy PSMs. Calculating q values. Final list yields 165187 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 608.0547 cpu seconds or 52 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.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: /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pin Started Sat Oct 5 11:51:28 2024 on nesvilab-ap-ps2a.med.umich.edu Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.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 43.0422DE 87.03203DE Found 719726 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 456293 positives and 263433 negatives, size ratio=1.7321 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 8 as initial direction. Could separate 91406 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 91039 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 91119 training set positives with q<0.01 in that direction. Found 136735 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 178.7366 cpu seconds or 8 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 154541 PSMs with q<0.01 Iteration 2: Estimated 159563 PSMs with q<0.01 Iteration 3: Estimated 160868 PSMs with q<0.01 Iteration 4: Estimated 161272 PSMs with q<0.01 Iteration 5: Estimated 161409 PSMs with q<0.01 Iteration 6: Estimated 161545 PSMs with q<0.01 Iteration 7: Estimated 161585 PSMs with q<0.01 Iteration 8: Estimated 161575 PSMs with q<0.01 Iteration 9: Estimated 161614 PSMs with q<0.01 Iteration 10: Estimated 161606 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 -0.5989 -0.6092 -0.4839 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0395 0.0546 0.0236 isotope_error_0 0.0386 0.0232 0.0175 isotope_error_1 -0.0803 -0.0802 -0.0423 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -1.2409 -1.1813 -1.1786 log10_evalue 0.7170 0.7648 0.6677 hyperscore 0.6999 0.7231 0.5685 delta_hyperscore 0.9013 0.9206 0.6279 matched_ion_num -0.0113 -0.0056 -0.0523 complementary_ions 0.3352 0.2945 0.2281 ion_series -0.2496 -0.2420 -0.1654 weighted_average_abs_fragment_ppm -0.0857 -0.0830 -0.0517 length_7 -0.0750 -0.0668 -0.0595 length_8 0.0937 0.0886 0.0640 length_9_30 0.0792 0.0666 0.0633 length_31 0.0000 0.0000 0.0000 ntt -0.3545 -0.3542 -0.2859 nmc -0.4416 -0.3530 -0.3257 charge_1 -0.0693 -0.0724 -0.0564 charge_2 0.1560 0.1205 0.1120 charge_3 0.0946 0.1111 0.0836 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.2800 -0.2669 -0.2398 15.9949M -1.3142 -1.2985 -0.9797 43.0422DE -1.7698 -1.6802 -1.2950 87.03203DE -2.8787 -2.7909 -2.4736 m0 Found 161340 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 456293 target PSMs and 263433 decoy PSMs. Calculating q values. Final list yields 161342 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 626.4163 cpu seconds or 50 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.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: /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/percolator_3_6_5/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 72 --results-psms 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_target_psms.tsv --decoy-results-psms 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pin Started Sat Oct 5 11:52:29 2024 on nesvilab-ap-ps2a.med.umich.edu Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.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 43.0422DE 87.03203DE Found 723842 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 457056 positives and 266786 negatives, size ratio=1.71319 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 8 as initial direction. Could separate 89929 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 89566 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 89378 training set positives with q<0.01 in that direction. Found 134362 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 183.0393 cpu seconds or 8 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 150806 PSMs with q<0.01 Iteration 2: Estimated 155058 PSMs with q<0.01 Iteration 3: Estimated 156317 PSMs with q<0.01 Iteration 4: Estimated 157074 PSMs with q<0.01 Iteration 5: Estimated 157311 PSMs with q<0.01 Iteration 6: Estimated 157365 PSMs with q<0.01 Iteration 7: Estimated 157415 PSMs with q<0.01 Iteration 8: Estimated 157483 PSMs with q<0.01 Iteration 9: Estimated 157512 PSMs with q<0.01 Iteration 10: Estimated 157522 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 -0.5849 -0.6058 -0.5894 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0415 0.0404 0.0302 isotope_error_0 0.0417 0.0331 0.0349 isotope_error_1 -0.0855 -0.0755 -0.0669 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -1.3585 -1.3072 -1.3050 log10_evalue 0.8733 0.9352 0.8963 hyperscore 0.7035 0.6864 0.7448 delta_hyperscore 0.7204 0.7289 0.7293 matched_ion_num 0.0159 0.0063 -0.0392 complementary_ions 0.2065 0.2298 0.2611 ion_series -0.2132 -0.2038 -0.1929 weighted_average_abs_fragment_ppm -0.0786 -0.0947 -0.0825 length_7 -0.0599 -0.0540 -0.0571 length_8 0.0844 0.0841 0.0813 length_9_30 0.0432 0.0662 0.0566 length_31 0.0000 0.0000 0.0000 ntt -0.3472 -0.3498 -0.3508 nmc -0.3045 -0.3258 -0.3685 charge_1 -0.0808 -0.0707 -0.0728 charge_2 0.1389 0.1400 0.1661 charge_3 0.0823 0.0750 0.0598 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.2240 -0.2092 -0.2204 15.9949M -1.2863 -1.2317 -1.2330 43.0422DE -1.9110 -1.5728 -1.7594 87.03203DE -2.9712 -2.6876 -2.8301 m0 Found 157306 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 457056 target PSMs and 266786 decoy PSMs. Calculating q values. Final list yields 157326 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 587.3820 cpu seconds or 50 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pin 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_target_psms.tsv 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_decoy_psms.tsv interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer DDA 0.5 /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_calibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pin 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_target_psms.tsv 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_decoy_psms.tsv interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer DDA 0.5 /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_calibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pin 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_target_psms.tsv 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_decoy_psms.tsv interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer DDA 0.5 /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_calibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pin 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_target_psms.tsv 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_decoy_psms.tsv interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer DDA 0.5 /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_calibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pin 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_target_psms.tsv 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_decoy_psms.tsv interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer DDA 0.5 /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_calibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pin 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_target_psms.tsv 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_decoy_psms.tsv interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer DDA 0.5 /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_calibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.github.chhh.utils.FileDelete /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 PTMProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/PTMProphet/PTMProphetParser KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,DE:43.0422,DE:87.03203 MINPROB=0.5 MAXTHREADS=1 interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pep.xml interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mod.pep.xml PTMProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/PTMProphet/PTMProphetParser KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,DE:43.0422,DE:87.03203 MINPROB=0.5 MAXTHREADS=1 interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pep.xml interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mod.pep.xml PTMProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/PTMProphet/PTMProphetParser KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,DE:43.0422,DE:87.03203 MINPROB=0.5 MAXTHREADS=1 interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pep.xml interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mod.pep.xml PTMProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/PTMProphet/PTMProphetParser KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,DE:43.0422,DE:87.03203 MINPROB=0.5 MAXTHREADS=1 interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pep.xml interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mod.pep.xml PTMProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/PTMProphet/PTMProphetParser KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,DE:43.0422,DE:87.03203 MINPROB=0.5 MAXTHREADS=1 interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pep.xml interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mod.pep.xml PTMProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/PTMProphet/PTMProphetParser KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,DE:43.0422,DE:87.03203 MINPROB=0.5 MAXTHREADS=1 interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pep.xml interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mod.pep.xml Please wait. PTMProphet is running. It can take a long time. Please wait. PTMProphet is running. It can take a long time. Please wait. PTMProphet is running. It can take a long time. Please wait. PTMProphet is running. It can take a long time. Please wait. PTMProphet is running. It can take a long time. Please wait. PTMProphet is running. It can take a long time. [INFO:] Using statically set 15 PPM tolerance ... [INFO:] Writing file interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pep.xml.tmp.V1e8M5 ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pep.xml ... ​ [INFO:] processed 46000/46297 spectrum_queries [INFO:] done ... [INFO:] Computing EM Models ... [INFO:] Iterating PTM Model: ....5...done [INFO:] done ... [INFO:] done ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pep.xml ... ​ [INFO:] written 46000/46297 spectrum_queries [INFO:] done ... [INFO:] Writing file interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mod.pep.xml ... [INFO:] done ... Process 'PTMProphet' finished, exit code: 0 [INFO:] Using statically set 15 PPM tolerance ... [INFO:] Writing file interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pep.xml.tmp.xDdoEA ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pep.xml ... ​ [INFO:] processed 83000/83825 spectrum_queries [INFO:] done ... [INFO:] Computing EM Models ... [INFO:] Iterating PTM Model: ....5...done [INFO:] done ... [INFO:] done ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pep.xml ... ​ [INFO:] written 83000/83825 spectrum_queries [INFO:] done ... [INFO:] Writing file interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mod.pep.xml ... [INFO:] done ... Process 'PTMProphet' finished, exit code: 0 [INFO:] Using statically set 15 PPM tolerance ... [INFO:] Writing file interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pep.xml.tmp.SgzFP8 ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pep.xml ... ​ [INFO:] processed 188000/188473 spectrum_queries [INFO:] done ... [INFO:] Computing EM Models ... [INFO:] Iterating PTM Model: ....5...done [INFO:] done ... [INFO:] done ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pep.xml ... ​ [INFO:] written 188000/188473 spectrum_queries [INFO:] done ... [INFO:] Writing file interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mod.pep.xml ... [INFO:] done ... Process 'PTMProphet' finished, exit code: 0 [INFO:] Using statically set 15 PPM tolerance ... [INFO:] Writing file interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pep.xml.tmp.kLcb5o ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pep.xml ... ​ [INFO:] processed 197000/197439 spectrum_queries [INFO:] done ... [INFO:] Computing EM Models ... [INFO:] Iterating PTM Model: ....5...done [INFO:] done ... [INFO:] done ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pep.xml ... ​ [INFO:] written 197000/197439 spectrum_queries [INFO:] done ... [INFO:] Writing file interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mod.pep.xml ... [INFO:] done ... Process 'PTMProphet' finished, exit code: 0 [INFO:] Using statically set 15 PPM tolerance ... [INFO:] Writing file interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pep.xml.tmp.Y8IWKg ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pep.xml ... ​ [INFO:] processed 200000/200828 spectrum_queries [INFO:] done ... [INFO:] Computing EM Models ... [INFO:] Iterating PTM Model: ....5...done [INFO:] done ... [INFO:] done ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pep.xml ... ​ [INFO:] written 200000/200828 spectrum_queries [INFO:] done ... [INFO:] Writing file interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mod.pep.xml ... [INFO:] done ... Process 'PTMProphet' finished, exit code: 0 [INFO:] Using statically set 15 PPM tolerance ... [INFO:] Writing file interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pep.xml.tmp.Cckyhx ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pep.xml ... ​ [INFO:] processed 192000/192159 spectrum_queries [INFO:] done ... [INFO:] Computing EM Models ... [INFO:] Iterating PTM Model: ....5....done [INFO:] done ... [INFO:] done ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pep.xml ... ​ [INFO:] written 192000/192159 spectrum_queries [INFO:] done ... [INFO:] Writing file interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mod.pep.xml ... [INFO:] done ... Process 'PTMProphet' finished, exit code: 0 ProteinProphet [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 proteinprophet --maxppmdiff 2000000 --output combined /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/filelist_proteinprophet.txt time="12:07:03" 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 /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.pep.xml... ...read in 13 1+, 49159 2+, 29948 3+, 4705 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.pep.xml... ...read in 13 1+, 108567 2+, 67482 3+, 12411 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.pep.xml... ...read in 26 1+, 113685 2+, 70635 3+, 13093 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.pep.xml... ...read in 10 1+, 32407 2+, 12823 3+, 1057 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.pep.xml... ...read in 129 1+, 108490 2+, 71203 3+, 12337 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.pep.xml... ...read in 19 1+, 113738 2+, 74157 3+, 12914 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 168016 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database /storage/yufe/2021-03-23-decoys-reviewed-contam-UP000005640.