System OS: Linux, Architecture: amd64 Java Info: 17.0.15, OpenJDK 64-Bit Server VM, Ubuntu .NET Core Info: 6.0.36 Version info: FragPipe version 23.1 DIA-Umpire version 2.3.3 diaTracer version 1.3.3 MSFragger version 4.3 Crystal-C version 1.5.9 MSBooster version 1.3.17 Percolator version 3.7.1 PTMProphet version 7.3.0 Metaproteomics version 1.0.1 Philosopher version 5.1.2 PTM-Shepherd version 3.0.2 IonQuant version 1.11.11 TMT-Integrator version 6.1.1 EasyPQP version 0.1.52 DIA-NN version 1.8.2 beta 8 Skyline version N/A Pandas version 2.3.1 Numpy version 1.26.4 LCMS files: Experiment/Group: (if "spectral library generation" is enabled, all files will be analyzed together) - /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.raw DIA 26 commands to execute: CheckCentroid java -Xmx194G -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/batmass-io-1.35.4.jar org.nesvilab.fragpipe.util.CheckCentroid /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.raw 31 WorkspaceCleanInit [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 workspace --init --nocheck --temp /tmp/1044b792-999e-4343-96b2-77038bf7bb2f MSFragger [Work dir: /home/projects/proteomics/workingdir01] java -jar -Dfile.encoding=UTF-8 -Xmx194G /fragpipe_bin/dependencies/MSFragger-4.3/MSFragger-4.3.jar /home/projects/proteomics/workingdir01/fragger_dia.params /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.raw MSFragger move pepxml java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/batmass-io-1.35.4.jar org.nesvilab.utils.FileMove --no-err /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank1.pepXML /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank1.pepXML MSFragger move pepxml java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/batmass-io-1.35.4.jar org.nesvilab.utils.FileMove --no-err /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank2.pepXML /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank2.pepXML MSFragger move pepxml java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/batmass-io-1.35.4.jar org.nesvilab.utils.FileMove --no-err /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank3.pepXML /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank3.pepXML MSFragger move pepxml java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/batmass-io-1.35.4.jar org.nesvilab.utils.FileMove --no-err /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank4.pepXML /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank4.pepXML MSFragger move pepxml java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/batmass-io-1.35.4.jar org.nesvilab.utils.FileMove --no-err /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank5.pepXML /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank5.pepXML MSFragger move pin java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/batmass-io-1.35.4.jar org.nesvilab.utils.FileMove --no-err /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.pin /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.pin MSBooster [Work dir: /home/projects/proteomics/workingdir01] java -Djava.awt.headless=true -Xmx194G -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/MSBooster-1.3.17.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/batmass-io-1.35.4.jar mainsteps.MainClass --paramsList /home/projects/proteomics/workingdir01/msbooster_params.txt Percolator [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/percolator_3_7_1/linux/percolator --no-terminate --post-processing-tdc --subset-max-train 500000 --num-threads 31 --results-peptides 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_target_psms.tsv --decoy-results-peptides 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_edited.pin Percolator: Convert to pepxml [Work dir: /home/projects/proteomics/workingdir01] java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.pin 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_target_psms.tsv 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_decoy_psms.tsv interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01 DIA 0.7 /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_uncalibrated.mzML Percolator delete temp java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar org.nesvilab.utils.FileDelete /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_target_psms.tsv Percolator delete temp java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar org.nesvilab.utils.FileDelete /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_decoy_psms.tsv ProteinProphet [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined /home/projects/proteomics/workingdir01/filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 database --annotate /home/projects/proteomics/UP000005640_9606_withDECOYS.fasta --prefix rev_ PhilosopherFilter [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 filter --picked --prot 0.01 --minPepLen 8 --tag rev_ --pepxml /home/projects/proteomics/workingdir01 --protxml /home/projects/proteomics/workingdir01/combined.prot.xml --razor PhilosopherReport [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 report WorkspaceClean [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 workspace --clean --nocheck SpecLibGen [Work dir: /home/projects/proteomics/workingdir01] python3 -u /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/speclib/gen_con_spec_lib.py /home/projects/proteomics/UP000005640_9606_withDECOYS.fasta /home/projects/proteomics/workingdir01 unused /home/projects/proteomics/workingdir01 True unused use_easypqp noiRT:noIM 31 "--max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.0" delete_intermediate_files /home/projects/proteomics/workingdir01/filelist_speclibgen.txt DIA-Quant run DIA-NN [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/diann/1.8.2_beta_8/linux/diann-1.8.1.8 --lib library.tsv --threads 31 --verbose 1 --out dia-quant-output/report.tsv --qvalue 0.01 --matrix-qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --cfg /home/projects/proteomics/workingdir01/filelist_diann.txt-- DIA-Quant move and rename speclib for skyline java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar org.nesvilab.utils.FileMoveWithExtension /home/projects/proteomics/workingdir01 .speclib /home/projects/proteomics/workingdir01/dia-quant-output/report-tsv.speclib DIA-Quant propagate information [Work dir: /home/projects/proteomics/workingdir01/dia-quant-output] java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/batmass-io-1.35.4.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar org.nesvilab.fragpipe.tools.diann.Propagation /home/projects/proteomics/workingdir01 - - - DIA-Quant convert DIA-NN output to MSstats.csv [Work dir: /home/projects/proteomics/workingdir01/dia-quant-output] java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/commons-io-2.18.0.