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Nesvilab / FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
http://fragpipe.nesvilab.org
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proteinprophet returned non-zero #1556

Closed HYCCHENG closed 2 months ago

HYCCHENG commented 2 months ago

Hello, I recently used open search to find an unknown modification of 60 AA peptides. The sample was analyzed after processing, but the results showed: Process 'ProteinProphet' finished, exit code: 1 Process returned non-zero exit code, stopping。 What could be the reason for this? Thanks! The search history is as follows

System OS: Windows 11, Architecture: AMD64 Java Info: 11.0.15.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation .NET Core Info: 6.0.7

Version info: FragPipe version 20.0 MSFragger version 3.8 IonQuant version 1.9.8 Philosopher version 5.0.0

LCMS files: Experiment/Group:

17 commands to execute: CheckCentroid java -Xmx47G -cp "C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin.raw 19 WorkspaceCleanInit [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\SZBL\AppData\Local\Temp\a6d22017-1214-4c9a-8252-fa512471e24e MSFragger [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] java -jar -Dfile.encoding=UTF-8 -Xmx47G C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\fragger.params D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin.raw MSFragger move pepxml java -cp C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/C:/Users/SZBL/Downloads/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin.pepXML D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\20240420_scut_100ng_60min_sin.pepXML MSFragger move tsv java -cp C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/C:/Users/SZBL/Downloads/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin.tsv D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\20240420_scut_100ng_60min_sin.tsv MSFragger move pin java -cp C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/C:/Users/SZBL/Downloads/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin.pin D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\20240420_scut_100ng_60min_sin.pin Crystal-C [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] java -Dlibs.thermo.dir="C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\thermo" -Xmx47G -cp "C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\original-crystalc-1.5.2.jar;C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar;C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\crystalc-0-20240420_scut_100ng_60min_sin.pepXML.params D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\20240420_scut_100ng_60min_sin.pepXML Crystal-C: Delete temp java -cp C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\crystalc-0-20240420_scut_100ng_60min_sin.pepXML.params PeptideProphet [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Proteomics data\Database_fasta\2024-04-25-decoys-contam-20240420_SCUT_TEST.fasta.fas --combine 20240420_scut_100ng_60min_sin_c.pepXML Rewrite pepxml [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] java -cp C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\interact.pep.xml D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin_uncalibrated.mzML ProteinProphet [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe database --annotate D:\Proteomics data\Database_fasta\2024-04-25-decoys-contam-20240420_SCUTTEST.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe filter --sequential --prot 0.01 --mapmods --tag rev --pepxml D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2 --protxml D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\combined.prot.xml --razor PhilosopherReport [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report PTMShepherd [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] java -Xmx47G -Dlibs.thermo.dir="C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\thermo" -cp "C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\ptmshepherd-2.0.5.jar;C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar;C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\commons-math3-3.6.1.jar;C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\hipparchus-1.8\hipparchus-core-1.8.jar;C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\hipparchus-1.8\hipparchus-stat-1.8.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\shepherd.config" WorkspaceClean [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2]
    Cmd: [CheckCentroid], Work dir: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2]
    Cmd: [MSFragger], Work dir: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2]
    Cmd: [Crystal-C], Work dir: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2]
    Cmd: [PeptideProphet], Work dir: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2]
    Cmd: [ProteinProphet], Work dir: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2]
    Cmd: [PhilosopherFilter], Work dir: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2]
    Cmd: [PhilosopherReport], Work dir: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2]
    Cmd: [PTMShepherd], Work dir: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2]
    Cmd: [WorkspaceClean], Work dir: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2]