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry rev_sp|P07203|GPX1_HUMAN : U ACSPGQSLLAEIDPEIDITQFRRSYRRLPVGDPGVLFKEFNWAVDNRCVPSWTILKPDTMLATADDSPAPLAERLFAFLPHAGAGNVECKEFLMFNPEFGGGPRVYKLSNLIEENKANEQHGFQNCPFGLVVLGRPGLRRQLENMQTYDRVTTGULSAVNEILLVKGRLSGLSVPEGGALPRASFAYVSQAAAAAAALRAACM .....:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry rev_sp|P18283|GPX2_HUMAN : U IAVKLLRKIDPEINITPFTRSYRRFPEGEPGILFKEFNWAVDSRRVPSWIILKPDTMLSFPDDYPYPLKDKLYAFVPHENQGNVECKQVLTFTPQYGGGPRVYKLSNLIEENQCNEQHGFQNCPFGLVVLRRPFRCQLENLQTFDRTTTGULSAVNEILVARGRFTNFDVKEGDLSIASLDYFSKAIFAM ........:.........:.........:.........5000 .........:.........:.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry rev_sp|P36969|GPX4_HUMAN : U FYHPLDKEIVLPEEMPGYRKVVCGNKDILFKTFNWKIANGLIGKGKPQIKMWKWLPHADDGNVCIKSFMDFKVNYGAAFEKIEENSGPEQKGFQNCPFALIRLGCEAYRAHLDVLQTYNVETKGUQSAVNTVICVFGRYKDLNVMHGDIDKASFEHMSRACRWDDRSACMTGALGPAALAGCLLAPKLLRCLRGLSM ......:.........:.........:.........:.........6000 ......WARNING: Found the following zero-mass residues in protein entry rev_sp|P49908|SEPP1_HUMAN : UUUUUUUUUU NSPUEUKKAQNKURUSASAETPILQQSIQUAAPPLRUQCSETINEEARLGQUSCLSPLNEKCQUTIASGTKEFILHRCHCCUSRPALESDTPLKCLLQNICRKRCLKKQLDQLDESAPMDRNEPHGQRHQGKHKHHHHLGPPAPHTPANPAGPQQNESLESSGLHQHGHNHHHEHHYHPSPTEVTKDVTALSVRKCFDEDKLTTLSCNGCKKECYAIKIAEEVYPFTLFSFPLGLHYVLRGCRDYILFDDKSGNLLTWVDTQNEEQQYVPIHESVKNKLHTYKLRSSIGQHNVVIYSINSYGEKKLKVRLDELKSAQLICLYUSAQLLAVVTVSGNSNLMPDQDRISWAPPQKCLSSQDQSETGGSPLLCLALALGLSRWM ...:.........:.........:.........:.........:.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry rev_sp|P62341|SELT_HUMAN : U SRHHPISDMHVNLKMENDLIQVLQQMSPLHGSELKSWVPVDNLTIEFAGTSMCQNEIMNSLFFVMMCAYVKNEQGWQWISPAQMGFFAFPDKGVIILGILVLKFVSLFSAIHRYIPQPLYNEGEIRIDPYRQSIVRMYEEFVRRYGUSVCIQFKLLPGTAYQMKLRKSPVGGLNASAESRVMASAAVLLLLLLRM .....:....WARNING: Found the following zero-mass residues in protein entry rev_sp|P63302|SELW_HUMAN : U GQALAAKIAAVLKLFKSETDVYGDGKKKSHILKGAVMVEFFGTAQPTGEGCIDLRGPFEDELKKKLQLYKSKYGUAGCYVVRVALAM .....7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry rev_sp|Q86VQ6|TRXR3_HUMAN : U GUCGKQTIDLGSSKTIELTTFVEGCTPHIGITDDLLQKTLGCKMAAAFGQTVEGANPGLIHFGIVRDHDFKNCIIKAYCTNNERGAVTWELPWFLTHYIELNEKKYVEIAKEESLGCCGYELPTFVTTPVNIYDCKELSAGFLRQALLKGSQIAVPTLEPKDELIDGVAYVYPVNTQEVDNVPIKGSKENIKVGIKELGIKRTCSDRGIALLVTNYVGEITETGETSKALVKLKGPSGKELQQVMVPIFKRLFKVGHQEMYSGVKEAMEQDFGRLLISRVMVTVDLGFGALFGACELAVYSAGVVLTKGPCYPLSFLDDSTICYEKDGQIGLYRPREGTAIVFQAATYYTEQGKKNTAKIKHHEVFEGYSNVYAVAKERLSLRYGWNLSSIHNQIAKTMTEWNHRVQQNYEWGFKRSDCLAQGLLAAQHMLKKPICGVNVCTGGLGWSTGQPSPVVFDLVMVKKGLIAAEKACSLGGSGGGIIILDYDYALDEQLLKQLLGSQYAQFTQDCGGVHVKNVFINPVTKQNTIESLVEQVRAGDDVQDLELVNCEVGLSSFLEKVRTSHPCYSKSFIVVRSREILGVLHRRLEERAESSRSPGPSSLRARRGPPSLVRAGRVHGSRRNPADGAKGPGPSQPPSREM ........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry rev_sp|Q8WWX9|SELM_HUMAN : U LDAHDSTEEPPKAPAWVYEPPVQADPAAKRYFGLEQVLANIEERTMESLPIRELEEYRRGLLVLEPDAGPLHKMVLNHYFPIDQTVFAKVEKLRNLQUGGCTEVRARTLGSLRNWDPRYATAATAPAVLAALLLLLALPPLLLSM ........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9BVL4|SELO_HUMAN : U SSUTVCLEAAWLPPKSSYSRQRGDAGDAETAEADTAAGAECHYPTELLKLVRRVESFDGREAAEIANQAIYNRLVYKPNNAHMVRVHEAQWAAADGAGELDKDLRARYAQLWDAWHGQNRSQLEAASLQELRSQQEVRELERAIGARTGMLAFLQPNSQALMLMMSLQRPDMQPRFALRLEELSACQEMLRALFEALGPSELEVPFSSLLYFTNTFDAGTLHMTELLKSVLAGDEELEVQVLGLKRRMKQLYHRQFEADFEEALIAEGLELPLEPQLAEALKRLNWRCVEPQKSYAYRGTNDSANCVHDPDYRDLFGFPGYDITLGLISMNDTNLVGHCFGVCQWEAVMRATRRTVERFFAANRQVSDSAHAAQIEPYFSSIVYDLLQVRIDNRGVSPGARGTHEDASKFIEFSGFRIFTSAVRLVVTCQEYKPNGDYFVDRVVTSESTVCAGARTTPVGLHFMAESCLFERISSRLVKRGDAQRSFPTPGAGKLQLEWREGTATCVEGLYMAAGDGLQGAFQGFQHGCYCHAAPEAGPLLANGSFFLAAEAEAERAPPAGLGLLALAPESLAVLRPQRLPTPQVRTFCAGPVPRPASPAGEPGPPPAEVPLARLARNDFRLGALWRPAPEMAAGSLTSRPAPSPSCRGLPLLRAAALSAGLAARYVAM ......:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9NZV5|SELN_HUMAN : UU PQLLPLGRRLGEKLFQMYTATSPDEFTSSFSFLNSEIEEPKVSTIDLFYNANIHHVVTGNPLCIMMEVPFSYKELHLGALKQHSSNEQNNQLEELEKVLSWTSIFSENLLTLIPSSELVTERLTRGSGUCSQDDLAGWLLISHVLKNEAKARDFAETFPLYSVKKFPYMAVELRRAAEEWSLEQQWKIEEFVFQLPEGSPLHSDIMSGDEDLIVSPVSPGTAELEMQPIYGIDVEMNSSESAGYLWEMDVNLSRHNPVFLRFDRVHTADKSLIIHGTFQAPSFWFPFDPPESLQFEAHIRFMVTYYFDSIATLCAVAGQPAFRTKVFPRPHFMSLLRHIIVEKGKPPPPYFRNNSLYGTFMSLESPIIWWPEGLEQGPPPLFPQFHRTAFVASPSAAATWNRLGSLALRSVGLFGDKSKTMTEPLLPQFRAEITLTEESPDPPLEEEECSAAPTSRLLSLCSSUNLWPLQPQLSSHSCWQVGTQTVSCSGTLKEAIPKFEEPSIYMDGDTDLSSFLFLGDTGLTKLALEQRAAAQAEAHRACVRVAAAAAAALLAGLLALSRARRRPPAPPQAAPGPSPPGRQGPRARGM ......:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........WARNING: Found the following zero-mass residues in protein entry sp|O60613|SEP15_HUMAN : U MVAMAAGPSGCLVPAFGLRLLLATVLQAVSAFGAEFSSEACRELGFSSNLLCSSCDLLGQFNLLQLDPDCRGCCQEEAQFETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEELSILKWNTDSVEEFLSEKLERI :.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|P07203|GPX1_HUMAN : U MCAARLAAAAAAAQSVYAFSARPLAGGEPVSLGSLRGKVLLIENVASLUGTTVRDYTQMNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGVPLRRYSRRFQTIDIEPDIEALLSQGPSCA ..24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|P22352|GPX3_HUMAN : U MARLLQASCLLSLLLAGFVSQSRGQEKSKMDCHGGISGTIYEYGALTIDGEEYIPFKQYAGKYVLFVNVASYUGLTGQYIELNALQEELAPFGLVILGFPCNQFGKQEPGENSEILPTLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTSELLGTSDRLFWEPMKVHDIRWNFEKFLVGPDGIPIMRWHHRTTVSNVKMDILSYMRRQAALGVKRK ..:.........:.........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|P36969|GPX4_HUMAN : U MSLGRLCRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF ...26000 .........:.........:.........:.........:.........:.........:.........:.........:.....WARNING: Found the following zero-mass residues in protein entry sp|P55073|IOD3_HUMAN : U MPRQATSRLVVGEGEGSQGASGPAATMLRSLLLHSLRLCAQTASCLVLFPRFLGTAFMLWLLDFLCIRKHFLGRRRRGQPEPEVELNSEGEEVPPDDPPICVSDDNRLCTLASLKAVWHGQKLDFFKQAHEGGPAPNSEVVLPDGFQSQHILDYAQGNRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIEEAHPSDGWVTTDSPYIIPQHRSLEDRVSAARVLQQGAPGCALVLDTMANSSSSAYGAYFERLYVIQSGTIMYQGGRGPDGYQVSELRTWLERYDEQLHGARPRRV ....:.........27000 .........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|P62341|SELT_HUMAN : U MRLLLLLLVAASAMVRSEASANLGGVPSKRLKMQYATGPLLKFQICVSUGYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKVYACMMVFFLSNMIENQCMSTGAFEITLNDVPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPHHRS ..:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.......WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG ..:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q86VQ6|TRXR3_HUMAN : U MERSPPQSPGPGKAGDAPNRRSGHVRGARVLSPPGRRARLSSPGPSRSSEAREELRRHLVGLIERSRVVIFSKSYCPHSTRVKELFSSLGVECNVLELDQVDDGARVQEVLSEITNQKTVPNIFVNKVHVGGCDQTFQAYQSGLLQKLLQEDLAYDYDLIIIGGGSGGLSCAKEAAILGKKVMVLDFVVPSPQGTSWGLGGTCVNVGCIPKKLMHQAALLGQALCDSRKFGWEYNQQVRHNWETMTKAIQNHISSLNWGYRLSLREKAVAYVNSYGEFVEHHKIKATNKKGQETYYTAAQFVIATGERPRYLGIQGDKEYCITSDDLFSLPYCPGKTLVVGASYVALECAGFLAGFGLDVTVMVRSILLRGFDQEMAEKVGSYMEQHGVKFLRKFIPVMVQQLEKGSPGKLKVLAKSTEGTETIEGVYNTVLLAIGRDSCTRKIGLEKIGVKINEKSGKIPVNDVEQTNVPYVYAVGDILEDKPELTPVAIQSGKLLAQRLFGASLEKCDYINVPTTVFTPLEYGCCGLSEEKAIEVYKKENLEIYHTLFWPLEWTVAGRENNTCYAKIICNKFDHDRVIGFHILGPNAGEVTQGFAAAMKCGLTKQLLDDTIGIHPTCGEVFTTLEITKSSGLDITQKGCUG .....:.........:.........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|Q8IZQ5|SELH_HUMAN : U MAPRGRKRKAEAAVVAVAEKREKLANGGEGMEEATVVIEHCTSURVYGRNAAALSQALRLEAPELPVKVNPTKPRRGSFEVTLLRPDGSSAELWTGIKKGPPRKLKFPEPQEVVEELKKYLS ..:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q8WWX9|SELM_HUMAN : U MSLLLPPLALLLLLAALVAPATAATAYRPDWNRLSGLTRARVETCGGUQLNRLKEVKAFVTQDIPFYHNLVMKHLPGADPELVLLGRRYEELERIPLSEMTREEINALVQELGFYRKAAPDAQVPPEYVWAPAKPPEETSDHADL .....:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|Q9BQE4|SELS_HUMAN : U MERQEESLSARPALETEGLRFLHTTVGSLLATYGWYIVFSCILLYVVFQKLSARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQLEEEKRRQKIEMWDSMQEGKSYKGNAKKPQEEDSPGPSTSSVLKRKSDRKPLRGGGYNPLSGEGGGACSWRPGRRGPSSGGUG ...:.........