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar org.nesvilab.fragpipe.tools.diann.DiannToMsstats report.tsv ./ /home/projects/proteomics/workingdir01/psm.tsv 0.01 1 0.01 0.01 /home/projects/proteomics/workingdir01/fragpipe-files.fp-manifest DIA-Quant generate site reports [Work dir: /home/projects/proteomics/workingdir01/dia-quant-output] java -jar /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/LFQ-SiteReporter-1.0.12.jar -pr /home/projects/proteomics/workingdir01/dia-quant-output/report.tsv -psm /home/projects/proteomics/workingdir01/psm.tsv -out_dir /home/projects/proteomics/workingdir01/dia-quant-output -mod_tag -min_site_prob 0.75 ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [/home/projects/proteomics/workingdir01] Cmd: [CheckCentroid], Work dir: [/home/projects/proteomics/workingdir01] Cmd: [WorkspaceCleanInit], Work dir: [/home/projects/proteomics/workingdir01] Cmd: [MSFragger], Work dir: [/home/projects/proteomics/workingdir01] Cmd: [MSBooster], Work dir: [/home/projects/proteomics/workingdir01] Cmd: [Percolator], Work dir: [/home/projects/proteomics/workingdir01] Cmd: [ProteinProphet], Work dir: [/home/projects/proteomics/workingdir01] Cmd: [PhilosopherDbAnnotate], Work dir: [/home/projects/proteomics/workingdir01] Cmd: [PhilosopherFilter], Work dir: [/home/projects/proteomics/workingdir01] Cmd: [PhilosopherReport], Work dir: [/home/projects/proteomics/workingdir01] Cmd: [WorkspaceClean], Work dir: [/home/projects/proteomics/workingdir01] Cmd: [SpecLibGen], Work dir: [/home/projects/proteomics/workingdir01] Cmd: [DIA-Quant], Work dir: [/home/projects/proteomics/workingdir01] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of /home/projects/proteomics/UP000005640_9606_withDECOYS.fasta~~~~~~~ >rev_sp|A0A024R1R8|TMA7B_HUMAN >rev_sp|O43915|VEGFD_HUMAN >rev_sp|P10124|SRGN_HUMAN >rev_sp|P51687|SUOX_HUMAN >rev_sp|Q14CX7|NAA25_HUMAN >rev_sp|Q6NVV3|NIPA3_HUMAN >rev_sp|Q8IZY5|BLID_HUMAN >rev_sp|Q92738|US6NL_HUMAN >rev_sp|Q9BX95|SGPP1_HUMAN >rev_sp|Q9NZJ7|MTCH1_HUMAN >rev_tr|Q9HB66|Q9HB66_HUMAN >sp|O43909|EXTL3_HUMAN Exostosin-like 3 OS=Homo sapiens OX=9606 GN=EXTL3 PE=1 SV=1 >sp|P10092|CALCB_HUMAN Calcitonin gene-related peptide 2 OS=Homo sapiens OX=9606 GN=CALCB PE=1 SV=1 >sp|P51684|CCR6_HUMAN C-C chemokine receptor type 6 OS=Homo sapiens OX=9606 GN=CCR6 PE=1 SV=2 >sp|Q14CS0|UBX2B_HUMAN UBX domain-containing protein 2B OS=Homo sapiens OX=9606 GN=UBXN2B PE=1 SV=1 >sp|Q6NVU6|UFSP1_HUMAN Ufm1-specific protease 1 OS=Homo sapiens OX=9606 GN=UFSP1 PE=1 SV=3 >sp|Q8IZW8|TENS4_HUMAN Tensin-4 OS=Homo sapiens OX=9606 GN=TNS4 PE=1 SV=3 >sp|Q92734|TFG_HUMAN Protein TFG OS=Homo sapiens OX=9606 GN=TFG PE=1 SV=2 >sp|Q9BX82|ZN471_HUMAN Zinc finger protein 471 OS=Homo sapiens OX=9606 GN=ZNF471 PE=1 SV=1 >sp|Q9NZJ4|SACS_HUMAN Sacsin OS=Homo sapiens OX=9606 GN=SACS PE=1 SV=2 >tr|Q9H052|Q9H052_HUMAN Uncharacterized protein DKFZp547L112 (Fragment) OS=Homo sapiens OX=9606 GN=DKFZp547L112 PE=2 SV=1 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v23.1ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=/home/projects/proteomics/UP000005640_9606_withDECOYS.fasta crystalc.run-crystalc=false database.decoy-tag=rev_ diann.channel-normalization-strategy=0 diann.cmd-opts= diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.medium= diann.min-site-prob=0.75 diann.mod-tag= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=2 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=true diatracer.mass-defect-offset=0.1 diatracer.rf-max=500 diatracer.run-diatracer=false diatracer.write-intermediate-files=false diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fpop.coadaptr.fpop.fpop_masses= fpop.coadaptr.fpop.run-fpop-coadaptr=false fpop.fragpipe.fpop.fpop-tmt=false fpop.fragpipe.fpop.label_control= fpop.fragpipe.fpop.label_fpop= fpop.fragpipe.fpop.region_size=1 fpop.fragpipe.fpop.run-fpop=false fpop.fragpipe.fpop.subtract-control=false fragpipe-config.bin-diann=/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/diann/1.8.2_beta_8/linux/diann-1.8.1.8 fragpipe-config.bin-python=python3 fragpipe-config.tools-folder=/fragpipe_bin/dependencies freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.formula= ionquant.heavy= ionquant.imtol=0.05 ionquant.intensitymode=0 ionquant.ionfdr=0.01 ionquant.light= ionquant.locprob=0.75 ionquant.maxlfq=1 ionquant.mbr=0 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=10 ionquant.medium= ionquant.minfreq=0 ionquant.minions=1 ionquant.minisotopes=1 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 metaproteomics.cmd-line-opts= metaproteomics.delta-hyperscore=0.0 metaproteomics.host-name=Homo sapiens metaproteomics.iterations=3 metaproteomics.min-pept-cnt-per-prot=1 metaproteomics.min-uniq-pept-cnt=3 metaproteomics.min-uniq-pept-cnt-per-prot=1 metaproteomics.qvalue=0.01 metaproteomics.run-metaproteomics=false msbooster.find-best-im-model=false msbooster.find-best-rt-model=false msbooster.find-best-spectra-model=false msbooster.fragmentation-type=0 msbooster.im-model=DIA-NN msbooster.koina-url= msbooster.predict-im=true msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.rt-model=DIA-NN msbooster.run-msbooster=true msbooster.spectra-model=DIA-NN msbooster.spectral-library-path= msfragger.Y_type_masses= msfragger.activation_types=all msfragger.allowed_missed_cleavage_1=1 msfragger.allowed_missed_cleavage_2=1 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=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.00 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=2 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=2 msfragger.output_format=pepXML_pin msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.output_report_topN_dda_plus=5 msfragger.output_report_topN_dia1=5 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2= 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,1; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 0.0,site_06,false,1; 0.0,site_07,false,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 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=1000 msfragger.write_calibrated_mzml=false msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 opair.activation1=HCD opair.activation2=ETD opair.allowed_sites= 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=--no-terminate --post-processing-tdc --subset-max-train 500000 percolator.keep-tsv-files=false percolator.min-prob=0.7 percolator.run-percolator=true phi-report.dont-use-prot-proph-file=false phi-report.filter=--picked --prot 0.01 --minPepLen 8 phi-report.pep-level-summary=false phi-report.print-decoys=false phi-report.prot-level-summary=false phi-report.remove-contaminants=false phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 protein-prophet.run-protein-prophet=true ptmprophet.cmdline= ptmprophet.override-defaults=false ptmprophet.run-ptmprophet=false ptmshepherd.adv_params=false ptmshepherd.annotate_assigned_mods=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=25 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=12.5 ptmshepherd.diagmine_fragMinSpecDiff=25 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=25 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.