>rev_sp|O00762|UBE2C_HUMAN Ubiquitin-conjugating enzyme E2 C OS=Homo sapiens OX=9606 GN=UBE2C PE=1 SV=1
>rev_sp|P00330|ADH1_YEAST Alcohol dehydrogenase 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=ADH1 PE=1 SV=5
>rev_sp|P00767|CTRB_BOVIN Chymotrypsinogen B OS=Bos taurus OX=9913 PE=1 SV=1
>rev_sp|P01127|PDGFB_HUMAN Platelet-derived growth factor subunit B OS=Homo sapiens OX=9606 GN=PDGFB PE=1 SV=1
>rev_sp|P02445|KRA34_SHEEP Keratin, high sulfur matrix protein, IIIB4 OS=Ovis aries OX=9940 PE=1 SV=1
>rev_sp|P02787|TRFE_HUMAN Serotransferrin OS=Homo sapiens OX=9606 GN=TF PE=1 SV=3
>rev_sp|P08758|ANXA5_HUMAN Annexin A5 OS=Homo sapiens OX=9606 GN=ANXA5 PE=1 SV=2
>rev_sp|P15241|K2M2_SHEEP Keratin, type II microfibrillar, component 7C OS=Ovis aries OX=9940 PE=1 SV=1
>rev_sp|P41159|LEP_HUMAN Leptin OS=Homo sapiens OX=9606 GN=LEP PE=1 SV=1
>rev_sp|P68871|HBB_HUMAN Hemoglobin subunit beta OS=Homo sapiens OX=9606 GN=HBB PE=1 SV=2
>rev_sp|Q14533|KRT81_HUMAN Keratin, type II cuticular Hb1 OS=Homo sapiens OX=9606 GN=KRT81 PE=1 SV=3
>sp|O76011|KRT34_HUMAN Keratin, type I cuticular Ha4 OS=Homo sapiens OX=9606 GN=KRT34 PE=1 SV=2
>sp|P00551|KKA1_ECOLX Aminoglycoside 3'-phosphotransferase OS=Escherichia coli OX=562 GN=aphA1 PE=3 SV=2
>sp|P00883|ALDOA_RABIT Fructose-bisphosphate aldolase A OS=Oryctolagus cuniculus OX=9986 GN=ALDOA PE=1 SV=2
>sp|P01375|TNFA_HUMAN Tumor necrosis factor OS=Homo sapiens OX=9606 GN=TNF PE=1 SV=1
>sp|P02662|CASA1_BOVIN Alpha-S1-casein OS=Bos taurus OX=9913 GN=CSN1S1 PE=1 SV=2
>sp|P04264|K2C1_HUMAN Keratin, type II cytoskeletal 1 OS=Homo sapiens OX=9606 GN=KRT1 PE=1 SV=6
>sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1
>sp|P16083|NQO2_HUMAN Ribosyldihydronicotinamide dehydrogenase [quinone] OS=Homo sapiens OX=9606 GN=NQO2 PE=1 SV=5
>sp|P55957|BID_HUMAN BH3-interacting domain death agonist OS=Homo sapiens OX=9606 GN=BID PE=1 SV=1
>sp|P78386|KRT85_HUMAN Keratin, type II cuticular Hb5 OS=Homo sapiens OX=9606 GN=KRT85 PE=1 SV=1
>sp|Q29463|TRY2_BOVIN Anionic trypsin OS=Bos taurus OX=9913 PE=2 SV=1
# FragPipe v20.0ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\Proteomics data\\Database_fasta\\2024-04-25-decoys-contam-20240420_SCUT_TEST.fasta.fas

Table.editor=439.1888
crystalc.run-crystalc=true
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
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
fragpipe-config.bin-ionquant=C\:\\Users\\SZBL\\Downloads\\FragPipe-20.0\\fragpipe\\tools\\IonQuant-1.9.8.jar
fragpipe-config.bin-msfragger=C\:\\Users\\SZBL\\Downloads\\FragPipe-20.0\\fragpipe\\tools\\MSFragger-3.8\\MSFragger-3.8.jar
fragpipe-config.bin-philosopher=C\:\\Users\\SZBL\\Downloads\\FragPipe-20.0\\fragpipe\\tools\\philosopher_v5.0.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\SZBL\\AppData\\Local\\Programs\\Python\\Python39\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=true
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=false
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.add_topN_complementary=0
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=true
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dia1=5
msfragger.output_report_topN_dia2=3
msfragger.override_charge=false
msfragger.precursor_mass_lower=-150
msfragger.precursor_mass_mode=corrected
msfragger.precursor_mass_units=0
msfragger.precursor_mass_upper=500
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),false,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
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=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=false
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 0.01 --mapmods
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
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.diagextract_mode=false
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_minIons=25
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_allowed_res=all
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=true
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
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=ciRT
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-10
tmtintegrator.dont-run-fq-lq=false
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_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=pool
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=D\:\\Proteomics_data_20240129\\OTHERS\\20240420_SCUT_100ng_60min_sin\\OPEN_2
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=19