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|Q9BVL4|SELO_HUMAN : U MAVYRAALGASLAAARLLPLGRCSPSPAPRSTLSGAAMEPAPRWLAGLRFDNRALRALPVEAPPPGPEGAPSAPRPVPGACFTRVQPTPLRQPRLVALSEPALALLGLGAPPAREAEAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTATGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGVPTTRAGACVTSESTVVRDVFYDGNPKYEQCTVVLRVASTFIRFGSFEIFKSADEHTGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASDSVQRNAAFFREVTRRTARMVAEWQCVGFCHGVLNTDNMSILGLTIDYGPFGFLDRYDPDHVCNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLELGEAILAEEFDAEFQRHYLQKMRRKLGLVQVELEEDGALVSKLLETMHLTGADFTNTFYLLSSFPVELESPGLAEFLARLMEQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSAAELQSRNQGHWADWLQAYRARLDKDLEGAGDAAAWQAEHVRVMHANNPKYVLRNYIAQNAIEAAERGDFSEVRRVLKLLETPYHCEAGAATDAEATEADGADGRQRSYSSKPPLWAAELCVTUSS ...37000 .........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|Q9C0D9|EPT1_HUMAN : U MAGYEYVSPEQLAGFDKYKYSAVDTNPLSLYVMHPFWNTIVKVFPTWLAPNLITFSGFLLVVFNFLLMAYFDPDFYASAPGHKHVPDWVWIVVGILNFVAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKYNTGILFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKNNTLKLNSVYEAMVPLFSPCLLFILSTAWILWSPSDILELHPRVFYFMVGTAFANSTCQLIVCQMSSTRCPTLNWLLVPLFLVVLVVNLGVASYVESILLYTLTTAFTLAHIHYGVRVVKQLSSHFQIYPFSLRKPNSDULGMEEKNIGL ..:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|Q9NNW7|TRXR2_HUMAN : U MAAMAVALRGLGGRFRWRTQAVAGGVRGAARGAAAGQRDYDLLVVGGGSGGLACAKEAAQLGRKVAVVDYVEPSPQGTRWGLGGTCVNVGCIPKKLMHQAALLGGLIQDAPNYGWEVAQPVPHDWRKMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVCGVAKGGKEILLSADHIIIATGGRPRYPTHIEGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTIMMRSIPLRGFDQQMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTVLWAIGRVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEGRPELTPIAIMAGRLLVQRLFGGSSDLMDYDNVPTTVFTPLEYGCVGLSEEEAVARHGQEHVEVYHAHYKPLEFTVAGRDASQCYVKMVCLREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG ......:.........:.........:.........:.........:.........:.........39000 .........:......WARNING: Found the following zero-mass residues in protein entry sp|Q9NZV5|SELN_HUMAN : UU MGRARPGQRGPPSPGPAAQPPAPPRRRARSLALLGALLAAAAAAAVRVCARHAEAQAAARQELALKTLGTDGLFLFSSLDTDGDMYISPEEFKPIAEKLTGSCSVTQTGVQWCSHSSLQPQLPWLNUSSCLSLLRSTPAASCEEEELPPDPSEETLTIEARFQPLLPETMTKSKDGFLGVSRLALSGLRNWTAAASPSAVFATRHFQPFLPPPGQELGEPWWIIPSELSMFTGYLSNNRFYPPPPKGKEVIIHRLLSMFHPRPFVKTRFAPQGAVACLTAISDFYYTVMFRIHAEFQLSEPPDFPFWFSPAQFTGHIILSKDATHVRDFRLFVPNHRSLNVDMEWLYGASESSNMEVDIGYIPQMELEATGPSVPSVILDEDGSMIDSHLPSGEPLQFVFEEIKWQQELSWEEAARRLEVAMYPFKKVSYLPFTEAFDRAKAENKLVHSILLWGALDDQSCUGSGRTLRETVLESSPILTLLNESFISTWSLVKELEELQNNQENSSHQKLAGLHLEKYSFPVEMMICLPNGTVVHHINANYFLDITSVKPEEIESNLFSFSSTFEDPSTATYMQFLKEGLRRGLPLLQP ...:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|Q9Y6D0|SELK_HUMAN : U MVYISNGQVLDSRSQSPWRLSLITDFFWGIAEFVVLFFKTLLQQDVKKRRSYGNSSDSRYDDGRGPPGNPPRRMGRINHLRGPSPPPMAGGUGR ...:...... Total: 40862 Computing degenerate peptides for 30056 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 30444 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 30444 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 30444 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 30444 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 30444 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 30444 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 30444 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=0.000566312, db_size=45499701 Computing MU for 30444 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% time="12:07:28" level=info msg=Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 database --annotate /storage/yufe/2021-03-23-decoys-reviewed-contam-UP000005640.fas --prefix rev_ time="12:07:28" level=info msg="Executing Database v5.1.1" time="12:07:28" level=info msg="Annotating the database" time="12:07:28" level=info msg=Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 filter --picked --prot 0.01 --tag rev_ --pepxml /storage/yufe/github_issues/github_fragpipe_1815/yufe_3 --protxml /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/combined.prot.xml --razor time="12:07:28" level=info msg="Executing Filter v5.1.1" time="12:07:28" level=info msg="Processing peptide identification files" time="12:07:28" level=info msg="Parsing /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mod.pep.xml" time="12:07:28" level=info msg="Parsing /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mod.pep.xml" time="12:07:28" level=info msg="Parsing /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mod.pep.xml" time="12:07:28" level=info msg="Parsing /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mod.pep.xml" time="12:07:28" level=info msg="Parsing /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mod.pep.xml" time="12:07:28" level=info msg="Parsing /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mod.pep.xml" time="12:07:42" level=info msg="1+ Charge profile" decoy=50 target=160 time="12:07:42" level=info msg="2+ Charge profile" decoy=28169 target=497877 time="12:07:42" level=info msg="3+ Charge profile" decoy=15278 target=310970 time="12:07:42" level=info msg="4+ Charge profile" decoy=2541 target=53976 time="12:07:42" level=info msg="5+ Charge profile" decoy=0 target=0 time="12:07:42" level=info msg="6+ Charge profile" decoy=0 target=0 time="12:07:44" level=info msg="Database search results" ions=167127 peptides=144247 psms=909021 time="12:07:46" level=info msg="Converged to 1.00 % FDR with 732720 PSMs" decoy=7327 threshold=0.872821 total=740047 time="12:07:46" level=info msg="Converged to 1.00 % FDR with 57691 Peptides" decoy=576 threshold=0.983237 total=58267 time="12:07:46" level=info msg="Converged to 1.00 % FDR with 72859 Ions" decoy=728 threshold=0.97915 total=73587 time="12:07:46" level=info msg="Protein inference results" decoy=13597 target=15790 time="12:07:46" level=info msg="Converged to 0.96 % FDR with 6634 Proteins" decoy=64 threshold=0.9948 total=6698 time="12:07:47" level=info msg="2D FDR estimation: Protein mirror image" decoy=6634 target=6634 time="12:07:50" level=info msg="Second filtering results" ions=121747 peptides=99918 psms=851881 time="12:07:51" level=info msg="Converged to 1.00 % FDR with 776479 PSMs" decoy=7764 threshold=0.735547 total=784243 time="12:07:52" level=info msg="Converged to 1.00 % FDR with 60784 Peptides" decoy=607 threshold=0.961506 total=61391 time="12:07:52" level=info msg="Converged to 1.00 % FDR with 77360 Ions" decoy=773 threshold=0.950805 total=78133 time="12:07:52" level=info msg="Post processing identifications" time="12:07:58" level=info msg="Assigning protein identifications to layers" time="12:10:12" level=info msg="Processing protein inference" time="12:10:14" level=info msg="Synchronizing PSMs and proteins" time="12:10:17" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=77360 peptides=60784 proteins=6634 psms=776475 time="12:10:17" level=info msg=Saving time="12:10:20" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 report --removecontam time="12:10:20" level=info msg="Executing Report v5.1.1" time="12:10:20" level=info msg="Creating reports" time="12:10:41" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/Philosopher/philosopher-v5.1.1 workspace --clean --nocheck time="12:10:41" level=info msg="Executing Workspace v5.1.1" time="12:10:41" level=info