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_condPeaks=150 ptmshepherd.spectra_condRatio=0.0001 ptmshepherd.spectra_maxPrecursorCharge=4 ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.use_msfragger_localization=false ptmshepherd.varmod_masses= quantitation.run-label-free-quant=false run-psm-validation=true run-validation-tab=true saintexpress.cmd-opts= saintexpress.max-replicates=10 saintexpress.run-saint-express=false saintexpress.virtual-controls=100 skyline.run-skyline=false skyline.skyline=false skyline.skyline-custom=false skyline.skyline-custom-path= skyline.skyline-daily=true skyline.skyline-fragment-tolerance=10 skyline.skyline-mods-mode=Default skyline.skyline-precursor-tolerance=10 skyline.use-ssl=false 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.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_temp_files=false tab-run.export_matched_fragments=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=-1 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_resolution=0 tmtintegrator.min_site_prob=-1 tmtintegrator.min_snr=0 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_d_tag=Pool tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=false tmtintegrator.tolerance=20 tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=false workdir=/home/projects/proteomics/workingdir01 workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.misc.sdrf-type=Default workflow.ram=0 workflow.threads=31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid java -Xmx194G -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/batmass-io-1.35.4.jar org.nesvilab.fragpipe.util.CheckCentroid /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.raw 31 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 workspace --clean --nocheck time="08:44:27" level=info msg="Executing Workspace v5.1.2" time="08:44:27" level=info msg="Removing workspace" time="08:44:27" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 workspace --init --nocheck --temp /tmp/1044b792-999e-4343-96b2-77038bf7bb2f time="08:44:27" level=info msg="Executing Workspace v5.1.2" time="08:44:27" level=info msg="Creating workspace" time="08:44:27" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: /home/projects/proteomics/workingdir01] java -jar -Dfile.encoding=UTF-8 -Xmx194G /fragpipe_bin/dependencies/MSFragger-4.3/MSFragger-4.3.jar /home/projects/proteomics/workingdir01/fragger_dia.params /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.raw MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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: 17.0.15, OpenJDK 64-Bit Server VM, Ubuntu JVM started with 194 GB memory data_type > 0. Will use the isolation window from the spectral file as precursor tolerance. Checking database... ***********************************FIRST SEARCH************************************ Parameters: num_threads = 31 database_name = /home/projects/proteomics/UP000005640_9606_withDECOYS.fasta decoy_prefix = rev_ precursor_mass_lower = -10.0 precursor_mass_upper = 10.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 10.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = 0 mass_offsets = 0 use_detailed_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 = 1 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 = 1.7976931348623157E308 report_alternative_proteins = 0 override_charge = 1 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 = 1000 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 0 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. 95510874 fragments to be searched in 1 slices (0.89 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.97 s 001. 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.raw 90.1 s | deisotoping 9.2 s [progress: 225928/225928 (100%) - 11970 spectra/s] 18.9s postprocessing 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.raw 0.7 s ***************************FIRST SEARCH DONE IN 2.027 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | -0.19 0.53 | 0.00 0.44 | 0.25 1.43 | -0.04 1.35 -----|---------------|---------------|---------------|--------------- New fragment_mass_tolerance = 6.000000 PPM New precursor_true_tolerance = 2.000000 PPM ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.945 MIN********* ************************************MAIN SEARCH************************************ data_type > 0. Will use the isolation window from the spectral file as precursor tolerance. Checking database... Parameters: num_threads = 31 database_name = /home/projects/proteomics/UP000005640_9606_withDECOYS.fasta decoy_prefix = rev_ precursor_mass_lower = isolation window lower precursor_mass_upper = isolation window upper precursor_mass_units = isolation window data_type = 1 precursor_true_tolerance = 2.0 precursor_true_units = 1 fragment_mass_tolerance = 6.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = 0 mass_offsets = 0.0 use_detailed_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 = 1 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 = 5 output_max_expect = 1.7976931348623157E308 report_alternative_proteins = 1 override_charge = 1 precursor_charge_low = 2 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 = 1000 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = isolation window 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 1 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 0.03 Da. 143298868 fragments to be searched in 1 slices (1.33 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.75 s 001. 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.mzBIN_calibrated 6.5 s [progress: 225928/225928 (100%) - 5331 spectra/s] 42.4s postprocessing 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.mzBIN_calibrated Building spectral index for the mzBIN_calibrated file: 97.6 s Preparing the PSMs 127.7 s Rescoring with peak tracing 118.2 s Picking top PSMs for each precursor 1.1 s Rescoring 5.6 s Writing results 4.1 s ***************************MAIN SEARCH DONE IN 5.141 MIN*************************** *******************************TOTAL TIME 8.113 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/batmass-io-1.35.4.jar org.nesvilab.utils.FileMove --no-err /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank1.pepXML /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/batmass-io-1.35.4.jar org.nesvilab.utils.FileMove --no-err /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank2.pepXML /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/batmass-io-1.35.4.jar org.nesvilab.utils.FileMove --no-err /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank3.pepXML /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/batmass-io-1.35.4.jar org.nesvilab.utils.FileMove --no-err /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank4.pepXML /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/batmass-io-1.35.4.jar org.nesvilab.utils.FileMove --no-err /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank5.pepXML /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank5.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/batmass-io-1.35.4.jar org.nesvilab.utils.FileMove --no-err /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.pin /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: /home/projects/proteomics/workingdir01] java -Djava.awt.headless=true -Xmx194G -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/MSBooster-1.3.17.