proteinprophet returned non-zero
Closed this issue · 7 comments
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:
- D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\20240420_scut_100ng_60min_sin.raw DDA
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_windows_amd64\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_SCUT_TEST.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_windows_amd64\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
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 = 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
001. 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
decoy_prefix = 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
001. 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_windows_amd64\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
- D:\Proteomics_data_20240129\OTHERS\20240420_SCUT_100ng_60min_sin\OPEN_2\interact.pep.xml
- Building Commentz-Walter keyword tree...
- Searching the tree...
- Linking duplicate entries...
- Printing results...
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
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.
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?
Could you share the log file?
Thanks,
Fengchao
log_2024-04-26_09-25-38.txt
The log file is attached
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