System OS: Windows 10, Architecture: AMD64 Java Info: 22.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation .NET Core Info: N/A Version info: FragPipe version 21.0 MSFragger version 4.0 IonQuant version 1.10.12 Philosopher version 5.1.0 LCMS files: Experiment/Group: PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58 (if "spectral library generation" is enabled, all files will be analyzed together) - C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw DDA 21 commands to execute: CheckCentroid java -Xmx15G -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\lib\fragpipe-21.0.jar;C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 2 WorkspaceCleanInit [Work dir: C:\Users\dawa726\braveQC\output] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\Users\dawa726\braveQC\output] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe workspace --init --nocheck --temp C:\Users\dawa726\AppData\Local\Temp\a6b77c6d-1d79-440c-ba08-12d7477f0c8a WorkspaceCleanInit [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe workspace --init --nocheck --temp C:\Users\dawa726\AppData\Local\Temp\f96dbcfa-da90-45d1-81a3-7e06d5d92463 MSFragger [Work dir: C:\Users\dawa726\braveQC\output] java -jar -Dfile.encoding=UTF-8 -Xmx15G C:\Users\dawa726\MSFragger-4.0\MSFragger-4.0.jar C:\Users\dawa726\braveQC\output\fragger.params C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw MSFragger move pepxml java -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\lib\fragpipe-21.0.jar;/C:/Users/dawa726/FragPipe-21.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pepXML C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pepXML MSFragger move pin java -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\lib\fragpipe-21.0.jar;/C:/Users/dawa726/FragPipe-21.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pin C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pin Percolator [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 2 --results-psms PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_target_psms.tsv --decoy-results-psms PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pin Percolator: Convert to pepxml [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] java -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pin PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58 PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_target_psms.tsv PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_decoy_psms.tsv interact-PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58 DDA 0.5 C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_uncalibrated.mzML Percolator: Delete temp java -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_target_psms.tsv Percolator: Delete temp java -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_decoy_psms.tsv ProteinProphet [Work dir: C:\Users\dawa726\braveQC\output] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined C:\Users\dawa726\braveQC\output\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe database --annotate C:\Users\dawa726\braveQC\2024-05-03-decoys-Sorghum_bicolor_UniProt_TrEMBL.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58 --protxml C:\Users\dawa726\braveQC\output\combined.prot.xml --razor PhilosopherReport [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe report WorkspaceClean [Work dir: C:\Users\dawa726\braveQC\output] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe workspace --clean --nocheck IonQuant [Work dir: C:\Users\dawa726\braveQC\output] java -Xmx15G -Dlibs.bruker.dir=C:\Users\dawa726\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=C:\Users\dawa726\MSFragger-4.0\ext\thermo -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\jfreechart-1.5.3.jar;C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\batmass-io-1.30.0.jar;C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 2 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 0 --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --multidir . --filelist C:\Users\dawa726\braveQC\output\filelist_ionquant.txt --modlist C:\Users\dawa726\braveQC\output\modmasses_ionquant.txt IonQuant [Work dir: C:\Users\dawa726\braveQC\output] java -Xmx15G -Dlibs.bruker.dir=C:\Users\dawa726\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=C:\Users\dawa726\MSFragger-4.0\ext\thermo -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\jfreechart-1.5.3.jar;C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\batmass-io-1.30.0.jar;C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 2 --perform-ms1quant 0 --perform-isoquant 1 --isotol 20.0 --isolevel 2 --isotype TMT-16 --ionmobility 0 --site-reports 0 --annotation C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\psm.tsv=C:\Users\dawa726\braveQC\TMT_A_annotation_test.txt_annotation.txt --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --multidir . --filelist C:\Users\dawa726\braveQC\output\filelist_ionquant.txt --modlist C:\Users\dawa726\braveQC\output\modmasses_ionquant.txt TmtIntegrator [Work dir: C:\Users\dawa726\braveQC\output] java -Xmx15G -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\tmt-integrator-5.0.7.jar TMTIntegrator C:\Users\dawa726\braveQC\output\tmt-integrator-conf.yml C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\psm.tsv ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [C:\Users\dawa726\braveQC\output] Cmd: [CheckCentroid], Work dir: [C:\Users\dawa726\braveQC\output] Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\dawa726\braveQC\output] Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] Cmd: [MSFragger], Work dir: [C:\Users\dawa726\braveQC\output] Cmd: [Percolator], Work dir: [C:\Users\dawa726\braveQC\output] Cmd: [ProteinProphet], Work dir: [C:\Users\dawa726\braveQC\output] Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\dawa726\braveQC\output] Cmd: [PhilosopherFilter], Work dir: [C:\Users\dawa726\braveQC\output] Cmd: [PhilosopherReport], Work dir: [C:\Users\dawa726\braveQC\output] Cmd: [WorkspaceClean], Work dir: [C:\Users\dawa726\braveQC\output] Cmd: [WorkspaceClean], Work