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Process 'MSBooster' finished, exit code: 1 Process returned non-zero exit code, stopping #1244

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gux2023 opened this issue Sep 12, 2023 · 7 comments

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@gux2023
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gux2023 commented Sep 12, 2023

I used MSConverter to convert Agilent .d file to .mzXML file. Then use Fragpipe for database searching.
The Run was stopped. Please help!

System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
.NET Core Info: N/A

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

LCMS files:
Experiment/Group:

  • H:\mzXML\Ingel_08282023_RP_E2.mzXML DDA

16 commands to execute:
CheckCentroid
C:\fragpipe\jre\bin\java.exe -Xmx8G -cp "C:\fragpipe\lib\fragpipe-20.0.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid H:\mzXML\Ingel_08282023_RP_E2.mzXML 11
WorkspaceCleanInit [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gux\AppData\Local\Temp\56e75c33-1551-434e-a3a6-55f88505beb9
MSFragger [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx8G C:\fragpipe\lib\MSFragger-3.8\MSFragger-3.8.jar D:\XiaorongGu\Proteomics\MGF\fragger.params H:\mzXML\Ingel_08282023_RP_E2.mzXML
MSFragger move pepxml
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err H:\mzXML\Ingel_08282023_RP_E2.pepXML D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2.pepXML
MSFragger move pin
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err H:\mzXML\Ingel_08282023_RP_E2.pin D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2.pin
MSBooster [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -Xmx8G -cp "C:\fragpipe\tools\msbooster-1.1.11.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" Features.MainClass --paramsList D:\XiaorongGu\Proteomics\MGF\msbooster_params.txt
Percolator [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms Ingel_08282023_RP_E2_percolator_target_psms.tsv --decoy-results-psms Ingel_08282023_RP_E2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Ingel_08282023_RP_E2_edited.pin
Percolator: Convert to pepxml [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Ingel_08282023_RP_E2.pin Ingel_08282023_RP_E2 Ingel_08282023_RP_E2_percolator_target_psms.tsv Ingel_08282023_RP_E2_percolator_decoy_psms.tsv interact-Ingel_08282023_RP_E2 DDA 0.5 H:\mzXML\Ingel_08282023_RP_E2.mzXML
Percolator: Delete temp
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2_percolator_target_psms.tsv
Percolator: Delete temp
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2_percolator_decoy_psms.tsv
ProteinProphet [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\XiaorongGu\Proteomics\MGF\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe database --annotate C:\fragpipe\bin\2023-09-12-decoys-contam-2023-09-06-decoys-reviewed-contam-UP000005640.fas.fas --prefix rev_
PhilosopherFilter [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\XiaorongGu\Proteomics\MGF --protxml D:\XiaorongGu\Proteomics\MGF\combined.prot.xml --razor
PhilosopherReport [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
WorkspaceClean [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [CheckCentroid], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [MSFragger], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [MSBooster], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [Percolator], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [ProteinProphet], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [PhilosopherFilter], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [PhilosopherReport], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [WorkspaceClean], Work dir: [D:\XiaorongGu\Proteomics\MGF]