msg="Removing workspace" time="12:10:41" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 SpecLibGen [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] python -u /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/speclib/gen_con_spec_lib.py /storage/yufe/2021-03-23-decoys-reviewed-contam-UP000005640.fas /storage/yufe/github_issues/github_fragpipe_1815/yufe_3 unused /storage/yufe/github_issues/github_fragpipe_1815/yufe_3 True unused use_easypqp noiRT:noIM 72 "--unimod /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.0" delete_intermediate_files /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/filelist_speclibgen.txt File list provided Spectral library building Commands to execute: /usr/local/bin/easypqp convert --unimod /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mod.pep.xml'"'"']' --spectra /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mzML --exclude-range -1.5,3.5 --psms 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.psmpkl --peaks 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.peakpkl /usr/local/bin/easypqp convert --unimod /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mod.pep.xml'"'"']' --spectra /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mzML --exclude-range -1.5,3.5 --psms 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.psmpkl --peaks 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.peakpkl /usr/local/bin/easypqp convert --unimod /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mod.pep.xml'"'"']' --spectra /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mzML --exclude-range -1.5,3.5 --psms 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.psmpkl --peaks 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.peakpkl /usr/local/bin/easypqp convert --unimod /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mod.pep.xml'"'"']' --spectra /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mzML --exclude-range -1.5,3.5 --psms 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.psmpkl --peaks 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.peakpkl /usr/local/bin/easypqp convert --unimod /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mod.pep.xml'"'"']' --spectra /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mzML --exclude-range -1.5,3.5 --psms 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.psmpkl --peaks 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.peakpkl /usr/local/bin/easypqp convert --unimod /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mod.pep.xml'"'"']' --spectra /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mzML --exclude-range -1.5,3.5 --psms 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.psmpkl --peaks 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.peakpkl /usr/local/bin/easypqp library --psmtsv /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/psm.tsv --peptidetsv /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/peptide.tsv --out easypqp_lib_openswath.tsv --rt_lowess_fraction 0.0 /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/filelist_easypqp_library.txt ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ easypqp, version 0.1.50rc1 Executing ['/usr/local/bin/easypqp', 'convert', '--unimod', '/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mod.pep.xml']", '--spectra', '/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mzML', '--exclude-range', '-1.5,3.5', '--psms', '20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.psmpkl', '--peaks', '20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.peakpkl'] 2024-10-05 12:10:44 - Info: Converting ['/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mod.pep.xml']. 2024-10-05 12:10:44 - Info: Parsing run 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer. 2024-10-05 12:10:45 - Info: Parsing pepXML: /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mod.pep.xml 2024-10-05 12:10:53 - Info: 83825 PSMs parsed. 2024-10-05 12:10:53 - Info: Generate theoretical spectra. Warning: unknown modification '216.074623' of residue 'E' - adding it to the database Warning: unknown modification '202.058973' of residue 'D' - adding it to the database Warning: unknown modification '259.116823' of residue 'E' - adding it to the database Warning: unknown modification '245.101173' of residue 'D' - adding it to the database 2024-10-05 12:10:59 - Info: Processing spectra from file /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.mzML. 2024-10-05 12:15:05 - Info: Loaded 1131371 spectra 2024-10-05 12:15:06 - Info: Collecting PSMs... /usr/local/lib64/python3.11/site-packages/numpy/core/fromnumeric.py:59: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead. return bound(*args, **kwds) 2024-10-05 12:15:16 - Info: Got 83825 PSMs 2024-10-05 12:15:16 - Info: Generating Transitions... 2024-10-05 12:15:17 - Info: Generated 1151799 transitions 2024-10-05 12:15:19 - Info: PSMs successfully converted and stored in 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.psmpkl. 2024-10-05 12:15:20 - Info: Peaks successfully converted and stored in 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.peakpkl. 2024-10-05 12:15:20 - Info: Total elapsed time 4.59 minutes. Executing ['/usr/local/bin/easypqp', 'convert', '--unimod', '/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mod.pep.xml']", '--spectra', '/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mzML', '--exclude-range', '-1.5,3.5', '--psms', '20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.psmpkl', '--peaks', '20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.peakpkl'] 2024-10-05 12:15:22 - Info: Converting ['/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mod.pep.xml']. 2024-10-05 12:15:22 - Info: Parsing run 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer. 2024-10-05 12:15:22 - Info: Parsing pepXML: /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mod.pep.xml 2024-10-05 12:15:40 - Info: 188473 PSMs parsed. 2024-10-05 12:15:40 - Info: Generate theoretical spectra. Warning: unknown modification '202.058973' of residue 'D' - adding it to the database Warning: unknown modification '216.074623' of residue 'E' - adding it to the database Warning: unknown modification '259.116823' of residue 'E' - adding it to the database Warning: unknown modification '245.101173' of residue 'D' - adding it to the database 2024-10-05 12:15:51 - Info: Processing spectra from file /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.mzML. 2024-10-05 12:19:34 - Info: Loaded 1055555 spectra 2024-10-05 12:19:35 - Info: Collecting PSMs... /usr/local/lib64/python3.11/site-packages/numpy/core/fromnumeric.py:59: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead. return bound(*args, **kwds) 2024-10-05 12:19:55 - Info: Got 188473 PSMs 2024-10-05 12:19:55 - Info: Generating Transitions... 2024-10-05 12:19:59 - Info: Generated 2687572 transitions 2024-10-05 12:20:04 - Info: PSMs successfully converted and stored in 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.psmpkl. 2024-10-05 12:20:04 - Info: Peaks successfully converted and stored in 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.peakpkl. 2024-10-05 12:20:04 - Info: Total elapsed time 4.71 minutes. Executing ['/usr/local/bin/easypqp', 'convert', '--unimod', '/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mod.pep.xml']", '--spectra', '/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mzML', '--exclude-range', '-1.5,3.5', '--psms', '20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.psmpkl', '--peaks', '20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.peakpkl'] 2024-10-05 12:20:07 - Info: Converting ['/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mod.pep.xml']. 