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/batmass-io-1.35.4.jar mainsteps.MainClass --paramsList /home/projects/proteomics/workingdir01/msbooster_params.txt 2025-08-07 08:52:47 [INFO] - MSBooster v1.3.17 2025-08-07 08:52:48 [INFO] - Creating output folder at /home/projects/proteomics/workingdir01/MSBooster 2025-08-07 08:52:48 [INFO] - Using 31 threads 2025-08-07 08:52:55 [INFO] - Instrument detected: Astral 2025-08-07 08:52:55 [INFO] - NCE and fragmentation type detected: {HCD=25.00} 2025-08-07 08:52:55 [INFO] - Creating input file for createFull 2025-08-07 08:52:56 [INFO] - 297066 PSMs for prediction 2025-08-07 08:52:56 [INFO] - createFull input file generation took 908 milliseconds 2025-08-07 08:52:56 [INFO] - Input file at /home/projects/proteomics/workingdir01/MSBooster/spectraRT_full.tsv 2025-08-07 08:52:56 [INFO] - Generating input file for DIA-NN 2025-08-07 08:52:56 [INFO] - Creating input file for Diann 2025-08-07 08:52:57 [INFO] - 297066 PSMs for prediction 2025-08-07 08:52:57 [INFO] - Writing DIA-NN input file 2025-08-07 08:52:57 [INFO] - Diann input file generation took 1456 milliseconds 2025-08-07 08:52:57 [INFO] - Input file at /home/projects/proteomics/workingdir01/MSBooster/spectraRT.tsv 2025-08-07 08:52:57 [INFO] - Generating DIA-NN predictions 2025-08-07 08:52:57 [INFO] - /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/diann/1.8.2_beta_8/linux/diann-1.8.1.8 --lib /home/projects/proteomics/workingdir01/MSBooster/spectraRT.tsv --predict --threads 31 --strip-unknown-mods --predict-n-frag 100 2025-08-07 08:52:57 [INFO] - DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks) 2025-08-07 08:52:57 [INFO] - Compiled on Dec 1 2022 14:47:06 2025-08-07 08:52:57 [INFO] - Current date and time: Thu Aug 7 08:52:57 2025 2025-08-07 08:52:57 [INFO] - Logical CPU cores: 32 2025-08-07 08:52:57 [INFO] - Predicted spectra will be saved in a binary format 2025-08-07 08:52:57 [INFO] - Thread number set to 31 2025-08-07 08:52:57 [INFO] - DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option 2025-08-07 08:52:57 [INFO] - Deep learning predictor will predict 100 fragments 2025-08-07 08:52:57 [INFO] - 2025-08-07 08:52:57 [INFO] - 0 files will be processed 2025-08-07 08:52:57 [INFO] - [0:00] Loading spectral library /home/projects/proteomics/workingdir01/MSBooster/spectraRT.tsv 2025-08-07 08:52:58 [INFO] - [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) 2025-08-07 08:52:58 [INFO] - [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 297066 precursors in 265158 elution groups. 2025-08-07 08:53:00 [INFO] - [0:02] Encoding peptides for spectra and RTs prediction 2025-08-07 08:53:00 [INFO] - [0:02] Predicting spectra and IMs 2025-08-07 08:53:52 [INFO] - [0:54] Predicting RTs 2025-08-07 08:54:03 [INFO] - [1:05] Decoding predicted spectra and IMs 2025-08-07 08:54:09 [INFO] - [1:11] Decoding RTs 2025-08-07 08:54:09 [INFO] - [1:11] Saving the list of predictions to /home/projects/proteomics/workingdir01/MSBooster/spectraRT.predicted.bin 2025-08-07 08:54:09 [INFO] - Finished 2025-08-07 08:54:10 [INFO] - Done generating DIA-NN predictions 2025-08-07 08:54:10 [INFO] - Model running took 72484 milliseconds 2025-08-07 08:54:10 [INFO] - Generating edited pin with following features: [unweightedSpectralEntropy, weightedSpectralEntropy, hypergeometricProbability, intersection, predRTrealUnits, deltaRTLOESS] 2025-08-07 08:54:10 [INFO] - Loading predicted spectra: /home/projects/proteomics/workingdir01/MSBooster/spectraRT.predicted.bin 2025-08-07 08:54:13 [INFO] - Loading predicted retention times: /home/projects/proteomics/workingdir01/MSBooster/spectraRT.predicted.bin 2025-08-07 08:54:13 [INFO] - /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.pin has 338504 PSMs 2025-08-07 08:54:13 [INFO] - Processing pin /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.pin 2025-08-07 08:54:13 [INFO] - Processing /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_uncalibrated.mzML ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-08-07 08:54:24 [INFO] - Setting pin entries ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-08-07 08:54:25 [INFO] - RT regression using 5000 PSMs Iteration 1...2...3...4...5... 2025-08-07 08:54:29 [INFO] - Best average bandwidth for mass from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.15 2025-08-07 08:54:35 [INFO] - Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-08-07 08:54:42 [INFO] - Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-08-07 08:54:44 [INFO] - Edited pin file at /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_edited.pin 2025-08-07 08:54:45 [INFO] - Feature calculation, edited pin writing, and QC plot generation done in 35119 ms Process 'MSBooster' finished, exit code: 0 Percolator [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/percolator_3_7_1/linux/percolator --no-terminate --post-processing-tdc --subset-max-train 500000 --num-threads 31 --results-peptides 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_target_psms.tsv --decoy-results-peptides 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_edited.pin Percolator version 3.07.1, Build Date Aug 27 2024 13:21:45 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: /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/percolator_3_7_1/linux/percolator --no-terminate --post-processing-tdc --subset-max-train 500000 --num-threads 31 --results-peptides 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_target_psms.tsv --decoy-results-peptides 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_edited.pin Started Thu Aug 7 08:54:49 2025 on 6a5180a20119 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_edited.pin Features: rank precursor_detected abs_ppm abs_rt_diff complementary_ions ion_series weighted_average_abs_fragment_ppm weighted_average_fragment_rt_deviation precursor_rt_deviation isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more isotopes log10_kl hyperscore matched_ion_num length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy weighted_spectral_entropy hypergeometric_probability intersection pred_RT_real_units delta_RT_loess Found 338504 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 225884 positives and 112620 negatives, size ratio=2.00572 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 38 as initial direction. Could separate 57443 training set positives with q<0.01 in that direction. Split 2: Selected feature 38 as initial direction. Could separate 57253 training set positives with q<0.01 in that direction. Split 3: Selected feature 38 as initial direction. Could separate 57989 training set positives with q<0.01 in that direction. Found 86321 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 212.7336 cpu seconds or 10 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 102729 PSMs with q<0.01 Iteration 2: Estimated 107113 PSMs with q<0.01 Iteration 3: Estimated 108313 PSMs with q<0.01 Iteration 4: Estimated 108754 PSMs with q<0.01 Iteration 5: Estimated 108900 PSMs with q<0.01 Iteration 6: Estimated 108929 PSMs with q<0.01 Iteration 7: Estimated 108945 PSMs with q<0.01 Iteration 8: Estimated 108955 PSMs with q<0.01 Iteration 9: Estimated 108950 