>rev_rev_sp|A0A024R1R8|TMA7B_HUMAN Translation machinery-associated protein 7B OS=Homo sapiens OX=9606 GN=TMA7B PE=3 SV=1
>rev_rev_sp|O95996|APCL_HUMAN Adenomatous polyposis coli protein 2 OS=Homo sapiens OX=9606 GN=APC2 PE=1 SV=1
>rev_rev_sp|P51504|ZNF80_HUMAN Zinc finger protein 80 OS=Homo sapiens OX=9606 GN=ZNF80 PE=1 SV=2
>rev_rev_sp|Q53H82|LACB2_HUMAN Endoribonuclease LACTB2 OS=Homo sapiens OX=9606 GN=LACTB2 PE=1 SV=2
>rev_rev_sp|Q8IYB5|SMAP1_HUMAN Stromal membrane-associated protein 1 OS=Homo sapiens OX=9606 GN=SMAP1 PE=1 SV=2
>rev_rev_sp|Q96KC9|CABS1_HUMAN Calcium-binding and spermatid-specific protein 1 OS=Homo sapiens OX=9606 GN=CABS1 PE=2 SV=3
>rev_rev_sp|Q9NWW0|HPIP_HUMAN Host cell factor C1 regulator 1 OS=Homo sapiens OX=9606 GN=HCFC1R1 PE=1 SV=1
>rev_sp|B4DYI2|S31C2_HUMAN Putative spermatogenesis-associated protein 31C2 OS=Homo sapiens OX=9606 GN=SPATA31C2 PE=5 SV=2
>rev_sp|P0DW14|TFKLJ_HUMAN TATA-box-binding protein-associated factor 11-like protein 10 OS=Homo sapiens OX=9606 GN=TAF11L10 PE=2 SV=1
>rev_sp|Q00537|CDK17_HUMAN Cyclin-dependent kinase 17 OS=Homo sapiens OX=9606 GN=CDK17 PE=1 SV=2
>rev_sp|Q6IAN0|DRS7B_HUMAN Dehydrogenase/reductase SDR family member 7B OS=Homo sapiens OX=9606 GN=DHRS7B PE=1 SV=2
>rev_sp|Q8NEB5|PLPP5_HUMAN Phospholipid phosphatase 5 OS=Homo sapiens OX=9606 GN=PLPP5 PE=1 SV=2
>rev_sp|Q9BSV6|SEN34_HUMAN tRNA-splicing endonuclease subunit Sen34 OS=Homo sapiens OX=9606 GN=TSEN34 PE=1 SV=1
>rev_sp|Q9UKZ9|PCOC2_HUMAN Procollagen C-endopeptidase enhancer 2 OS=Homo sapiens OX=9606 GN=PCOLCE2 PE=1 SV=1
>sp|O43927|CXL13_HUMAN C-X-C motif chemokine 13 OS=Homo sapiens OX=9606 GN=CXCL13 PE=1 SV=1
>sp|P27540|ARNT_HUMAN Aryl hydrocarbon receptor nuclear translocator OS=Homo sapiens OX=9606 GN=ARNT PE=1 SV=1
>sp|Q14444|CAPR1_HUMAN Caprin-1 OS=Homo sapiens OX=9606 GN=CAPRIN1 PE=1 SV=2
>sp|Q71F78|LCA10_HUMAN Putative lung carcinoma-associated protein 10 OS=Homo sapiens OX=9606 GN=LCA10 PE=2 SV=1
>sp|Q8WWI5|CTL1_HUMAN Choline transporter-like protein 1 OS=Homo sapiens OX=9606 GN=SLC44A1 PE=1 SV=1
>sp|Q9H444|CHM4B_HUMAN Charged multivesicular body protein 4b OS=Homo sapiens OX=9606 GN=CHMP4B PE=1 SV=1
>sp|Q9Y6Z5|AFDDT_HUMAN Putative uncharacterized protein AFDN-DT OS=Homo sapiens OX=9606 GN=AFDN-DT PE=5 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=C\:\\fragpipe\\bin\\2023-09-12-decoys-contam-2023-09-06-decoys-reviewed-contam-UP000005640.fas.fas

crystalc.run-crystalc=false
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\:\\fragpipe\\tools\\IonQuant-1.9.8.jar
fragpipe-config.bin-msfragger=C\:\\fragpipe\\lib\\MSFragger-3.8\\MSFragger-3.8.jar
fragpipe-config.bin-philosopher=C\:\\fragpipe\\tools\\philosopher_v5.0.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=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=true
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=0
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=0/1/2/3
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.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=trypsin
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=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=true
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=trypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=P
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,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_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=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=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
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=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_mode=false
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_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
ptmshepherd.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.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=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=D\:\\XiaorongGu\\Proteomics\\MGF
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=8
workflow.threads=11