dir: [C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] Cmd: [IonQuant], Work dir: [C:\Users\dawa726\braveQC\output] Cmd: [IonQuant], Work dir: [C:\Users\dawa726\braveQC\output] Cmd: [TmtIntegrator], Work dir: [C:\Users\dawa726\braveQC\output] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of C:\Users\dawa726\braveQC\2024-05-03-decoys-Sorghum_bicolor_UniProt_TrEMBL.fasta.fas~~~~~~~ >rev_sp|A1E9Q2|RR12_SORBI 30S ribosomal protein S12, chloroplastic OS=Sorghum bicolor OX=4558 GN=rps12-A PE=3 SV=1 >rev_tr|A0A1B6PCE5|A0A1B6PCE5_SORBI MFS domain-containing protein OS=Sorghum bicolor OX=4558 GN=SORBI_3008G084800 PE=4 SV=1 >rev_tr|A0A1B6Q6N4|A0A1B6Q6N4_SORBI TPT domain-containing protein OS=Sorghum bicolor OX=4558 GN=SORBI_3003G327600 PE=4 SV=1 >rev_tr|A0A1W0VSL1|A0A1W0VSL1_SORBI CBFD_NFYB_HMF domain-containing protein OS=Sorghum bicolor OX=4558 GN=SORBI_3010G119200 PE=3 SV=1 >rev_tr|A0A1Z5R198|A0A1Z5R198_SORBI Uncharacterized protein OS=Sorghum bicolor OX=4558 GN=SORBI_3009G068350 PE=4 SV=1 >rev_tr|A0A1Z5RHP2|A0A1Z5RHP2_SORBI Uncharacterized protein OS=Sorghum bicolor OX=4558 GN=SORBI_3005G102750 PE=4 SV=1 >rev_tr|A0A1Z5SC20|A0A1Z5SC20_SORBI Uncharacterized protein OS=Sorghum bicolor OX=4558 GN=SORBI_3001G543100 PE=4 SV=1 >rev_tr|C5X734|C5X734_SORBI Uncharacterized protein OS=Sorghum bicolor OX=4558 GN=SORBI_3002G002200 PE=4 SV=2 >rev_tr|C5XWB2|C5XWB2_SORBI Glutamine amidotransferase type-1 domain-containing protein OS=Sorghum bicolor OX=4558 GN=SORBI_3004G064500 PE=4 SV=1 >rev_tr|C5YQB1|C5YQB1_SORBI Uncharacterized protein OS=Sorghum bicolor OX=4558 GN=SORBI_3008G139000 PE=4 SV=1 >rev_tr|V5NZK0|V5NZK0_SORBI NAC1 protein (Fragment) OS=Sorghum bicolor OX=4558 GN=NAC1 PE=4 SV=1 >tr|A0A1B6PCC8|A0A1B6PCC8_SORBI Uncharacterized protein OS=Sorghum bicolor OX=4558 GN=SORBI_3008G063500 PE=3 SV=1 >tr|A0A1B6Q6M2|A0A1B6Q6M2_SORBI PsbP domain-containing protein OS=Sorghum bicolor OX=4558 GN=SORBI_3003G328200 PE=4 SV=1 >tr|A0A1W0VSK2|A0A1W0VSK2_SORBI Aldo_ket_red domain-containing protein OS=Sorghum bicolor OX=4558 GN=SORBI_3010G117900 PE=4 SV=1 >tr|A0A1Z5R182|A0A1Z5R182_SORBI Uncharacterized protein (Fragment) OS=Sorghum bicolor OX=4558 GN=SORBI_3009G024600 PE=4 SV=1 >tr|A0A1Z5RHN3|A0A1Z5RHN3_SORBI Dirigent protein OS=Sorghum bicolor OX=4558 GN=SORBI_3005G101500 PE=3 SV=1 >tr|A0A1Z5SC05|A0A1Z5SC05_SORBI Cation_ATPase_N domain-containing protein OS=Sorghum bicolor OX=4558 GN=SORBI_3001G539400 PE=4 SV=1 >tr|C5X718|C5X718_SORBI Uncharacterized protein OS=Sorghum bicolor OX=4558 GN=SORBI_3002G285800 PE=3 SV=1 >tr|C5XW92|C5XW92_SORBI FAS1 domain-containing protein OS=Sorghum bicolor OX=4558 GN=SORBI_3004G062300 PE=3 SV=1 >tr|C5YQ93|C5YQ93_SORBI Uncharacterized protein OS=Sorghum bicolor OX=4558 GN=SORBI_3008G136900 PE=4 SV=1 >tr|T1RSA4|T1RSA4_SORBI Soluble acid invertase OS=Sorghum bicolor OX=4558 GN=SAI PE=3 SV=1 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~annotation files~~~~~~~ C:\Users\dawa726\braveQC\TMT_A_annotation_test.txt_annotation.txt: 126 sample-01 127N sample-02 127C sample-03 128N sample-04 128C sample-05 129N sample-06 129C sample-07 130N sample-08 130C sample-09 131N sample-10 131C sample-11 132N sample-12 132C sample-13 133N sample-14 133C sample-15 134N sample-16 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v21.0ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=C\:\\Users\\dawa726\\braveQC\\2024-05-03-decoys-Sorghum_bicolor_UniProt_TrEMBL.fasta.fas crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.medium= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=QuantUMS (high accuracy) diann.run-dia-nn=false diann.run-dia-plex=false diann.run-specific-protein-q-value=false diann.unrelated-runs=false diann.use-predicted-spectra=true diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fpop.fpop-tmt=false fpop.label_control= fpop.label_fpop= fpop.region_size=1 fpop.run-fpop=false fpop.subtract-control=false fragpipe-config.bin-diann=C\:\\Users\\dawa726\\FragPipe-21.0\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe fragpipe-config.bin-ionquant=C\:\\Users\\dawa726\\FragPipe-21.0\\fragpipe\\tools\\IonQuant-1.10.12.jar fragpipe-config.bin-msfragger=C\:\\Users\\dawa726\\MSFragger-4.0\\MSFragger-4.0.jar fragpipe-config.bin-philosopher=C\:\\Users\\dawa726\\FragPipe-21.0\\fragpipe\\philosopher.exe fragpipe-config.bin-python=C\:\\Users\\dawa726\\AppData\\Local\\Programs\\Python\\Python39\\python.exe freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.heavy= ionquant.imtol=0.05 ionquant.ionfdr=0.01 ionquant.light= ionquant.locprob=0.75 ionquant.maxlfq=1 ionquant.mbr=0 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=10 ionquant.medium= ionquant.minfreq=0 ionquant.minions=2 ionquant.minisotopes=2 ionquant.minscans=3 ionquant.mztol=10 ionquant.normalization=1 ionquant.peptidefdr=1 ionquant.proteinfdr=1 ionquant.requantify=1 ionquant.rttol=0.4 ionquant.run-ionquant=true ionquant.tp=0 ionquant.uniqueness=0 ionquant.use-labeling=false ionquant.use-lfq=true ionquant.writeindex=0 msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.run-msbooster=false msbooster.use-correlated-features=false msfragger.Y_type_masses= msfragger.activation_types=all msfragger.allowed_missed_cleavage_1=2 msfragger.allowed_missed_cleavage_2=2 msfragger.calibrate_mass=2 msfragger.check_spectral_files=true msfragger.clip_nTerm_M=true msfragger.deisotope=1 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) msfragger.deneutralloss=1 msfragger.diagnostic_fragments= msfragger.diagnostic_intensity_filter=0 msfragger.digest_max_length=50 msfragger.digest_min_length=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=-1/0/1/2/3 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.mass_offsets_detailed= msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.01 msfragger.misc.fragger.clear-mz-hi=134.5 msfragger.misc.fragger.clear-mz-lo=125.5 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=200 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=-18.01056 79.96633 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; 