PSMs with q<0.01 Iteration 10: Estimated 108956 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.0360 -0.0372 -0.0409 rank 0.0000 0.0000 0.0000 precursor_detected -0.1500 -0.1619 -0.1669 abs_ppm 0.0084 0.0160 0.0223 abs_rt_diff 0.1481 0.1543 0.1732 complementary_ions 0.1052 0.1114 0.0972 ion_series -0.0125 -0.0215 -0.0193 weighted_average_abs_fragment_ppm -0.0199 -0.0291 -0.0233 weighted_average_fragment_rt_deviation -0.0285 -0.0428 -0.0289 precursor_rt_deviation 0.0000 0.0000 0.0000 isotope_error_negative 0.0301 0.0231 0.0292 isotope_error_0 -0.0301 -0.0231 -0.0292 isotope_error_1 0.0000 0.0000 0.0000 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more 0.0547 0.0416 0.0605 isotopes -0.0595 -0.0860 -0.0659 log10_kl 1.1327 1.0463 1.2274 hyperscore -0.2082 -0.1983 -0.3362 matched_ion_num -0.0721 -0.0645 -0.0651 length_7 -0.0233 -0.0249 -0.0136 length_8 0.0539 0.0486 0.0529 length_9_30 0.0049 0.0087 -0.0123 length_31 0.0000 0.0000 0.0000 ntt -0.0254 -0.0356 -0.0427 nmc 0.0000 0.0000 0.0000 charge_1 -0.0861 -0.1076 -0.0984 charge_2 0.1051 0.1010 0.0769 charge_3 -0.0213 0.0084 0.0255 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 -0.1381 -0.1345 -0.1161 15.9949M 1.0197 0.9959 0.9849 unweighted_spectral_entropy 0.3364 0.3833 0.2968 weighted_spectral_entropy 0.7302 0.7083 0.7205 hypergeometric_probability 0.2791 0.2958 0.2516 intersection -0.0122 0.0055 0.0002 pred_RT_real_units -3.8575 -3.7656 -3.7376 delta_RT_loess -3.1378 -3.0816 -2.9935 m0 Found 108944 test set PSMs with q<0.01. Scoring full list of PSMs with trained SVMs. Features: rank precursor_detected abs_ppm abs_rt_diff complementary_ions ion_series weighted_average_abs_fragment_ppm weighted_average_fragment_rt_deviation precursor_rt_deviation isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more isotopes log10_kl hyperscore matched_ion_num length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy weighted_spectral_entropy hypergeometric_probability intersection pred_RT_real_units delta_RT_loess Found 338504 PSMs Evaluated set contained 225884 positives and 112620 negatives. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 225884 target PSMs and 112620 decoy PSMs. Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. Calculating q values. Final list yields 90267 target peptides with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 630.4191 cpu seconds or 43 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/projects/proteomics/workingdir01] java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.pin 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_target_psms.tsv 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_decoy_psms.tsv interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01 DIA 0.7 /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator delete temp java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar org.nesvilab.utils.FileDelete /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_target_psms.tsv Process 'Percolator delete temp' finished, exit code: 0 Percolator delete temp java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar org.nesvilab.utils.FileDelete /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_percolator_decoy_psms.tsv Process 'Percolator delete temp' finished, exit code: 0 ProteinProphet [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined /home/projects/proteomics/workingdir01/filelist_proteinprophet.txt time="08:55:48" level=info msg="Executing ProteinProphet v5.1.2" 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 /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank1.pep.xml... ...read in 0 1+, 29832 2+, 26254 3+, 5384 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5 Reading in /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank2.pep.xml... ...read in 0 1+, 11143 2+, 7407 3+, 1380 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5 Reading in /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank3.pep.xml... ...read in 0 1+, 3633 2+, 2204 3+, 428 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5 Reading in /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank4.pep.xml... ...read in 0 1+, 1255 2+, 773 3+, 164 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5 Reading in /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank5.pep.xml... ...read in 0 1+, 434 2+, 304 3+, 44 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5 Initializing 90639 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database /home/projects/proteomics/UP000005640_9606_withDECOYS.fasta .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|O60613|SEP15_HUMAN : U MVAMAAGPSGCLVPAFGLRLLLATVLQAVSAFGAEFSSEACRELGFSSNLLCSSCDLLGQFNLLQLDPDCRGCCQEEAQFETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEELSILKWNTDSVEEFLSEKLERI ..26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|Q8IZQ5|SELH_HUMAN : U MAPRGRKRKAEAAVVAVAEKREKLANGGEGMEEATVVIEHCTSURVYGRNAAALSQALRLEAPELPVKVNPTKPRRGSFEVTLLRPDGSSAELWTGIKKGPPRKLKFPEPQEVVEELKKYLS ......:.........:.........:.........:.....WARNING: Found the following zero-mass residues in protein entry sp|Q9NNW7|TRXR2_HUMAN : U MAAMAVALRGLGGRFRWRTQAVAGGVRGAARGAAAGQRDYDLLVVGGGSGGLACAKEAAQLGRKVAVVDYVEPSPQGTRWGLGGTCVNVGCIPKKLMHQAALLGGLIQDAPNYGWEVAQPVPHDWRKMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVCGVAKGGKEILLSADHIIIATGGRPRYPTHIEGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTIMMRSIPLRGFDQQMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTVLWAIGRVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEGRPELTPIAIMAGRLLVQRLFGGSSDLMDYDNVPTTVFTPLEYGCVGLSEEEAVARHGQEHVEVYHAHYKPLEFTVAGRDASQCYVKMVCLREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG ....28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........WARNING: Found the following zero-mass residues in protein entry sp|P62341|SELT_HUMAN : U MRLLLLLLVAASAMVRSEASANLGGVPSKRLKMQYATGPLLKFQICVSUGYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKVYACMMVFFLSNMIENQCMSTGAFEITLNDVPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPHHRS :......WARNING: Found the following zero-mass residues in protein entry sp|Q9Y6D0|SELK_HUMAN : U MVYISNGQVLDSRSQSPWRLSLITDFFWGIAEFVVLFFKTLLQQDVKKRRSYGNSSDSRYDDGRGPPGNPPRRMGRINHLRGPSPPPMAGGUGR ...:.........:.........:.........:.........30000 .........:.........WARNING: Found the following zero-mass residues in protein entry sp|P63302|SELW_HUMAN : U MALAVRVVYCGAUGYKSKYLQLKKKLEDEFPGRLDICGEGTPQATGFFEVMVAGKLIHSKKKGDGYVDTESKFLKLVAAIKAALAQG :.