CheckCentroid
C:\fragpipe\jre\bin\java.exe -Xmx8G -cp "C:\fragpipe\lib\fragpipe-20.0.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid H:\mzXML\Ingel_08282023_RP_E2.mzXML 11
Done in 2.5 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[14:02:44] Executing Workspace v5.0.0
INFO[14:02:44] Removing workspace
INFO[14:02:44] Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gux\AppData\Local\Temp\56e75c33-1551-434e-a3a6-55f88505beb9
INFO[14:02:45] Executing Workspace v5.0.0
INFO[14:02:45] Creating workspace
INFO[14:02:45] Done
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx8G C:\fragpipe\lib\MSFragger-3.8\MSFragger-3.8.jar D:\XiaorongGu\Proteomics\MGF\fragger.params H:\mzXML\Ingel_08282023_RP_E2.mzXML
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 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
JVM started with 8 GB memory
Checking database...
Checking spectral files...
H:\mzXML\Ingel_08282023_RP_E2.mzXML: Scans = 5335

MAIN SEARCH
Checking database...
Parameters:
num_threads = 11
database_name = C:\fragpipe\bin\2023-09-12-decoys-contam-2023-09-06-decoys-reviewed-contam-UP000005640.fas.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 = 0
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 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 = trypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = P
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 = 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_C_cysteine = 57.02146
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.10 Da.
314040894 fragments to be searched in 1 slices (4.68 GB total)
Operating on slice 1 of 1:
Fragment index slice generated in 5.22 s
001. Ingel_08282023_RP_E2.mzXML 4.2 s | deisotoping 0.6 s
[progress: 5335/5335 (100%) - 4271 spectra/s] 1.2s | remapping alternative proteins and postprocessing 2.3 s
MAIN SEARCH DONE IN 0.268 MIN

TOTAL TIME 0.416 MIN*
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err H:\mzXML\Ingel_08282023_RP_E2.pepXML D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err H:\mzXML\Ingel_08282023_RP_E2.pin D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2.pin
Process 'MSFragger move pin' finished, exit code: 0
MSBooster [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -Xmx8G -cp "C:\fragpipe\tools\msbooster-1.1.11.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" Features.MainClass --paramsList D:\XiaorongGu\Proteomics\MGF\msbooster_params.txt
MSBooster v1.1.11
Using 11 threads
java.lang.IllegalArgumentException: No matching mzml/mgf file for Ingel_08282023_RP_E2.pin, please check that provided mzml/mgf directories contain proper mzml/mgf files.
at Features.PinMzmlMatcher.(PinMzmlMatcher.java:93)
at Features.MainClass.main(MainClass.java:507)
Process 'MSBooster' finished, exit code: 1
Process returned non-zero exit code, stopping

Cancelling 10 remaining tasks
@yangkl96
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Member

Hello,

MSBooster only supports mzml and mgf files. Could you please convert your .d file to mzml instead and try again?

Thanks,
Kevin

@gux2023
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gux2023 commented Sep 12, 2023 via email

@gux2023
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gux2023 commented Sep 13, 2023

Hi Kevin
Tried mzml and it is still not working. Please advise!

System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
.NET Core Info: N/A

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

LCMS files:
Experiment/Group:

  • H:\mzXML\Ingel_08282023_RP_E2.mzML DDA

16 commands to execute:
CheckCentroid
C:\fragpipe\jre\bin\java.exe -Xmx8G -cp "C:\fragpipe\lib\fragpipe-20.0.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid H:\mzXML\Ingel_08282023_RP_E2.mzML 11
WorkspaceCleanInit [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gux\AppData\Local\Temp\9bbda1e6-c982-4e7b-98f2-33e0b57b591b
MSFragger [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx8G C:\fragpipe\lib\MSFragger-3.8\MSFragger-3.8.jar D:\XiaorongGu\Proteomics\MGF\fragger.params H:\mzXML\Ingel_08282023_RP_E2.mzML
MSFragger move pepxml
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err H:\mzXML\Ingel_08282023_RP_E2.pepXML D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2.pepXML
MSFragger move pin
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err H:\mzXML\Ingel_08282023_RP_E2.pin D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2.pin
MSBooster [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -Xmx8G -cp "C:\fragpipe\tools\msbooster-1.1.11.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" Features.MainClass --paramsList D:\XiaorongGu\Proteomics\MGF\msbooster_params.txt
Percolator [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms Ingel_08282023_RP_E2_percolator_target_psms.tsv --decoy-results-psms Ingel_08282023_RP_E2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Ingel_08282023_RP_E2_edited.pin
Percolator: Convert to pepxml [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Ingel_08282023_RP_E2.pin Ingel_08282023_RP_E2 Ingel_08282023_RP_E2_percolator_target_psms.tsv Ingel_08282023_RP_E2_percolator_decoy_psms.tsv interact-Ingel_08282023_RP_E2 DDA 0.5 H:\mzXML\Ingel_08282023_RP_E2.mzML
Percolator: Delete temp
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2_percolator_target_psms.tsv
Percolator: Delete temp
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2_percolator_decoy_psms.tsv
ProteinProphet [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\XiaorongGu\Proteomics\MGF\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe database --annotate C:\fragpipe\bin\2023-09-12-decoys-contam-2023-09-06-decoys-reviewed-contam-UP000005640.fas.fas --prefix rev_
PhilosopherFilter [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\XiaorongGu\Proteomics\MGF --protxml D:\XiaorongGu\Proteomics\MGF\combined.prot.xml --razor
PhilosopherReport [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
WorkspaceClean [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [CheckCentroid], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [MSFragger], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [MSBooster], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [Percolator], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [ProteinProphet], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [PhilosopherFilter], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [PhilosopherReport], Work dir: [D:\XiaorongGu\Proteomics\MGF]
    Cmd: [WorkspaceClean], Work dir: [D:\XiaorongGu\Proteomics\MGF]

>rev_rev_sp|A0A024R1R8|TMA7B_HUMAN Translation machinery-associated protein 7B OS=Homo sapiens OX=9606 GN=TMA7B PE=3 SV=1
>rev_rev_sp|O95996|APCL_HUMAN Adenomatous polyposis coli protein 2 OS=Homo sapiens OX=9606 GN=APC2 PE=1 SV=1
>rev_rev_sp|P51504|ZNF80_HUMAN Zinc finger protein 80 OS=Homo sapiens OX=9606 GN=ZNF80 PE=1 SV=2
>rev_rev_sp|Q53H82|LACB2_HUMAN Endoribonuclease LACTB2 OS=Homo sapiens OX=9606 GN=LACTB2 PE=1 SV=2
>rev_rev_sp|Q8IYB5|SMAP1_HUMAN Stromal membrane-associated protein 1 OS=Homo sapiens OX=9606 GN=SMAP1 PE=1 SV=2
>rev_rev_sp|Q96KC9|CABS1_HUMAN Calcium-binding and spermatid-specific protein 1 OS=Homo sapiens OX=9606 GN=CABS1 PE=2 SV=3
>rev_rev_sp|Q9NWW0|HPIP_HUMAN Host cell factor C1 regulator 1 OS=Homo sapiens OX=9606 GN=HCFC1R1 PE=1 SV=1
>rev_sp|B4DYI2|S31C2_HUMAN Putative spermatogenesis-associated protein 31C2 OS=Homo sapiens OX=9606 GN=SPATA31C2 PE=5 SV=2
>rev_sp|P0DW14|TFKLJ_HUMAN TATA-box-binding protein-associated factor 11-like protein 10 OS=Homo sapiens OX=9606 GN=TAF11L10 PE=2 SV=1
>rev_sp|Q00537|CDK17_HUMAN Cyclin-dependent kinase 17 OS=Homo sapiens OX=9606 GN=CDK17 PE=1 SV=2
>rev_sp|Q6IAN0|DRS7B_HUMAN Dehydrogenase/reductase SDR family member 7B OS=Homo sapiens OX=9606 GN=DHRS7B PE=1 SV=2
>rev_sp|Q8NEB5|PLPP5_HUMAN Phospholipid phosphatase 5 OS=Homo sapiens OX=9606 GN=PLPP5 PE=1 SV=2
>rev_sp|Q9BSV6|SEN34_HUMAN tRNA-splicing endonuclease subunit Sen34 OS=Homo sapiens OX=9606 GN=TSEN34 PE=1 SV=1
>rev_sp|Q9UKZ9|PCOC2_HUMAN Procollagen C-endopeptidase enhancer 2 OS=Homo sapiens OX=9606 GN=PCOLCE2 PE=1 SV=1
>sp|O43927|CXL13_HUMAN C-X-C motif chemokine 13 OS=Homo sapiens OX=9606 GN=CXCL13 PE=1 SV=1
>sp|P27540|ARNT_HUMAN Aryl hydrocarbon receptor nuclear translocator OS=Homo sapiens OX=9606 GN=ARNT PE=1 SV=1
>sp|Q14444|CAPR1_HUMAN Caprin-1 OS=Homo sapiens OX=9606 GN=CAPRIN1 PE=1 SV=2
>sp|Q71F78|LCA10_HUMAN Putative lung carcinoma-associated protein 10 OS=Homo sapiens OX=9606 GN=LCA10 PE=2 SV=1
>sp|Q8WWI5|CTL1_HUMAN Choline transporter-like protein 1 OS=Homo sapiens OX=9606 GN=SLC44A1 PE=1 SV=1
>sp|Q9H444|CHM4B_HUMAN Charged multivesicular body protein 4b OS=Homo sapiens OX=9606 GN=CHMP4B PE=1 SV=1
>sp|Q9Y6Z5|AFDDT_HUMAN Putative uncharacterized protein AFDN-DT OS=Homo sapiens OX=9606 GN=AFDN-DT PE=5 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=C\:\\fragpipe\\bin\\2023-09-12-decoys-contam-2023-09-06-decoys-reviewed-contam-UP000005640.fas.fas