304.20715,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,true,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 304.20715,n^,true,1; 229.16293,S,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=150 msfragger.write_calibrated_mzml=false msfragger.write_uncalibrated_mgf=false msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 opair.activation1=HCD opair.activation2=ETD opair.filterOxonium=true opair.glyco_db= opair.max_glycans=4 opair.max_isotope_error=2 opair.min_isotope_error=0 opair.ms1_tol=20 opair.ms2_tol=20 opair.oxonium_filtering_file= opair.oxonium_minimum_intensity=0.05 opair.reverse_scan_order=false opair.run-opair=false opair.single_scan_type=false peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore peptide-prophet.combine-pepxml=false peptide-prophet.run-peptide-prophet=false percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc percolator.keep-tsv-files=false percolator.min-prob=0.5 percolator.run-percolator=true phi-report.dont-use-prot-proph-file=false phi-report.filter=--sequential --picked --prot 0.01 phi-report.pep-level-summary=false phi-report.philosoher-msstats=false phi-report.print-decoys=false phi-report.prot-level-summary=false phi-report.remove-contaminants=false phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 protein-prophet.run-protein-prophet=true ptmprophet.cmdline= ptmprophet.run-ptmprophet=false ptmshepherd.adv_params=false ptmshepherd.annotation-common=false ptmshepherd.annotation-custom=false ptmshepherd.annotation-glyco=false ptmshepherd.annotation-unimod=true ptmshepherd.annotation_file= ptmshepherd.annotation_tol=0.01 ptmshepherd.cap_y_ions= ptmshepherd.decoy_type=1 ptmshepherd.diag_ions= ptmshepherd.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=00.2 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=00.1 ptmshepherd.diagmine_fragMinSpecDiff=00.1 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=00.2 ptmshepherd.glyco_adducts= ptmshepherd.glyco_fdr=1.00 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_ppm_tol=50 ptmshepherd.glycodatabase= ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=false ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=false ptmshepherd.localization_allowed_res= ptmshepherd.localization_background=4 ptmshepherd.max_adducts=0 ptmshepherd.n_glyco=true ptmshepherd.normalization-psms=true ptmshepherd.normalization-scans=false ptmshepherd.output_extended=false ptmshepherd.peakpicking_mass_units=0 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=0.002 ptmshepherd.precursor_mass_units=0 ptmshepherd.precursor_tol=0.01 ptmshepherd.print_decoys=false ptmshepherd.prob_dhexOx=2,0.5,0.1 ptmshepherd.prob_dhexY=2,0.5 ptmshepherd.prob_neuacOx=2,0.05,0.2 ptmshepherd.prob_neugcOx=2,0.05,0.2 ptmshepherd.prob_phosphoOx=2,0.05,0.2 ptmshepherd.prob_regY=5,0.5 ptmshepherd.prob_sulfoOx=2,0.05,0.2 ptmshepherd.remainder_masses= ptmshepherd.remove_glycan_delta_mass=true ptmshepherd.run-shepherd=false ptmshepherd.run_diagextract_mode=false ptmshepherd.run_diagmine_mode=false ptmshepherd.run_glyco_mode=false ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses= quantitation.run-label-free-quant=false run-psm-validation=true run-validation-tab=true saintexpress.fragpipe.cmd-opts= saintexpress.max-replicates=3 saintexpress.run-saint-express=true saintexpress.virtual-controls=100 speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.rt_lowess_fraction=0 speclibgen.easypqp.fragment.a=false speclibgen.easypqp.fragment.b=true speclibgen.easypqp.fragment.c=false speclibgen.easypqp.fragment.x=false speclibgen.easypqp.fragment.y=true speclibgen.easypqp.fragment.z=false speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.neutral_loss=false speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=false tab-run.delete_calibrated_mzml=false tab-run.delete_temp_files=false tab-run.sub_mzml_prob_threshold=0.5 tab-run.write_sub_mzml=false tmtintegrator.add_Ref=1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=false tmtintegrator.best_psm=true tmtintegrator.channel_num=TMT-16 tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=-1 tmtintegrator.groupby=0 tmtintegrator.log2transformed=true tmtintegrator.max_pep_prob_thres=0.9 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=1 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=true tmtintegrator.tolerance=20 tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=false workdir=C\:\\Users\\dawa726\\braveQC\\output workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.ram=15 workflow.threads=2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid java -Xmx15G -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\lib\fragpipe-21.0.jar;C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 2 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\Users\dawa726\braveQC\output] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe workspace --clean --nocheck INFO[10:32:35] Executing Workspace v5.1.0 INFO[10:32:35] Removing workspace INFO[10:32:35] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\Users\dawa726\braveQC\output] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe workspace --init --nocheck --temp C:\Users\dawa726\AppData\Local\Temp\a6b77c6d-1d79-440c-ba08-12d7477f0c8a INFO[10:32:35] Executing Workspace v5.1.0 INFO[10:32:35] Creating workspace INFO[10:32:35] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe workspace --clean --nocheck INFO[10:32:36] Executing Workspace v5.1.0 INFO[10:32:36] Removing workspace INFO[10:32:36] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe workspace --init --nocheck --temp C:\Users\dawa726\AppData\Local\Temp\f96dbcfa-da90-45d1-81a3-7e06d5d92463 INFO[10:32:36] Executing Workspace v5.1.0 INFO[10:32:36] Creating workspace INFO[10:32:36] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: C:\Users\dawa726\braveQC\output] java -jar -Dfile.encoding=UTF-8 -Xmx15G C:\Users\dawa726\MSFragger-4.0\MSFragger-4.0.jar C:\Users\dawa726\braveQC\output\fragger.params C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw MSFragger version MSFragger-4.0 Batmass-IO version 1.30.0 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 22.