CheckCentroid java -Xmx47G -cp "C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin.raw 19 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[18:53:21] Executing Workspace v5.0.0
INFO[18:53:21] Removing workspace
WARN[18:53:21] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[18:53:21] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\SZBL\AppData\Local\Temp\a6d22017-1214-4c9a-8252-fa512471e24e INFO[18:53:22] Executing Workspace v5.0.0
INFO[18:53:22] Creating workspace
INFO[18:53:22] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] java -jar -Dfile.encoding=UTF-8 -Xmx47G C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\fragger.params D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin.raw MSFragger version MSFragger-3.8 Batmass-IO version 1.28.12 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 11, Architecture: AMD64 Java Info: 11.0.15.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 47 GB memory Checking database... Checking spectral files... D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin.raw: Scans = 15647 ***FIRST SEARCH**** Parameters: num_threads = 19 database_name = D:\Proteomics data\Database_fasta\2024-04-25-decoys-contam-20240420_SCUT_TEST.fasta.fas decoyprefix = 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 = CORRECTED 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 = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 789 of length 8: 804 of length 9: 942 of length 10: 713 of length 11: 815 of length 12: 820 of length 13: 718 of length 14: 703 of length 15: 647 of length 16: 718 of length 17: 571 of length 18: 600 of length 19: 650 of length 20: 642 of length 21: 682 of length 22: 445 of length 23: 428 of length 24: 382 of length 25: 368 of length 26: 389 of length 27: 419 of length 28: 329 of length 29: 289 of length 30: 295 of length 31: 304 of length 32: 240 of length 33: 216 of length 34: 208 of length 35: 199 of length 36: 222 of length 37: 182 of length 38: 182 of length 39: 108 of length 40: 157 of length 41: 151 of length 42: 120 of length 43: 115 of length 44: 87 of length 45: 75 of length 46: 43 of length 47: 45 of length 48: 22 of length 49: 15 of length 50: 10 In total 16859 peptides. Generated 24560 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 995204 fragments to be searched in 1 slices (0.01 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.07 s

  1. 20240420_scut_100ng_60min_sin.raw 9.3 s | deisotoping 0.3 s [progress: 12771/12771 (100%) - 39175 spectra/s] 0.3s | postprocessing 0.0 s ***FIRST SEARCH DONE IN 0.226 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 Not enough data to perform mass calibration. Using the uncalibrated data.
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 51 60 60 55 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- -------
Peaks 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- -------
Count 60 60 60 60 60 60
------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 65
------- -------
------- -------
Rm P. 0
------- -------
Count 65
------- -------

New fragment_mass_tolerance = 7 PPM New use_topN_peaks = 100 New minimum_ratio = 0.010000 New intensity_transform = 1 New remove_precursor_peak = 0 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.646 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 19 database_name = D:\Proteomics data\Database_fasta\2024-04-25-decoys-contam-20240420_SCUT_TEST.fasta.fas decoyprefix = rev precursor_mass_lower = -150.0 precursor_mass_upper = 500.0 precursor_mass_units = 0 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 = 0 mass_offsets = 0.0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = CORRECTED localize_delta_mass = 1 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 100 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 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 = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 789 of length 8: 804 of length 9: 942 of length 10: 713 of length 11: 815 of length 12: 820 of length 13: 718 of length 14: 703 of length 15: 647 of length 16: 718 of length 17: 571 of length 18: 600 of length 19: 650 of length 20: 642 of length 21: 682 of length 22: 445 of length 23: 428 of length 24: 382 of length 25: 368 of length 26: 389 of length 27: 419 of length 28: 329 of length 29: 289 of length 30: 295 of length 31: 304 of length 32: 240 of length 33: 216 of length 34: 208 of length 35: 199 of length 36: 222 of length 37: 182 of length 38: 182 of length 39: 108 of length 40: 157 of length 41: 151 of length 42: 120 of length 43: 115 of length 44: 87 of length 45: 75 of length 46: 43 of length 47: 45 of length 48: 22 of length 49: 15 of length 50: 10 In total 16859 peptides. Generated 24560 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.01 Da. 1990408 fragments to be searched in 1 slices (0.03 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.29 s

  1. 20240420_scut_100ng_60min_sin.raw 2.8 s | deisotoping 0.0 s [progress: 12771/12771 (100%) - 4395 spectra/s] 2.9s | remapping alternative proteins and postprocessing 0.8 s MAIN SEARCH DONE IN 0.124 MIN