2024-10-05 12:20:07 - Info: Parsing run 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer. 2024-10-05 12:20:07 - Info: Parsing pepXML: /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mod.pep.xml 2024-10-05 12:20:25 - Info: 197439 PSMs parsed. 2024-10-05 12:20:25 - Info: Generate theoretical spectra. Warning: unknown modification '202.058973' of residue 'D' - adding it to the database Warning: unknown modification '216.074623' of residue 'E' - adding it to the database Warning: unknown modification '259.116823' of residue 'E' - adding it to the database Warning: unknown modification '245.101173' of residue 'D' - adding it to the database 2024-10-05 12:20:37 - Info: Processing spectra from file /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.mzML. 2024-10-05 12:24:25 - Info: Loaded 1079478 spectra 2024-10-05 12:24:25 - Info: Collecting PSMs... /usr/local/lib64/python3.11/site-packages/numpy/core/fromnumeric.py:59: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead. return bound(*args, **kwds) 2024-10-05 12:24:46 - Info: Got 197439 PSMs 2024-10-05 12:24:46 - Info: Generating Transitions... 2024-10-05 12:24:51 - Info: Generated 2781108 transitions 2024-10-05 12:24:54 - Info: PSMs successfully converted and stored in 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.psmpkl. 2024-10-05 12:24:55 - Info: Peaks successfully converted and stored in 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.peakpkl. 2024-10-05 12:24:55 - Info: Total elapsed time 4.80 minutes. Executing ['/usr/local/bin/easypqp', 'convert', '--unimod', '/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mod.pep.xml']", '--spectra', '/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mzML', '--exclude-range', '-1.5,3.5', '--psms', '20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.psmpkl', '--peaks', '20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.peakpkl'] 2024-10-05 12:24:57 - Info: Converting ['/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mod.pep.xml']. 2024-10-05 12:24:57 - Info: Parsing run 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer. 2024-10-05 12:24:57 - Info: Parsing pepXML: /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mod.pep.xml 2024-10-05 12:25:02 - Info: 46297 PSMs parsed. 2024-10-05 12:25:02 - Info: Generate theoretical spectra. Warning: unknown modification '216.074623' of residue 'E' - adding it to the database Warning: unknown modification '202.058973' of residue 'D' - adding it to the database Warning: unknown modification '245.101173' of residue 'D' - adding it to the database Warning: unknown modification '259.116823' of residue 'E' - adding it to the database 2024-10-05 12:25:04 - Info: Processing spectra from file /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.mzML. 2024-10-05 12:27:47 - Info: Loaded 742211 spectra 2024-10-05 12:27:47 - Info: Collecting PSMs... /usr/local/lib64/python3.11/site-packages/numpy/core/fromnumeric.py:59: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead. return bound(*args, **kwds) 2024-10-05 12:27:53 - Info: Got 46297 PSMs 2024-10-05 12:27:53 - Info: Generating Transitions... 2024-10-05 12:27:54 - Info: Generated 548140 transitions 2024-10-05 12:27:55 - Info: PSMs successfully converted and stored in 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.psmpkl. 2024-10-05 12:27:55 - Info: Peaks successfully converted and stored in 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.peakpkl. 2024-10-05 12:27:55 - Info: Total elapsed time 2.97 minutes. Executing ['/usr/local/bin/easypqp', 'convert', '--unimod', '/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mod.pep.xml']", '--spectra', '/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mzML', '--exclude-range', '-1.5,3.5', '--psms', '20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.psmpkl', '--peaks', '20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.peakpkl'] 2024-10-05 12:27:57 - Info: Converting ['/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mod.pep.xml']. 2024-10-05 12:27:57 - Info: Parsing run 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer. 2024-10-05 12:27:57 - Info: Parsing pepXML: /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mod.pep.xml 2024-10-05 12:28:16 - Info: 192159 PSMs parsed. 2024-10-05 12:28:16 - Info: Generate theoretical spectra. Warning: unknown modification '216.074623' of residue 'E' - adding it to the database Warning: unknown modification '202.058973' of residue 'D' - adding it to the database Warning: unknown modification '259.116823' of residue 'E' - adding it to the database Warning: unknown modification '245.101173' of residue 'D' - adding it to the database 2024-10-05 12:28:27 - Info: Processing spectra from file /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.mzML. 2024-10-05 12:32:15 - Info: Loaded 1082366 spectra 2024-10-05 12:32:15 - Info: Collecting PSMs... /usr/local/lib64/python3.11/site-packages/numpy/core/fromnumeric.py:59: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead. return bound(*args, **kwds) 2024-10-05 12:32:35 - Info: Got 192159 PSMs 2024-10-05 12:32:35 - Info: Generating Transitions... 2024-10-05 12:32:39 - Info: Generated 2770414 transitions 2024-10-05 12:32:42 - Info: PSMs successfully converted and stored in 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.psmpkl. 2024-10-05 12:32:42 - Info: Peaks successfully converted and stored in 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.peakpkl. 2024-10-05 12:32:42 - Info: Total elapsed time 4.76 minutes. Executing ['/usr/local/bin/easypqp', 'convert', '--unimod', '/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mod.pep.xml']", '--spectra', '/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mzML', '--exclude-range', '-1.5,3.5', '--psms', '20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.psmpkl', '--peaks', '20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.peakpkl'] 2024-10-05 12:32:44 - Info: Converting ['/nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mod.pep.xml']. 2024-10-05 12:32:44 - Info: Parsing run 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer. 2024-10-05 12:32:44 - Info: Parsing pepXML: /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/interact-20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mod.pep.xml 2024-10-05 12:33:03 - Info: 200828 PSMs parsed. 2024-10-05 12:33:03 - Info: Generate theoretical spectra. Warning: unknown modification '216.074623' of residue 'E' - adding it to the database Warning: unknown modification '259.116823' of residue 'E' - adding it to the database Warning: unknown modification '202.058973' of residue 'D' - adding it to the database Warning: unknown modification '245.101173' of residue 'D' - adding it to the database 2024-10-05 12:33:15 - Info: Processing spectra from file /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.mzML. 2024-10-05 12:37:09 - Info: Loaded 1113895 spectra 2024-10-05 12:37:09 - Info: Collecting PSMs... /usr/local/lib64/python3.11/site-packages/numpy/core/fromnumeric.py:59: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead. return bound(*args, **kwds) 2024-10-05 12:37:31 - Info: Got 200828 PSMs 2024-10-05 12:37:31 - Info: Generating Transitions... 2024-10-05 12:37:35 - Info: Generated 2856310 transitions 2024-10-05 12:37:37 - Info: PSMs successfully converted and stored in 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.psmpkl. 