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 15 GB memory Checking database... Checking spectral files... C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw: Scans = 56972; Isolation sizes = [0.7] ***********************************FIRST SEARCH************************************ Parameters: num_threads = 2 database_name = C:\Users\dawa726\braveQC\2024-05-03-decoys-Sorghum_bicolor_UniProt_TrEMBL.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 0 override_charge = 0 precursor_charge_low = 2 precursor_charge_high = 3 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_03 = 79.96633 STY 2 variable_mod_06 = 304.20715 n^ 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 = 304.20715 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: 322169 of length 8: 319898 of length 9: 305131 of length 10: 293164 of length 11: 287547 of length 12: 275980 of length 13: 265397 of length 14: 249772 of length 15: 238538 of length 16: 226947 of length 17: 216843 of length 18: 204018 of length 19: 194291 of length 20: 184181 of length 21: 176257 of length 22: 166193 of length 23: 157039 of length 24: 150309 of length 25: 140334 of length 26: 133120 of length 27: 125745 of length 28: 119779 of length 29: 112331 of length 30: 104071 of length 31: 98713 of length 32: 92099 of length 33: 85959 of length 34: 81490 of length 35: 75267 of length 36: 70046 of length 37: 65475 of length 38: 61741 of length 39: 57379 of length 40: 52526 of length 41: 48387 of length 42: 44653 of length 43: 40043 of length 44: 33598 of length 45: 26836 of length 46: 19583 of length 47: 13017 of length 48: 8448 of length 49: 4860 of length 50: 2833 In total 5952007 peptides. Generated 179376681 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 10083796310 fragments to be searched in 16 slices (150.26 GB total) Operating on slice 1 of 16: Fragment index slice generated in 26.87 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 40.0 s | deisotoping 2.8 s [progress: 56970/56970 (100%) - 2902 spectra/s] 19.6s Operating on slice 2 of 16: Fragment index slice generated in 20.59 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 20.8 s | deisotoping 2.4 s [progress: 56970/56970 (100%) - 7128 spectra/s] 8.0s Operating on slice 3 of 16: Fragment index slice generated in 22.69 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 25.2 s | deisotoping 3.5 s [progress: 56970/56970 (100%) - 8661 spectra/s] 6.6s Operating on slice 4 of 16: Fragment index slice generated in 23.78 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 25.4 s | deisotoping 3.5 s [progress: 56970/56970 (100%) - 10044 spectra/s] 5.7s Operating on slice 5 of 16: Fragment index slice generated in 22.58 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 17.3 s | deisotoping 3.6 s [progress: 56970/56970 (100%) - 9833 spectra/s] 5.8s Operating on slice 6 of 16: Fragment index slice generated in 22.47 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 12.5 s | deisotoping 3.5 s [progress: 56970/56970 (100%) - 13478 spectra/s] 4.2s Operating on slice 7 of 16: Fragment index slice generated in 21.57 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 25.8 s | deisotoping 3.6 s [progress: 56970/56970 (100%) - 10390 spectra/s] 5.5s Operating on slice 8 of 16: Fragment index slice generated in 16.95 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 20.2 s | deisotoping 2.2 s [progress: 56970/56970 (100%) - 12825 spectra/s] 4.4s Operating on slice 9 of 16: Fragment index slice generated in 18.22 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 19.7 s | deisotoping 2.2 s [progress: 56970/56970 (100%) - 11734 spectra/s] 4.9s Operating on slice 10 of 16: Fragment index slice generated in 18.63 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 10.3 s | deisotoping 2.4 s [progress: 56970/56970 (100%) - 12231 spectra/s] 4.7s Operating on slice 11 of 16: Fragment index slice generated in 18.76 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 17.2 s | deisotoping 2.3 s [progress: 56970/56970 (100%) - 11084 spectra/s] 5.1s Operating on slice 12 of 16: Fragment index slice generated in 17.99 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 19.5 s | deisotoping 2.2 s [progress: 56970/56970 (100%) - 7403 spectra/s] 7.7s Operating on slice 13 of 16: Fragment index slice generated in 18.27 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 26.6 s | deisotoping 4.0 s [progress: 56970/56970 (100%) - 7905 spectra/s] 7.2s Operating on slice 14 of 16: Fragment index slice generated in 24.39 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 23.2 s | deisotoping 3.5 s [progress: 56970/56970 (100%) - 10887 spectra/s] 5.2s Operating on slice 15 of 16: Fragment index slice generated in 19.72 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 20.2 s | deisotoping 2.8 s [progress: 56970/56970 (100%) - 8599 spectra/s] 6.6s Operating on slice 16 of 16: Fragment index slice generated in 19.75 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw 19.4 s | deisotoping 2.2 s [progress: 56970/56970 (100%) - 12186 spectra/s] 4.7s | postprocessing 9.5 s ***************************FIRST SEARCH DONE IN 15.306 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | 3.52 1.26 | -0.03 1.06 | 1.58 0.69 | 0.06 0.60 -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|------- MS2 | 7 | 10 | 15 | 20 | 25 | 30 -------|-------|-------|-------|-------|-------|------- Count | 10794| 10575| skip rest -------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 150_1 | 100_1 -------|-------|-------|-------|------- Count | 11024| 11012| skip rest -------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 11138 -------|------- -------|------- Rm P. | 0 -------|------- Count | 11183 -------|------- New fragment_mass_tolerance = 7.000000 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 47.353 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 2 database_name = C:\Users\dawa726\braveQC\2024-05-03-decoys-Sorghum_bicolor_UniProt_TrEMBL.