***TOTAL TIME 0.995 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/C:/Users/SZBL/Downloads/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin.pepXML D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\20240420_scut_100ng_60min_sin.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move tsv java -cp C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/C:/Users/SZBL/Downloads/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin.tsv D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\20240420_scut_100ng_60min_sin.tsv Process 'MSFragger move tsv' finished, exit code: 0 MSFragger move pin java -cp C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/C:/Users/SZBL/Downloads/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin.pin D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\20240420_scut_100ng_60min_sin.pin Process 'MSFragger move pin' finished, exit code: 0 Crystal-C [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] java -Dlibs.thermo.dir="C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\thermo" -Xmx47G -cp "C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\original-crystalc-1.5.2.jar;C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar;C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\crystalc-0-20240420_scut_100ng_60min_sin.pepXML.params D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\20240420_scut_100ng_60min_sin.pepXML 20240420_scut_100ng_60min_sin.pepXML Done! The execution time is 0.07105 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C: Delete temp java -cp C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\crystalc-0-20240420_scut_100ng_60min_sin.pepXML.params Process 'Crystal-C: Delete temp' finished, exit code: 0 PeptideProphet [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Proteomics data\Database_fasta\2024-04-25-decoys-contam-20240420_SCUT_TEST.fasta.fas --combine 20240420_scut_100ng_60min_sin_c.pepXML Please wait. PeptideProphet is running. It can take a long time. INFO[18:54:29] Executing PeptideProphet v5.0.0
Unknown file type. No file loaded.D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2/20240420_scut_100ng_60min_sin.raw Unknown file type. No file loaded.D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2/20240420_scut_100ng_60min_sin.raw file 1: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\20240420_scut_100ng_60min_sin_c.pepXML processed altogether 6966 results INFO: Results written to file: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\interact.pep.xml

Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) using search_offsets in mass mixture distr: 0.0 init with X! Tandem stricttrypsin PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 3398 2+, 2453 3+, 774 4+, 270 5+, 57 6+, and 14 7+ spectra. Found 3245 Decoys, and 3721 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .........10.........20...WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (2+). .. WARNING: Mixture model quality test failed for charge (3+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 26 iterations INFO[18:54:35] Done
Process 'PeptideProphet' finished, exit code: 0 Rewrite pepxml [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] java -cp C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\interact.pep.xml D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin_uncalibrated.mzML Fixing pepxml: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\interact.pep.xml Writing output to: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\interact.pep.xml4425358284813464914.temp-rewrite Deleting file: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\interact.pep.xml Moving rewritten file to original location: [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\interact.pep.xml4425358284813464914.temp-rewrite] -> [D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\interact.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2] C:\Users\SZBL\Downloads\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\filelist_proteinprophet.txt INFO[18:54:36] Executing ProteinProphet v5.0.0
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 D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\interact.pep.xml... did not find any PeptideProphet results in input data! Did you forget to run PeptideProphet? ...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

WARNING: no data - output file will be empty ERRO[18:54:36] Cannot execute program. there was an error with ProteinProphet, please check your parameters and input files Process 'ProteinProphet' finished, exit code: 1 Process returned non-zero exit code, stopping


Cancelling 6 remaining tasks
danielgeiszler commented 2 months ago

The FDR modeling couldn't converge because your database was too small, so there were no peptides identified in your dataset. It may work if you try appending your peptide to a full database. If that doesn't work, someone else might have other ideas about how to get this through the pipeline.

HYCCHENG commented 2 months ago

The FDR modeling couldn't converge because your database was too small, so there were no peptides identified in your dataset. It may work if you try appending your peptide to a full database. If that doesn't work, someone else might have other ideas about how to get this through the pipeline.

Thank you. My database has indeed only added one type of protein. But when I added this protein to a large database and searched here, I still received the same error message. I think there may be other reasons?

fcyu commented 2 months ago

Could you share the log file?

Thanks,

Fengchao

HYCCHENG commented 2 months ago

log_2024-04-26_09-25-38.txt The log file is attached

fcyu commented 2 months ago

Thanks for the log file. Does your fasta D:\Proteomics data\Database_fasta\20240425_scut_test.fasta contain decoys with prefix rev_?

Also, could you remove the spaces in your folder name, such as D:\Proteomics data\Database_fasta\?

Best,

Fengchao

HYCCHENG commented 2 months ago

Yes, I set a decoy library for this database

---- Replied Message ---- | From | @.> | | Date | 04/26/2024 09:32 | | To | Nesvilab/FragPipe @.> | | Cc | HYCCHENG @.>, Author @.> | | Subject | Re: [Nesvilab/FragPipe] proteinprophet returned non-zero (Issue #1556) |

Thanks for the log file. Does your fasta D:\Proteomics data\Database_fasta\20240425_scuttest.fasta contain decoys with prefix rev?

Best,

Fengchao

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fcyu commented 2 months ago

I doube that because there is a warning in your log file:

Found 0 Decoys, and 11306 Non-Decoys
WARNING: No decoys with label rev_ were found in this dataset. reverting to fully unsupervised method.

Could you zip and upload your fasta file to https://github.com/Nesvilab/FragPipe/issues/1556?

Thanks,

Fengchao