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|P07203|GPX1_HUMAN : U MCAARLAAAAAAAQSVYAFSARPLAGGEPVSLGSLRGKVLLIENVASLUGTTVRDYTQMNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGVPLRRYSRRFQTIDIEPDIEALLSQGPSCA ..:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .....WARNING: Found the following zero-mass residues in protein entry sp|Q9NZV5|SELN_HUMAN : UU MGRARPGQRGPPSPGPAAQPPAPPRRRARSLALLGALLAAAAAAAVRVCARHAEAQAAARQELALKTLGTDGLFLFSSLDTDGDMYISPEEFKPIAEKLTGSCSVTQTGVQWCSHSSLQPQLPWLNUSSCLSLLRSTPAASCEEEELPPDPSEETLTIEARFQPLLPETMTKSKDGFLGVSRLALSGLRNWTAAASPSAVFATRHFQPFLPPPGQELGEPWWIIPSELSMFTGYLSNNRFYPPPPKGKEVIIHRLLSMFHPRPFVKTRFAPQGAVACLTAISDFYYTVMFRIHAEFQLSEPPDFPFWFSPAQFTGHIILSKDATHVRDFRLFVPNHRSLNVDMEWLYGASESSNMEVDIGYIPQMELEATGPSVPSVILDEDGSMIDSHLPSGEPLQFVFEEIKWQQELSWEEAARRLEVAMYPFKKVSYLPFTEAFDRAKAENKLVHSILLWGALDDQSCUGSGRTLRETVLESSPILTLLNESFISTWSLVKELEELQNNQENSSHQKLAGLHLEKYSFPVEMMICLPNGTVVHHINANYFLDITSVKPEEIESNLFSFSSTFEDPSTATYMQFLKEGLRRGLPLLQP ....:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry sp|Q86VQ6|TRXR3_HUMAN : U MERSPPQSPGPGKAGDAPNRRSGHVRGARVLSPPGRRARLSSPGPSRSSEAREELRRHLVGLIERSRVVIFSKSYCPHSTRVKELFSSLGVECNVLELDQVDDGARVQEVLSEITNQKTVPNIFVNKVHVGGCDQTFQAYQSGLLQKLLQEDLAYDYDLIIIGGGSGGLSCAKEAAILGKKVMVLDFVVPSPQGTSWGLGGTCVNVGCIPKKLMHQAALLGQALCDSRKFGWEYNQQVRHNWETMTKAIQNHISSLNWGYRLSLREKAVAYVNSYGEFVEHHKIKATNKKGQETYYTAAQFVIATGERPRYLGIQGDKEYCITSDDLFSLPYCPGKTLVVGASYVALECAGFLAGFGLDVTVMVRSILLRGFDQEMAEKVGSYMEQHGVKFLRKFIPVMVQQLEKGSPGKLKVLAKSTEGTETIEGVYNTVLLAIGRDSCTRKIGLEKIGVKINEKSGKIPVNDVEQTNVPYVYAVGDILEDKPELTPVAIQSGKLLAQRLFGASLEKCDYINVPTTVFTPLEYGCCGLSEEKAIEVYKKENLEIYHTLFWPLEWTVAGRENNTCYAKIICNKFDHDRVIGFHILGPNAGEVTQGFAAAMKCGLTKQLLDDTIGIHPTCGEVFTTLEITKSSGLDITQKGCUG .......:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q99611|SPS2_HUMAN : U MAEASATGACGEAMAAAEGSSGPAGLTLGRSFSNYRPFEPQALGLSPSWRLTGFSGMKGUGCKVPQEALLKLLAGLTRPDVRPPLGRGLVGGQEEASQEAGLPAGAGPSPTFPALGIGMDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQSMSEEEREKVTPLMVKGFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQPNEFIMPDSAVVGDVLVLTKPLGTQVAVNAHQWLDNPERWNKVKMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFGILGHSQNLAKQQRNEVSFVIHNLPIIAKMAAVSKASGRFGLLQGTSAETSGGLLICLPREQAARFCSEIKSSKYGEGHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGATAAVLAPDSSNASSEPSS .....:.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q9C0D9|EPT1_HUMAN : U MAGYEYVSPEQLAGFDKYKYSAVDTNPLSLYVMHPFWNTIVKVFPTWLAPNLITFSGFLLVVFNFLLMAYFDPDFYASAPGHKHVPDWVWIVVGILNFVAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKYNTGILFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKNNTLKLNSVYEAMVPLFSPCLLFILSTAWILWSPSDILELHPRVFYFMVGTAFANSTCQLIVCQMSSTRCPTLNWLLVPLFLVVLVVNLGVASYVESILLYTLTTAFTLAHIHYGVRVVKQLSSHFQIYPFSLRKPNSDULGMEEKNIGL .....:.........:.........:.........:.........:.........39000 WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG .........:.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q9BVL4|SELO_HUMAN : U MAVYRAALGASLAAARLLPLGRCSPSPAPRSTLSGAAMEPAPRWLAGLRFDNRALRALPVEAPPPGPEGAPSAPRPVPGACFTRVQPTPLRQPRLVALSEPALALLGLGAPPAREAEAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTATGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGVPTTRAGACVTSESTVVRDVFYDGNPKYEQCTVVLRVASTFIRFGSFEIFKSADEHTGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASDSVQRNAAFFREVTRRTARMVAEWQCVGFCHGVLNTDNMSILGLTIDYGPFGFLDRYDPDHVCNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLELGEAILAEEFDAEFQRHYLQKMRRKLGLVQVELEEDGALVSKLLETMHLTGADFTNTFYLLSSFPVELESPGLAEFLARLMEQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSAAELQSRNQGHWADWLQAYRARLDKDLEGAGDAAAWQAEHVRVMHANNPKYVLRNYIAQNAIEAAERGDFSEVRRVLKLLETPYHCEAGAATDAEATEADGADGRQRSYSSKPPLWAAELCVTUSS .....:.........:.........:.........:.........:.........:.........:.........40000 .........:...WARNING: Found the following zero-mass residues in protein entry sp|Q8WWX9|SELM_HUMAN : U MSLLLPPLALLLLLAALVAPATAATAYRPDWNRLSGLTRARVETCGGUQLNRLKEVKAFVTQDIPFYHNLVMKHLPGADPELVLLGRRYEELERIPLSEMTREEINALVQELGFYRKAAPDAQVPPEYVWAPAKPPEETSDHADL ......WARNING: Found the following zero-mass residues in protein entry sp|P36969|GPX4_HUMAN : U MSLGRLCRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF :.........:.........:.........:.........:.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q9BQE4|SELS_HUMAN : U MERQEESLSARPALETEGLRFLHTTVGSLLATYGWYIVFSCILLYVVFQKLSARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQLEEEKRRQKIEMWDSMQEGKSYKGNAKKPQEEDSPGPSTSSVLKRKSDRKPLRGGGYNPLSGEGGGACSWRPGRRGPSSGGUG .....41000 .........:.........:.........:.. Total: 41326 Computing degenerate peptides for 10658 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10857 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10857 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10857 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10857 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=2.1752e-05, db_size=45830204 Computing MU for 10857 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% time="08:55:54" level=info msg=Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 database --annotate /home/projects/proteomics/UP000005640_9606_withDECOYS.fasta --prefix rev_ time="08:55:54" level=info msg="Executing Database v5.1.2" time="08:55:54" level=info msg="Annotating the database" time="08:55:54" level=info msg=Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 filter --picked --prot 0.01 --minPepLen 8 --tag rev_ --pepxml /home/projects/proteomics/workingdir01 --protxml /home/projects/proteomics/workingdir01/combined.prot.xml --razor time="08:55:54" level=info msg="Executing Filter v5.1.2" time="08:55:54" level=info msg="Processing peptide identification files" time="08:55:54" level=info msg="Parsing /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank5.pep.xml" time="08:55:54" level=info msg="Parsing /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank1.pep.xml" time="08:55:54" level=info msg="Parsing /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank2.pep.xml" time="08:55:54" level=info msg="Parsing /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank3.pep.xml" time="08:55:54" level=info msg="Parsing /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank4.pep.xml" time="08:55:57" level=info msg="1+ Charge profile" decoy=0 target=0 time="08:55:57" level=info msg="2+ Charge profile" decoy=415 target=45882 time="08:55:57" level=info msg="3+ Charge profile" decoy=300 target=36642 time="08:55:57" level=info msg="4+ Charge profile" decoy=73 target=7327 time="08:55:57" level=info msg="5+ Charge profile" decoy=0 target=0 time="08:55:57" level=info msg="6+ Charge profile" decoy=0 target=0 time="08:55:57" level=info msg="Database search results" ions=90451 peptides=72032 psms=90639 time="08:55:57" level=info msg="Converged to 0.88 % FDR with 89850 PSMs" decoy=788 threshold=0.700108 total=90638 time="08:55:57" level=info msg="Converged to 1.00 % FDR with 71012 Peptides" decoy=710 threshold=0.735823 total=71722 time="08:55:57" level=info msg="Converged to 0.88 % FDR with 89662 Ions" decoy=788 threshold=0.700108 total=90450 time="08:55:57" level=info msg="Protein inference results" decoy=802 target=9537 time="08:55:58" level=info msg="Converged to 0.99 % FDR with 8560 Proteins" decoy=85 threshold=0.9101 total=8645 time="08:55:58" level=info msg="2D FDR estimation: Protein mirror image" decoy=8560 target=8560 time="08:55:58" level=info msg="Second filtering results" ions=89734 peptides=71319 psms=89922 time="08:55:58" level=info msg="Converged to 0.51 % FDR with 89469 PSMs" decoy=452 threshold=0.700526 total=89921 time="08:55:58" level=info msg="Converged to 0.64 % FDR with 70867 Peptides" decoy=451 threshold=0.700526 total=71318 time="08:55:58" level=info msg="Converged to 0.51 % FDR with 89281 Ions" decoy=452 threshold=0.700526 total=89733 time="08:55:58" level=info msg="Post processing