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 7.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = -1/0/1/2/3 mass_offsets = 0.0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_03 = 79.96633 STY 3 variable_mod_06 = 304.20715 n^ 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 = 304.20715 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: 322169 of length 8: 319898 of length 9: 305131 of length 10: 293164 of length 11: 287547 of length 12: 275980 of length 13: 265397 of length 14: 249772 of length 15: 238538 of length 16: 226947 of length 17: 216843 of length 18: 204018 of length 19: 194291 of length 20: 184181 of length 21: 176257 of length 22: 166193 of length 23: 157039 of length 24: 150309 of length 25: 140334 of length 26: 133120 of length 27: 125745 of length 28: 119779 of length 29: 112331 of length 30: 104071 of length 31: 98713 of length 32: 92099 of length 33: 85959 of length 34: 81490 of length 35: 75267 of length 36: 70046 of length 37: 65475 of length 38: 61741 of length 39: 57379 of length 40: 52526 of length 41: 48387 of length 42: 44653 of length 43: 40043 of length 44: 33598 of length 45: 26836 of length 46: 19583 of length 47: 13017 of length 48: 8448 of length 49: 4860 of length 50: 2833 In total 5952007 peptides. Generated 248686113 modified peptides. Number of peptides with more than 5000 modification patterns: 10 Selected fragment index width 0.03 Da. 14688612162 fragments to be searched in 25 slices (218.88 GB total) Operating on slice 1 of 25: Fragment index slice generated in 32.68 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 1.2 s [progress: 56853/56853 (100%) - 1533 spectra/s] 37.1s Operating on slice 2 of 25: Fragment index slice generated in 29.88 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 1.1 s [progress: 56853/56853 (100%) - 3170 spectra/s] 17.9s Operating on slice 3 of 25: Fragment index slice generated in 19.85 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.6 s [progress: 56853/56853 (100%) - 4027 spectra/s] 14.1s Operating on slice 4 of 25: Fragment index slice generated in 21.52 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.8 s [progress: 56853/56853 (100%) - 6147 spectra/s] 9.2s Operating on slice 5 of 25: Fragment index slice generated in 16.06 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.7 s [progress: 56853/56853 (100%) - 7336 spectra/s] 7.8s Operating on slice 6 of 25: Fragment index slice generated in 15.85 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.6 s [progress: 56853/56853 (100%) - 7659 spectra/s] 7.4s Operating on slice 7 of 25: Fragment index slice generated in 15.55 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.6 s [progress: 56853/56853 (100%) - 7997 spectra/s] 7.1s Operating on slice 8 of 25: Fragment index slice generated in 17.46 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.7 s [progress: 56853/56853 (100%) - 6412 spectra/s] 8.9s Operating on slice 9 of 25: Fragment index slice generated in 15.51 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.7 s [progress: 56853/56853 (100%) - 7541 spectra/s] 7.5s Operating on slice 10 of 25: Fragment index slice generated in 15.29 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.7 s [progress: 56853/56853 (100%) - 7511 spectra/s] 7.6s Operating on slice 11 of 25: Fragment index slice generated in 15.03 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.7 s [progress: 56853/56853 (100%) - 7501 spectra/s] 7.6s Operating on slice 12 of 25: Fragment index slice generated in 16.17 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.7 s [progress: 56853/56853 (100%) - 7193 spectra/s] 7.9s Operating on slice 13 of 25: Fragment index slice generated in 16.71 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.7 s [progress: 56853/56853 (100%) - 6717 spectra/s] 8.5s Operating on slice 14 of 25: Fragment index slice generated in 16.41 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.7 s [progress: 56853/56853 (100%) - 7266 spectra/s] 7.8s Operating on slice 15 of 25: Fragment index slice generated in 16.81 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.7 s [progress: 56853/56853 (100%) - 6731 spectra/s] 8.4s Operating on slice 16 of 25: Fragment index slice generated in 15.00 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.7 s [progress: 56853/56853 (100%) - 7554 spectra/s] 7.5s Operating on slice 17 of 25: Fragment index slice generated in 16.19 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.7 s [progress: 56853/56853 (100%) - 7294 spectra/s] 7.8s Operating on slice 18 of 25: Fragment index slice generated in 15.79 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 1.2 s [progress: 56853/56853 (100%) - 6594 spectra/s] 8.6s Operating on slice 19 of 25: Fragment index slice generated in 20.09 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 0.7 s [progress: 56853/56853 (100%) - 5357 spectra/s] 10.6s Operating on slice 20 of 25: Fragment index slice generated in 19.87 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 1.1 s [progress: 56853/56853 (100%) - 5389 spectra/s] 10.5s Operating on slice 21 of 25: Fragment index slice generated in 20.55 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 1.1 s [progress: 56853/56853 (100%) - 5524 spectra/s] 10.3s Operating on slice 22 of 25: Fragment index slice generated in 24.19 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 1.1 s [progress: 56853/56853 (100%) - 5583 spectra/s] 10.2s Operating on slice 23 of 25: Fragment index slice generated in 19.52 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 1.1 s [progress: 56853/56853 (100%) - 4716 spectra/s] 12.1s Operating on slice 24 of 25: Fragment index slice generated in 19.26 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 1.2 s [progress: 56853/56853 (100%) - 5731 spectra/s] 9.9s Operating on slice 25 of 25: Fragment index slice generated in 19.80 s 001. PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.mzBIN_calibrated 1.0 s [progress: 56853/56853 (100%) - 5754 spectra/s] 9.9s | remapping alternative proteins and postprocessing 24.0 s ***************************MAIN SEARCH DONE IN 14.647 MIN*************************** *******************************TOTAL TIME 77.306 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\lib\fragpipe-21.0.jar;/C:/Users/dawa726/FragPipe-21.