2024-10-05 12:37:38 - Info: Peaks successfully converted and stored in 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.peakpkl. 2024-10-05 12:37:38 - Info: Total elapsed time 4.89 minutes. 2024-10-05 12:37:40 - Info: There are psm.tsv and peptide.tsv. Will ignore --psm_fdr_threshold, --peptide_fdr_threshold, --protein_fdr_threshold, --pi0_lambda, --proteotypic, and --no-proteotypic. 2024-10-05 12:37:40 - Info: Reading file /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.psmpkl. 2024-10-05 12:37:40 - Info: Reading file /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.psmpkl. 2024-10-05 12:37:40 - Info: Reading file /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.psmpkl. 2024-10-05 12:37:41 - Info: Reading file /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.psmpkl. 2024-10-05 12:37:41 - Info: Reading file /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.psmpkl. 2024-10-05 12:37:41 - Info: Reading file /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.psmpkl. 2024-10-05 12:37:42 - Info: In total 909020 PSMs loaded. 2024-10-05 12:37:53 - Info: 756580 redundant PSMs identified after filtering with /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/psm.tsv and /nfs/corexfs/proteomic/yufe/github_issues/github_fragpipe_1815/yufe_3/peptide.tsv 2024-10-05 12:37:53 - base_name modified_peptide 0 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer 24381 1 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer 55557 2 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer 58182 3 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer 13787 4 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer 55886 5 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer 58761 2024-10-05 12:37:54 - Info: easypqp_rt_alignment_20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer; Peptide overlap between run and reference: 18015. 2024-10-05 12:37:56 - Info: easypqp_rt_alignment_20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer; Lowess fraction used: 0.08. 2024-10-05 12:37:57 - Info: easypqp_rt_alignment_20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer; Peptide overlap between run and reference: 46712. 2024-10-05 12:37:59 - Info: easypqp_rt_alignment_20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer; Lowess fraction used: 0.01. 2024-10-05 12:38:00 - Info: easypqp_rt_alignment_20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer; Peptide overlap between run and reference: 49273. 2024-10-05 12:38:02 - Info: easypqp_rt_alignment_20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer; Lowess fraction used: 0.02. 2024-10-05 12:38:03 - Info: easypqp_rt_alignment_20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer; Peptide overlap between run and reference: 11290. 2024-10-05 12:38:04 - Info: easypqp_rt_alignment_20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer; Lowess fraction used: 0.02. 2024-10-05 12:38:04 - Info: easypqp_rt_alignment_20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer; Peptide overlap between run and reference: 47219. 2024-10-05 12:38:05 - Info: easypqp_rt_alignment_20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer; Lowess fraction used: 0.01. 2024-10-05 12:38:06 - Info: easypqp_rt_alignment_20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer; Peptide overlap between run and reference: 58761. 2024-10-05 12:38:07 - Info: easypqp_rt_alignment_20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer; Lowess fraction used: 0.08. 2024-10-05 12:38:08 - base_name modified_peptide 0 20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer 24381 1 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer 55557 2 20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer 58182 3 20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer 13787 4 20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer 55886 5 20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer 58761 2024-10-05 12:38:08 - Info: easypqp_im_alignment_20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer; Peptide overlap between run and reference: 18015. 2024-10-05 12:38:09 - Info: easypqp_im_alignment_20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer; Peptide overlap between run and reference: 46712. 2024-10-05 12:38:10 - Info: easypqp_im_alignment_20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer; Peptide overlap between run and reference: 49273. 2024-10-05 12:38:10 - Info: easypqp_im_alignment_20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer; Peptide overlap between run and reference: 11290. 2024-10-05 12:38:11 - Info: easypqp_im_alignment_20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer; Peptide overlap between run and reference: 47219. 2024-10-05 12:38:12 - Info: easypqp_im_alignment_20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer; Peptide overlap between run and reference: 58761. 2024-10-05 12:38:14 - Info: Parsing file /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_PLD_Slot2-38_1_8058_diatracer.peakpkl. 2024-10-05 12:38:17 - Info: Parsing file /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.peakpkl. 2024-10-05 12:38:24 - Info: Parsing file /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S1_total_Slot2-36_1_8055_diatracer.peakpkl. 2024-10-05 12:38:32 - Info: Parsing file /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_PLD_Slot2-41_1_8063_diatracer.peakpkl. 2024-10-05 12:38:33 - Info: Parsing file /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_sup_Slot2-40_1_8061_diatracer.peakpkl. 2024-10-05 12:38:41 - Info: Parsing file /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/20240927_SW-KF_S2_total_Slot2-39_1_8060_diatracer.peakpkl. 2024-10-05 12:39:02 - Info: Library successfully generated. 2024-10-05 12:39:02 - Info: Total elapsed time: 1.36 minutes. /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/speclib/gen_con_spec_lib.py:375: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method. The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy. For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object. df_lib['Proteotypic'].fillna(0, inplace=True) Done generating spectral library 2024-10-05 12:39:40,919:INFO:took 0:28:58.883194 Process 'SpecLibGen' finished, exit code: 0 DIA-NN [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3] /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/diann/1.8.2_beta_8/linux/diann-1.8.1.8 --lib library.tsv --threads 72 --verbose 1 --out diann-output/report.tsv --qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --cfg /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/filelist_diann.txt-- DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks) Compiled on Dec 1 2022 14:47:06 Current date and time: Sat Oct 5 12:39:41 2024 Logical CPU cores: 72 Thread number set to 72 Output will be filtered at 0.01 FDR Precursor/protein x samples expression level matrices will be saved along with the main report Protein inference will not be performed When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones .quant files will not be saved to the disk Fixed-width center of each elution peak will be used for quantification Interference removal from fragment elution curves disabled WARNING: unrecognised option [--] DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme. 6 files will be processed [0:00] Loading spectral library library.tsv [0:02] Spectral library loaded: 6634 protein isoforms, 6634 protein groups and 80222 precursors in 67684 elution groups. [0:02] Initialising