crystalc.run-crystalc=false
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\:\\fragpipe\\tools\\IonQuant-1.9.8.jar
fragpipe-config.bin-msfragger=C\:\\fragpipe\\lib\\MSFragger-3.8\\MSFragger-3.8.jar
fragpipe-config.bin-philosopher=C\:\\fragpipe\\tools\\philosopher_v5.0.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=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=true
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=0
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=0/1/2/3
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.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=trypsin
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=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=true
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=trypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=P
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,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_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=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=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
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=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_mode=false
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_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
ptmshepherd.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.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=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=D\:\\XiaorongGu\\Proteomics\\MGF
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=8
workflow.threads=11

CheckCentroid
C:\fragpipe\jre\bin\java.exe -Xmx8G -cp "C:\fragpipe\lib\fragpipe-20.0.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid H:\mzXML\Ingel_08282023_RP_E2.mzML 11
H:\mzXML\Ingel_08282023_RP_E2.mzML has non-centroid scans. Please re-convert it with peakPeaking (https://fragpipe.nesvilab.org/docs/tutorial_convert.html).
Process 'CheckCentroid' finished, exit code: 1
Process returned non-zero exit code, stopping

Cancelling 16 remaining tasks

@fcyu
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fcyu commented Sep 13, 2023

H:\mzXML\Ingel_08282023_RP_E2.mzML has non-centroid scans. Please re-convert it with peakPeaking (https://fragpipe.nesvilab.org/docs/tutorial_convert.html).

It seems that you did not add the peakPicking filter when converting the file to mzML. You should use that to make the peak centroid. Please check our tutorial in detail: https://fragpipe.nesvilab.org/docs/tutorial_convert.html

Best,

Fengchao

@gux2023
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gux2023 commented Sep 13, 2023 via email

@gux2023
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gux2023 commented Sep 13, 2023

It worked. Thank you very much!

@fcyu
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fcyu commented Sep 13, 2023

No problem.

Best,

Fengchao

@fcyu fcyu closed this as completed Sep 13, 2023
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