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pepXML C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\lib\fragpipe-21.0.jar;/C:/Users/dawa726/FragPipe-21.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pin C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pin Process 'MSFragger move pin' finished, exit code: 0 Percolator [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 2 --results-psms PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_target_psms.tsv --decoy-results-psms PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 2 --results-psms PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_target_psms.tsv --decoy-results-psms PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pin Started Thu May 23 11:49:58 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 304.20715n^ 79.96633STY Found 52849 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 33560 positives and 19289 negatives, size ratio=1.73985 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 7691 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 7670 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 7765 training set positives with q<0.01 in that direction. Found 11536 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 1.4190 cpu seconds or 2 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 12214 PSMs with q<0.01 Iteration 2: Estimated 12313 PSMs with q<0.01 Iteration 3: Estimated 12343 PSMs with q<0.01 Iteration 4: Estimated 12363 PSMs with q<0.01 Iteration 5: Estimated 12355 PSMs with q<0.01 Iteration 6: Estimated 12354 PSMs with q<0.01 Iteration 7: Estimated 12359 PSMs with q<0.01 Iteration 8: Estimated 12360 PSMs with q<0.01 Iteration 9: Estimated 12359 PSMs with q<0.01 Iteration 10: Estimated 12361 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 -0.4105 -0.3173 -0.2773 abs_ppm -0.2708 -0.1653 -0.2062 isotope_errors -2.2095 -1.9269 -1.9744 log10_evalue 1.2707 0.7781 0.7042 hyperscore 0.9111 0.8080 0.7121 delta_hyperscore 0.2877 0.6530 0.5175 matched_ion_num -0.3615 -0.2035 -0.0479 complementary_ions 0.7020 0.6975 0.6446 ion_series -0.5216 -0.4959 -0.3334 weighted_average_abs_fragment_ppm 0.1751 0.1278 0.1496 length_7 0.0471 0.0675 0.0636 length_8 -0.1156 -0.1164 -0.1055 length_9_30 -0.1364 -0.0726 -0.1498 length_31 0.0000 0.0000 0.0000 ntt -0.0738 -0.1185 -0.2173 nmc 0.0000 0.0000 0.0000 charge_1 -0.2100 -0.2554 -0.2761 charge_2 0.1680 0.1744 0.1784 charge_3 0.1408 0.1267 0.1879 charge_4 -0.1967 0.0241 -0.0708 charge_5 0.0259 0.0200 0.0192 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 0.0407 -0.0496 -0.0018 15.9949M -0.0133 -0.0310 -0.0371 304.20715n^ -0.8369 -0.5310 -0.6047 79.96633STY -0.9523 -0.7357 -0.7071 m0 Found 12305 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 33560 target PSMs and 19289 decoy PSMs. Calculating q values. Final list yields 12306 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 11.9940 cpu seconds or 12 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] java -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pin PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58 PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_target_psms.tsv PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_decoy_psms.tsv interact-PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58 DDA 0.5 C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: C:\Users\dawa726\braveQC\output] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined C:\Users\dawa726\braveQC\output\filelist_proteinprophet.txt INFO[11:50:15] Executing ProteinProphet v5.1.0 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64)) (no FPKM) (no groups) (using degen pep info) Reading in C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\interact-PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pep.xml... ...read in 0 1+, 6584 2+, 5368 3+, 1119 4+, 88 5+, 4 6+, 0 7+ spectra with min prob 0.5 Initializing 11436 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database C:\Users\dawa726\braveQC\2024-05-03-decoys-Sorghum_bicolor_UniProt_TrEMBL.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 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.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........43000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........44000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........45000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........46000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........47000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........48000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........49000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........50000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........51000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........52000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........53000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........54000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........55000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........56000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........57000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........58000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........59000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........60000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........61000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........62000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........63000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........64000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........65000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........66000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........67000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........68000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........78000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........82000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........85000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........86000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........87000 ..... Total: 87058 Computing degenerate peptides for 6009 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 6954 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6954 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6954 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6954 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=5.67408e-06, db_size=69245268 Computing MU for 6954 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO[11:50:20] Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe database --annotate C:\Users\dawa726\braveQC\2024-05-03-decoys-Sorghum_bicolor_UniProt_TrEMBL.fasta.fas --prefix rev_ INFO[11:50:20] Executing Database v5.1.0 INFO[11:50:20] Annotating the database INFO[11:50:21] Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58 --protxml C:\Users\dawa726\braveQC\output\combined.prot.xml --razor INFO[11:50:21] Executing Filter v5.1.0 INFO[11:50:21] Processing peptide identification files INFO[11:50:21] Parsing C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\interact-PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.pep.xml INFO[11:50:22] 1+ Charge profile decoy=0 target=0 INFO[11:50:22] 2+ Charge profile decoy=154 target=6430 INFO[11:50:22] 3+ Charge profile decoy=137 target=5231 INFO[11:50:22] 4+ Charge profile decoy=28 target=1091 INFO[11:50:22] 5+ Charge profile decoy=1 target=87 INFO[11:50:22] 6+ Charge profile decoy=0 target=4 INFO[11:50:22] Database search results ions=11398 peptides=9100 psms=13163 INFO[11:50:22] Converged to 1.00 % FDR with 12306 PSMs decoy=123 threshold=0.755524 total=12429 INFO[11:50:22] Converged to 0.99 % FDR with 8348 Peptides decoy=83 threshold=0.813514 total=8431 INFO[11:50:22] Converged to 1.00 % FDR with 10626 Ions decoy=106 threshold=0.772328 total=10732 INFO[11:50:22] Protein inference results decoy=310 target=3939 INFO[11:50:22] Converged to 0.99 % FDR with 2917 Proteins decoy=29 threshold=0.9252 total=2946 INFO[11:50:23] Applying sequential FDR estimation ions=10548 peptides=8306 psms=12197 INFO[11:50:23] Converged to 0.25 % FDR with 12166 PSMs decoy=31 threshold=0.756763 total=12197 INFO[11:50:23] Converged to 0.34 % FDR with 8278 Peptides decoy=28 threshold=0.756763 total=8306 INFO[11:50:23] Converged to 0.29 % FDR with 10517 Ions decoy=31 threshold=0.756763 total=10548 INFO[11:50:23] Post processing identifications INFO[11:50:23] Assigning protein identifications to layers INFO[11:50:25] Processing protein inference INFO[11:50:25] Synchronizing PSMs and proteins INFO[11:50:25] Final report numbers after FDR filtering, and post-processing ions=10514 peptides=8275 proteins=2916 psms=12163 INFO[11:50:25] Saving INFO[11:50:26] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe report INFO[11:50:26] Executing Report v5.1.0 INFO[11:50:26] Creating reports INFO[11:50:26] Done Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: C:\Users\dawa726\braveQC\output] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe workspace --clean --nocheck INFO[11:50:26] Executing Workspace v5.1.0 INFO[11:50:26] Removing workspace INFO[11:50:26] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58] C:\Users\dawa726\FragPipe-21.0\fragpipe\philosopher.exe workspace --clean --nocheck INFO[11:50:27] Executing Workspace v5.1.0 INFO[11:50:27] Removing workspace INFO[11:50:27] Done Process 'WorkspaceClean' finished, exit code: 0 IonQuant [Work dir: C:\Users\dawa726\braveQC\output] java -Xmx15G -Dlibs.bruker.dir=C:\Users\dawa726\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=C:\Users\dawa726\MSFragger-4.0\ext\thermo -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\jfreechart-1.5.3.jar;C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\batmass-io-1.30.0.jar;C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 2 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 0 --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --multidir . --filelist C:\Users\dawa726\braveQC\output\filelist_ionquant.txt --modlist C:\Users\dawa726\braveQC\output\modmasses_ionquant.txt IonQuant version IonQuant-1.10.12 Batmass-IO version 1.30.0 timsdata library version timsdata-2-21-0-4 (c) University of Michigan System OS: Windows 10, Architecture: AMD64 Java Info: 22.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 15 GB memory 2024-05-23 11:50:27 [INFO] - Collecting variable modifications from all psm.tsv files... 2024-05-23 11:50:28 [INFO] - Loading and indexing all psm.tsv files... 2024-05-23 11:50:28 [INFO] - Collecting all compensation voltages if applicable... 2024-05-23 11:50:38 [INFO] - Parameters: 2024-05-23 11:50:38 [INFO] - perform-ms1quant = 1 2024-05-23 11:50:38 [INFO] - perform-isoquant = 0 2024-05-23 11:50:38 [INFO] - isotol = 20.0 2024-05-23 11:50:38 [INFO] - isolevel = 2 2024-05-23 11:50:38 [INFO] - isotype = tmt10 2024-05-23 11:50:38 [INFO] - site-reports = 0 2024-05-23 11:50:38 [INFO] - threads = 2 2024-05-23 11:50:38 [INFO] - mztol = 10.0 2024-05-23 11:50:38 [INFO] - rttol = 1.0 2024-05-23 11:50:38 [INFO] - imtol = 0.05 2024-05-23 11:50:38 [INFO] - minisotopes = 1 2024-05-23 11:50:38 [INFO] - minscans = 1 2024-05-23 11:50:38 [INFO] - psm = C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\psm.tsv 2024-05-23 11:50:38 [INFO] - multidir = C:\Users\dawa726\braveQC\output\.