identifications" time="08:55:59" level=info msg="Assigning protein identifications to layers" time="08:56:12" level=info msg="Processing protein inference" time="08:56:12" level=info msg="Synchronizing PSMs and proteins" time="08:56:13" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=89281 peptides=70867 proteins=8560 psms=89469 time="08:56:13" level=info msg=Saving time="08:56:13" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 report time="08:56:13" level=info msg="Executing Report v5.1.2" time="08:56:13" level=info msg="Creating reports" time="08:56:14" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/Philosopher/philosopher-v5.1.2 workspace --clean --nocheck time="08:56:15" level=info msg="Executing Workspace v5.1.2" time="08:56:15" level=info msg="Removing workspace" time="08:56:15" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 SpecLibGen [Work dir: /home/projects/proteomics/workingdir01] python3 -u /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/speclib/gen_con_spec_lib.py /home/projects/proteomics/UP000005640_9606_withDECOYS.fasta /home/projects/proteomics/workingdir01 unused /home/projects/proteomics/workingdir01 True unused use_easypqp noiRT:noIM 31 "--max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.0" delete_intermediate_files /home/projects/proteomics/workingdir01/filelist_speclibgen.txt File list provided Using (un)calibrated.mzML files. Spectral library building Commands to execute: /usr/local/bin/easypqp convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank1.pep.xml'"'"', '"'"'/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank2.pep.xml'"'"', '"'"'/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank3.pep.xml'"'"', '"'"'/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank4.pep.xml'"'"', '"'"'/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank5.pep.xml'"'"']' --spectra /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_uncalibrated.mzML --exclude-range -1.5,3.5 --psms 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.psmpkl --peaks 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.peakpkl /usr/local/bin/easypqp library --psmtsv /home/projects/proteomics/workingdir01/psm.tsv --peptidetsv /home/projects/proteomics/workingdir01/peptide.tsv --out easypqp_lib_openswath.tsv --rt_lowess_fraction 0.0 /home/projects/proteomics/workingdir01/filelist_easypqp_library.txt ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ easypqp, version 0.1.52 Executing "/usr/local/bin/easypqp convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types ['b','y',] --enable_unannotated --pepxml ['/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank1.pep.xml', '/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank2.pep.xml', '/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank3.pep.xml', '/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank4.pep.xml', '/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank5.pep.xml'] --spectra /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_uncalibrated.mzML --exclude-range -1.5,3.5 --psms 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.psmpkl --peaks 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.peakpkl" 2025-08-07 08:56:20 - Info: Converting ['/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank1.pep.xml', '/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank2.pep.xml', '/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank3.pep.xml', '/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank4.pep.xml', '/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank5.pep.xml']. 2025-08-07 08:56:20 - Info: Parsing run 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01. 2025-08-07 08:56:20 - Info: Parsing pepXML: /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank1.pep.xml 2025-08-07 08:56:24 - Info: 61470 PSMs parsed. 2025-08-07 08:56:24 - Info: Parsing pepXML: /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank2.pep.xml 2025-08-07 08:56:25 - Info: 19930 PSMs parsed. 2025-08-07 08:56:25 - Info: Parsing pepXML: /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank3.pep.xml 2025-08-07 08:56:26 - Info: 6265 PSMs parsed. 2025-08-07 08:56:26 - Info: Parsing pepXML: /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank4.pep.xml 2025-08-07 08:56:26 - Info: 2192 PSMs parsed. 2025-08-07 08:56:26 - Info: Parsing pepXML: /home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank5.pep.xml 2025-08-07 08:56:26 - Info: 782 PSMs parsed. 2025-08-07 08:56:26 - Info: Generate theoretical spectra. 2025-08-07 08:56:33 - Info: Processing spectra from file /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_uncalibrated.mzML. 2025-08-07 08:57:28 - Info: Loaded 230519 spectra 2025-08-07 08:57:28 - Info: Collecting PSMs... /usr/local/lib/python3.12/dist-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) 2025-08-07 08:57:39 - Info: Got 90639 PSMs 2025-08-07 08:57:39 - Info: Generating Transitions... 2025-08-07 08:57:42 - Info: Generated 2166313 transitions 2025-08-07 08:57:42 - Info: PSMs successfully converted and stored in 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.psmpkl. 2025-08-07 08:57:42 - Info: Peaks successfully converted and stored in 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.peakpkl. 2025-08-07 08:57:42 - Info: Total elapsed time 1.38 minutes. Executing "/usr/local/bin/easypqp library --psmtsv /home/projects/proteomics/workingdir01/psm.tsv --peptidetsv /home/projects/proteomics/workingdir01/peptide.tsv --out easypqp_lib_openswath.tsv --rt_lowess_fraction 0.0 /home/projects/proteomics/workingdir01/filelist_easypqp_library.txt" 2025-08-07 08:57:45 - 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. 2025-08-07 08:57:45 - Info: Reading file /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.psmpkl. 2025-08-07 08:57:45 - Info: In total 90639 PSMs loaded. 2025-08-07 08:57:46 - Info: 89305 redundant PSMs identified after filtering with /home/projects/proteomics/workingdir01/psm.tsv and /home/projects/proteomics/workingdir01/peptide.tsv 2025-08-07 08:57:46 - base_name modified_peptide 0 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Co... 89305 2025-08-07 08:57:46 - Info: easypqp_rt_alignment_20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01; Peptide overlap between run and reference: 89305. 2025-08-07 08:58:24 - Info: easypqp_rt_alignment_20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01; Lowess fraction used: 0.08. /usr/local/lib/python3.12/dist-packages/easypqp/library.py:392: FutureWarning: DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning. aligned_runs = aligned_runs.groupby('base_name', as_index=False, group_keys=False).apply(lambda x: lowess(x, rt_reference_run, 'retention_time', 'irt', rt_lowess_frac, rt_psm_fdr_threshold, min_peptides, "easypqp_rt_alignment_" + x.name, main_path)) 2025-08-07 08:58:26 - Info: Parsing file /home/projects/proteomics/workingdir01/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.peakpkl. 2025-08-07 08:58:44 - Info: Library successfully generated. 