yangkl96
commented
10 months ago Hello,
MSBooster only supports mzml and mgf files. Could you please convert your .d file to mzml instead and try again?
Thanks, Kevin
Closed gux2023 closed 10 months ago
yangkl96
commented
10 months ago Hello,
MSBooster only supports mzml and mgf files. Could you please convert your .d file to mzml instead and try again?
Thanks, Kevin
gux2023
commented
10 months ago Thank you!, Trying now...
From: yangkl96 @.> Sent: Tuesday, September 12, 2023 3:30 PM To: Nesvilab/FragPipe @.> Cc: Gu, PhD Xiaorong @.>; Author @.> Subject: [EXT] Re: [Nesvilab/FragPipe] Process 'MSBooster' finished, exit code: 1 Process returned non-zero exit code, stopping (Issue #1244)
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Hello,
MSBooster only supports mzml and mgf files. Could you please convert your .d file to mzml instead and try again?
Thanks, Kevin
— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/1244#issuecomment-1716300500, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BCMRLYCJT2CNX72SHKH5WBLX2CZ57ANCNFSM6AAAAAA4VHEH4A. You are receiving this because you authored the thread.Message ID: @.***>
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gux2023
commented
10 months ago 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:
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_decoypsms.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_windowsamd64\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_windowsamd64\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
commented
10 months ago 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
commented
10 months ago Thank you! Trying it now, will keep you posted.
From: Fengchao @.> Sent: Wednesday, September 13, 2023 9:22 AM To: Nesvilab/FragPipe @.> Cc: Gu, PhD Xiaorong @.>; Author @.> Subject: [EXT] Re: [Nesvilab/FragPipe] Process 'MSBooster' finished, exit code: 1 Process returned non-zero exit code, stopping (Issue #1244)
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H:\mzXML\Ingel_08282023_RP_E2.mzML has non-centroid scans. Please re-convert it with peakPeaking (https://fragpipe.nesvilab.org/docs/tutorial_convert.htmlhttps://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.htmlhttps://fragpipe.nesvilab.org/docs/tutorial_convert.html
Best,
Fengchao
— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/1244#issuecomment-1717627856, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BCMRLYFWF2S6KED5GEC63W3X2GXRVANCNFSM6AAAAAA4VHEH4A. You are receiving this because you authored the thread.Message ID: @.***>
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gux2023
commented
10 months ago It worked. Thank you very much!
fcyu
commented
10 months ago No problem.
Best,
Fengchao
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:
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_decoypsms.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_windowsamd64\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_windowsamd64\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
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 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 = 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
***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