\ 2024-05-23 11:50:38 [INFO] - excludemods = 2024-05-23 11:50:38 [INFO] - minions = 1 2024-05-23 11:50:38 [INFO] - maxlfq = 0 2024-05-23 11:50:38 [INFO] - ibaq = 0 2024-05-23 11:50:38 [INFO] - normalization = 0 2024-05-23 11:50:38 [INFO] - minexps = 1 2024-05-23 11:50:38 [INFO] - minfreq = 0.0 2024-05-23 11:50:38 [INFO] - tp = 0 2024-05-23 11:50:38 [INFO] - mbr = 0 2024-05-23 11:50:38 [INFO] - mbrrttol = 1.0 2024-05-23 11:50:38 [INFO] - mbrimtol = 0.05 2024-05-23 11:50:38 [INFO] - mbrtoprun = 10 2024-05-23 11:50:38 [INFO] - mbrmincorr = 0.0 2024-05-23 11:50:38 [INFO] - ionmobility = 0 2024-05-23 11:50:38 [INFO] - ionfdr = 0.01 2024-05-23 11:50:38 [INFO] - peptidefdr = 1.0 2024-05-23 11:50:38 [INFO] - proteinfdr = 1.0 2024-05-23 11:50:38 [INFO] - light = 2024-05-23 11:50:38 [INFO] - medium = 2024-05-23 11:50:38 [INFO] - heavy = 2024-05-23 11:50:38 [INFO] - requantify = 0 2024-05-23 11:50:38 [INFO] - writeindex = 0 2024-05-23 11:50:38 [INFO] - locprob = 0.0 2024-05-23 11:50:38 [INFO] - uniqueness = 0 2024-05-23 11:50:38 [INFO] - filelist = C:\Users\dawa726\braveQC\output\filelist_ionquant.txt 2024-05-23 11:50:38 [INFO] - specdir = C:\Users\dawa726\braveQC 2024-05-23 11:50:38 [INFO] - modlist = C:\Users\dawa726\braveQC\output\modmasses_ionquant.txt 2024-05-23 11:50:38 [INFO] - mod masses: 2024-05-23 11:50:38 [INFO] - 15.9949 2024-05-23 11:50:38 [INFO] - 42.0106 2024-05-23 11:50:38 [INFO] - 57.02146 2024-05-23 11:50:38 [INFO] - 79.96633 2024-05-23 11:50:38 [INFO] - 304.20715 2024-05-23 11:50:38 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2024-05-23 11:50:39 [INFO] - Loading C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw... 2024-05-23 11:51:04 [INFO] - Building index... 2024-05-23 11:51:04 [INFO] - Quantifying... 2024-05-23 11:51:05 [INFO] - Updating Philosopher's tables... 2024-05-23 11:51:06 [INFO] - Combining experiments and estimating protein intensity... 2024-05-23 11:51:07 [INFO] - Done! Process 'IonQuant' finished, exit code: 0 IonQuant [Work dir: C:\Users\dawa726\braveQC\output] java -Xmx15G -Dlibs.bruker.dir=C:\Users\dawa726\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=C:\Users\dawa726\MSFragger-4.0\ext\thermo -cp C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\jfreechart-1.5.3.jar;C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\batmass-io-1.30.0.jar;C:\Users\dawa726\FragPipe-21.0\fragpipe\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 2 --perform-ms1quant 0 --perform-isoquant 1 --isotol 20.0 --isolevel 2 --isotype TMT-16 --ionmobility 0 --site-reports 0 --annotation C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\psm.tsv=C:\Users\dawa726\braveQC\TMT_A_annotation_test.txt_annotation.txt --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --multidir . --filelist C:\Users\dawa726\braveQC\output\filelist_ionquant.txt --modlist C:\Users\dawa726\braveQC\output\modmasses_ionquant.txt IonQuant version IonQuant-1.10.12 Batmass-IO version 1.30.0 timsdata library version timsdata-2-21-0-4 (c) University of Michigan System OS: Windows 10, Architecture: AMD64 Java Info: 22.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 15 GB memory 2024-05-23 11:51:07 [INFO] - Collecting variable modifications from all psm.tsv files... 2024-05-23 11:51:08 [INFO] - Loading and indexing all psm.tsv files... 2024-05-23 11:51:08 [INFO] - Collecting all compensation voltages if applicable... 2024-05-23 11:51:17 [INFO] - Parameters: 2024-05-23 11:51:17 [INFO] - perform-ms1quant = 0 2024-05-23 11:51:17 [INFO] - perform-isoquant = 1 2024-05-23 11:51:17 [INFO] - isotol = 20.0 2024-05-23 11:51:17 [INFO] - isolevel = 2 2024-05-23 11:51:17 [INFO] - isotype = tmt-16 2024-05-23 11:51:17 [INFO] - annotation = PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58/psm.tsv=C:\Users\dawa726\braveQC\TMT_A_annotation_test.txt_annotation.txt 2024-05-23 11:51:17 [INFO] - site-reports = 0 2024-05-23 11:51:17 [INFO] - threads = 2 2024-05-23 11:51:17 [INFO] - mztol = 10.0 2024-05-23 11:51:18 [INFO] - rttol = 1.0 2024-05-23 11:51:18 [INFO] - imtol = 0.05 2024-05-23 11:51:18 [INFO] - minisotopes = 1 2024-05-23 11:51:18 [INFO] - minscans = 1 2024-05-23 11:51:18 [INFO] - psm = C:\Users\dawa726\braveQC\output\PremixQC_Magill_A_22May24_Titus_BEHCoA_24_04_58\psm.tsv 2024-05-23 11:51:18 [INFO] - multidir = C:\Users\dawa726\braveQC\output\.\ 2024-05-23 11:51:18 [INFO] - excludemods = 2024-05-23 11:51:18 [INFO] - minions = 1 2024-05-23 11:51:18 [INFO] - maxlfq = 0 2024-05-23 11:51:18 [INFO] - ibaq = 0 2024-05-23 11:51:18 [INFO] - normalization = 0 2024-05-23 11:51:18 [INFO] - minexps = 1 2024-05-23 11:51:18 [INFO] - minfreq = 0.0 2024-05-23 11:51:18 [INFO] - tp = 0 2024-05-23 11:51:18 [INFO] - mbr = 0 2024-05-23 11:51:18 [INFO] - mbrrttol = 1.0 2024-05-23 11:51:18 [INFO] - mbrimtol = 0.05 2024-05-23 11:51:18 [INFO] - mbrtoprun = 10 2024-05-23 11:51:18 [INFO] - mbrmincorr = 0.0 2024-05-23 11:51:18 [INFO] - ionmobility = 0 2024-05-23 11:51:18 [INFO] - ionfdr = 0.01 2024-05-23 11:51:18 [INFO] - peptidefdr = 1.0 2024-05-23 11:51:18 [INFO] - proteinfdr = 1.0 2024-05-23 11:51:18 [INFO] - light = 2024-05-23 11:51:18 [INFO] - medium = 2024-05-23 11:51:18 [INFO] - heavy = 2024-05-23 11:51:18 [INFO] - requantify = 0 2024-05-23 11:51:18 [INFO] - writeindex = 0 2024-05-23 11:51:18 [INFO] - locprob = 0.0 2024-05-23 11:51:18 [INFO] - uniqueness = 0 2024-05-23 11:51:18 [INFO] - filelist = C:\Users\dawa726\braveQC\output\filelist_ionquant.txt 2024-05-23 11:51:18 [INFO] - specdir = C:\Users\dawa726\braveQC 2024-05-23 11:51:18 [INFO] - modlist = C:\Users\dawa726\braveQC\output\modmasses_ionquant.txt 2024-05-23 11:51:18 [INFO] - mod masses: 2024-05-23 11:51:18 [INFO] - 15.9949 2024-05-23 11:51:18 [INFO] - 42.0106 2024-05-23 11:51:18 [INFO] - 57.02146 2024-05-23 11:51:18 [INFO] - 79.96633 2024-05-23 11:51:18 [INFO] - 304.20715 2024-05-23 11:51:18 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2024-05-23 11:51:18 [INFO] - Loading and quantifying C:\Users\dawa726\braveQC\PremixQC_Magill_A_22May24_Titus_BEHCoA-24-04-58.raw... java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 63458 at m.(Unknown Source) at p.(Unknown Source) at ionquant.IonQuant.main(Unknown Source) 2024-05-23 11:51:28 [ERROR] - Index -1 out of bounds for length 63458 Process 'IonQuant' finished, exit code: 1 Process returned non-zero exit code, stopping ~~~~~~~~~~~~~~~~~~~~ Cancelling 2 remaining tasks