2025-08-07 08:58:44 - Info: Total elapsed time: 0.98 minutes. Done generating spectral library 2025-08-07 08:59:00,019:INFO:took 0:02:44.002357 Process 'SpecLibGen' finished, exit code: 0 DIA-Quant run DIA-NN [Work dir: /home/projects/proteomics/workingdir01] /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/diann/1.8.2_beta_8/linux/diann-1.8.1.8 --lib library.tsv --threads 31 --verbose 1 --out dia-quant-output/report.tsv --qvalue 0.01 --matrix-qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --cfg /home/projects/proteomics/workingdir01/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: Thu Aug 7 08:59:01 2025 Logical CPU cores: 32 Thread number set to 31 Output will be filtered at 0.01 FDR Precursor/protein x sample matrices will be filtered at 0.01 precursor & protein-level 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. 1 files will be processed [0:00] Loading spectral library library.tsv [0:01] Spectral library loaded: 8559 protein isoforms, 8559 protein groups and 89305 precursors in 72702 elution groups. [0:01] Initialising library [0:01] Saving the library to library.tsv.speclib [0:01] File #1/1 [0:01] Loading run /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_uncalibrated.mzML WARNING: more than 1000 different isolation windows - is this intended? [1:34] 50015 library precursors are potentially detectable [1:34] Processing... [1:34] RT window set to 0.697154 [1:34] Peak width: 3.056 [1:34] Scan window radius set to 6 [1:34] Recommended MS1 mass accuracy setting: 2.78215 ppm [1:37] Optimised mass accuracy: 13.791 ppm [1:41] Removing low confidence identifications [1:41] Removing interfering precursors [1:43] Training neural networks: 49526 targets, 44934 decoys [1:45] Number of IDs at 0.01 FDR: 49483 [1:45] Calculating protein q-values [1:45] Number of protein isoforms identified at 1% FDR: 7631 (precursor-level), 7631 (protein-level) (inference performed using proteotypic peptides only) [1:45] Quantification [1:47] Cross-run analysis [1:47] Reading quantification information: 1 files [1:47] Quantifying peptides [1:47] Quantifying proteins [1:47] Calculating q-values for protein and gene groups [1:47] Calculating global q-values for protein and gene groups [1:47] Writing report [1:48] Report saved to dia-quant-output/report.tsv. [1:48] Saving precursor levels matrix [1:48] Precursor levels matrix (1% precursor and protein group FDR) saved to dia-quant-output/report.pr_matrix.tsv. [1:48] Saving protein group levels matrix [1:48] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to dia-quant-output/report.pg_matrix.tsv. [1:48] Saving gene group levels matrix [1:48] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to dia-quant-output/report.gg_matrix.tsv. [1:48] Saving unique genes levels matrix [1:48] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to dia-quant-output/report.unique_genes_matrix.tsv. [1:48] Stats report saved to dia-quant-output/report.stats.tsv [1:48] Log saved to dia-quant-output/report.log.txt Finished Process 'DIA-Quant run DIA-NN' finished, exit code: 0 DIA-Quant move and rename speclib for skyline java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar org.nesvilab.utils.FileMoveWithExtension /home/projects/proteomics/workingdir01 .speclib /home/projects/proteomics/workingdir01/dia-quant-output/report-tsv.speclib Moving /home/projects/proteomics/workingdir01/library.tsv.speclib to /home/projects/proteomics/workingdir01/dia-quant-output/report-tsv.speclib Process 'DIA-Quant move and rename speclib for skyline' finished, exit code: 0 DIA-Quant propagate information [Work dir: /home/projects/proteomics/workingdir01/dia-quant-output] java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/batmass-io-1.35.4.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar org.nesvilab.fragpipe.tools.diann.Propagation /home/projects/proteomics/workingdir01 - - - Done in 1.25 seconds. Process 'DIA-Quant propagate information' finished, exit code: 0 DIA-Quant convert DIA-NN output to MSstats.csv [Work dir: /home/projects/proteomics/workingdir01/dia-quant-output] java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/commons-io-2.18.0.jar:/fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar org.nesvilab.fragpipe.tools.diann.DiannToMsstats report.tsv ./ /home/projects/proteomics/workingdir01/psm.tsv 0.01 1 0.01 0.01 /home/projects/proteomics/workingdir01/fragpipe-files.fp-manifest Done in 1.82 seconds. Process 'DIA-Quant convert DIA-NN output to MSstats.csv' finished, exit code: 0 DIA-Quant generate site reports [Work dir: /home/projects/proteomics/workingdir01/dia-quant-output] java -jar /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/LFQ-SiteReporter-1.0.12.jar -pr /home/projects/proteomics/workingdir01/dia-quant-output/report.tsv -psm /home/projects/proteomics/workingdir01/psm.tsv -out_dir /home/projects/proteomics/workingdir01/dia-quant-output -mod_tag -min_site_prob 0.75 2025-08-07 09:00:54 [INFO] - LFQ-SiteReporter Version: 1.0.12 2025-08-07 09:00:54 [INFO] - Load PSM data 2025-08-07 09:00:54 [INFO] - Abort creating site reports as no modification tag is specified. Process 'DIA-Quant generate site reports' finished, exit code: 0 Please cite: (Any searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods. 14:513 (2017) (Any searches) Fast deisotoping algorithm and its implementation in the MSFragger search engine. J Proteome Res. 20:498 (2021) (timsTOF ddaPASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics. 19:1575 (2020) (Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020) (Glyco search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods. 17:1125 (2020) (Labile search) MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics. Mol Cell Proteomics. 22:100538 (2023) (DDA+ search) MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search. Nat Commun. 16:3329 (2025) (MSBooster) MSBooster: improving peptide identification rates using deep learning-based features. Nat Commun. 14:4539 (2023) (PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods. 4:923 (2007) (Protein inference with ProteinProphet)A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem. 75:4646 (2003) (FDR filtering and reporting) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods. 17:869 (2020) (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) Task Runtimes: CheckCentroid: 0.00 minutes WorkspaceCleanInit: 0.01 minutes MSFragger: 8.31 minutes MSFragger move pepxml: 0.02 minutes MSFragger move pin: 0.00 minutes MSBooster: 2.03 minutes Percolator: 0.92 minutes Percolator: Convert to pepxml: 0.06 minutes Percolator delete temp: 0.01 minutes ProteinProphet: 0.10 minutes PhilosopherDbAnnotate: 0.01 minutes PhilosopherFilter: 0.32 minutes PhilosopherReport: 0.02 minutes WorkspaceClean: 0.01 minutes SpecLibGen: 2.74 minutes DIA-Quant run DIA-NN: 1.84 minutes DIA-Quant move and rename speclib for skyline: 0.00 minutes DIA-Quant propagate information: 0.02 minutes DIA-Quant convert DIA-NN output to MSstats.csv: 0.03 minutes DIA-Quant generate site reports: 0.00 minutes Finalizer Task: 0.01 minutes =============================================================ALL JOBS DONE IN 16.5 MINUTES=============================================================