library [0:02] Saving the library to library.tsv.speclib [0:02] File #1/6 [0:02] Loading run /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_PLD_Slot2-38_1_8058.d For most diaPASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to values in the range 10-15 ppm. [0:19] 80222 library precursors are potentially detectable [0:19] Processing... [0:22] RT window set to 0.990714 [0:22] Ion mobility window set to 0.0142942 [0:22] Peak width: 4.948 [0:22] Scan window radius set to 10 [0:22] Recommended MS1 mass accuracy setting: 13.8739 ppm [0:25] Optimised mass accuracy: 15.8471 ppm [0:32] Removing low confidence identifications [0:32] Removing interfering precursors [0:34] Training neural networks: 75994 targets, 76954 decoys [0:37] Number of IDs at 0.01 FDR: 51851 [0:39] Calculating protein q-values [0:39] Number of protein isoforms identified at 1% FDR: 5646 (precursor-level), 5496 (protein-level) (inference performed using proteotypic peptides only) [0:39] Quantification [0:41] File #2/6 [0:41] Loading run /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_sup_Slot2-40_1_8061.d [0:56] 80222 library precursors are potentially detectable [0:56] Processing... [0:57] RT window set to 0.973446 [0:57] Ion mobility window set to 0.0139766 [0:57] Recommended MS1 mass accuracy setting: 12.8428 ppm [1:03] Removing low confidence identifications [1:03] Removing interfering precursors [1:07] Training neural networks: 76790 targets, 76154 decoys [1:10] Number of IDs at 0.01 FDR: 72770 [1:12] Calculating protein q-values [1:12] Number of protein isoforms identified at 1% FDR: 6480 (precursor-level), 6458 (protein-level) (inference performed using proteotypic peptides only) [1:12] Quantification [1:13] File #3/6 [1:13] Loading run /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_total_Slot2-39_1_8060.d [1:28] 80222 library precursors are potentially detectable [1:28] Processing... [1:29] RT window set to 0.980173 [1:29] Ion mobility window set to 0.0140599 [1:29] Recommended MS1 mass accuracy setting: 13.1522 ppm [1:36] Removing low confidence identifications [1:36] Removing interfering precursors [1:39] Training neural networks: 76766 targets, 76112 decoys [1:42] Number of IDs at 0.01 FDR: 73690 [1:44] Calculating protein q-values [1:44] Number of protein isoforms identified at 1% FDR: 6491 (precursor-level), 6487 (protein-level) (inference performed using proteotypic peptides only) [1:44] Quantification [1:46] File #4/6 [1:46] Loading run /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_sup_Slot2-37_1_8056.d [1:59] 80222 library precursors are potentially detectable [1:59] Processing... [2:01] RT window set to 0.966287 [2:01] Ion mobility window set to 0.0136224 [2:01] Recommended MS1 mass accuracy setting: 12.064 ppm [2:07] Removing low confidence identifications [2:07] Removing interfering precursors [2:10] Training neural networks: 76413 targets, 75265 decoys [2:13] Number of IDs at 0.01 FDR: 72783 [2:15] Calculating protein q-values [2:15] Number of protein isoforms identified at 1% FDR: 6464 (precursor-level), 6448 (protein-level) (inference performed using proteotypic peptides only) [2:15] Quantification [2:17] File #5/6 [2:17] Loading run /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S1_total_Slot2-36_1_8055.d [2:31] 80222 library precursors are potentially detectable [2:31] Processing... [2:32] RT window set to 0.980188 [2:32] Ion mobility window set to 0.0131563 [2:32] Recommended MS1 mass accuracy setting: 12.7711 ppm [2:38] Removing low confidence identifications [2:38] Removing interfering precursors [2:42] Training neural networks: 76778 targets, 75291 decoys [2:45] Number of IDs at 0.01 FDR: 73751 [2:47] Calculating protein q-values [2:47] Number of protein isoforms identified at 1% FDR: 6488 (precursor-level), 6473 (protein-level) (inference performed using proteotypic peptides only) [2:47] Quantification [2:48] File #6/6 [2:48] Loading run /storage/yufe/github_issues/github_fragpipe_1815/raw/20240927_SW-KF_S2_PLD_Slot2-41_1_8063.d [3:01] 80222 library precursors are potentially detectable [3:01] Processing... [3:05] RT window set to 0.979658 [3:05] Ion mobility window set to 0.0136531 [3:05] Recommended MS1 mass accuracy setting: 13.7537 ppm [3:12] Removing low confidence identifications [3:12] Removing interfering precursors [3:14] Training neural networks: 74198 targets, 73311 decoys [3:18] Number of IDs at 0.01 FDR: 41087 [3:19] Calculating protein q-values [3:19] Number of protein isoforms identified at 1% FDR: 5211 (precursor-level), 5011 (protein-level) (inference performed using proteotypic peptides only) [3:19] Quantification [3:20] Cross-run analysis [3:20] Reading quantification information: 6 files [3:20] Quantifying peptides [3:23] Quantifying proteins [3:24] Calculating q-values for protein and gene groups [3:24] Calculating global q-values for protein and gene groups [3:24] Writing report [3:40] Report saved to diann-output/report.tsv. [3:40] Saving precursor levels matrix [3:41] Precursor levels matrix (1% precursor and protein group FDR) saved to diann-output/report.pr_matrix.tsv. [3:41] Saving protein group levels matrix [3:41] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to diann-output/report.pg_matrix.tsv. [3:41] Saving gene group levels matrix [3:41] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to diann-output/report.gg_matrix.tsv. [3:41] Saving unique genes levels matrix [3:41] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to diann-output/report.unique_genes_matrix.tsv. [3:41] Stats report saved to diann-output/report.stats.tsv [3:41] Log saved to diann-output/report.log.txt Finished Process 'DIA-NN' finished, exit code: 0 DIA-NN: Propagate information [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/diann-output] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/tools/batmass-io-1.33.4.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.Propagation /storage/yufe/github_issues/github_fragpipe_1815/yufe_3 Done in 2298.24 seconds. Process 'DIA-NN: Propagate information' finished, exit code: 0 DIA-NN: Convert DIA-NN output to MSstats.csv [Work dir: /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/diann-output] java -cp /nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar:/nfs/corexfs/proteomic/yufe/tools/FragPipe-22.0/fragpipe/lib/fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.DiannToMsstats report.tsv ./ /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/psm.tsv 0.01 1 0.01 0.01 /storage/yufe/github_issues/github_fragpipe_1815/yufe_3/fragpipe-files.fp-manifest Done in 15.56 seconds. Process 'DIA-NN: Convert DIA-NN output to MSstats.csv' finished, exit code: 0 Please cite: (pseudo-MS/MS generation with diaTracer) diaTracer enables spectrum-centric analysis of diaPASEF proteomics data. bioRxiv (2024) (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) (PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923 (2007) (PTM localization with PTMProphet)PTMProphet: fast and accurate mass modification localization for the trans-proteomic pipeline . J. Proteome Res. 18:4262 (2019) (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) (Spectral library generation and DIA analysis) Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform. Nat Commun. 14:4154 (2023) (DIA quantification with DIA-NN) dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts. Nat Commun. 13:3944 (2022) (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 136.5 MINUTES=============================================================