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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Switch off MBR for one file queries #341

Closed kabalak closed 3 years ago

kabalak commented 3 years ago

If the user selects MBR for IonQuant, but supplies just one file/experiment, then IonQuant crashes and FragPipe stops - but it should rather check for such cases and simply ignore MBR in these cases (in my case, it was an accident, as I reused an old query for a new, single file and forgot to tick off MBR in the IonQuant tab). `System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 15.0 MSFragger version 3.2 Philosopher version 3.4.13 (build 1611589727)

LCMS files: Experiment/Group: HeLa_Triple_LOW_RES

19 commands to execute: WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx108G C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\MSFragger-3.2.jar E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\fragger.params E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw MSFragger move pepxml C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar;/C:/MSPrograms/fragpipe-15/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML MSFragger move tsv C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar;/C:/MSPrograms/fragpipe-15/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.tsv E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.tsv PeptideProphet: Workspace init [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML-temp] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWERRES.pepXML-temp] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database E:\PHILOSOPHER_FASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas ..\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML PeptideProphet: Delete temp C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML-temp Rewrite pepxml [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib/* com.dmtavt.fragpipe.util.RewritePepxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw ProteinProphet [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml PhilosopherDbAnnotate [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe database --annotate E:\PHILOSOPHERFASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe database --annotate E:\PHILOSOPHERFASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherFilter [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOWRES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe filter --sequential --razor --picked --prot 0.01 --tag rev --pepxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES --protxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\combined.prot.xml PhilosopherReport [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe report IonQuant [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\jre\bin\java.exe -Xmx108G -Dlibs.bruker.dir="C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\ext\bruker" -Dlibs.thermo.dir="C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\ext\thermo" -cp "C:\MSPrograms\fragpipe-15\tools\ionquant-1.5.5.jar;C:\MSPrograms\fragpipe-15\tools\batmass-io-1.22.1.jar" ionquant.IonQuant --threads 0 --ionmobility 0 --mbr 1 --proteinquant 2 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 3 --minfreq 0.5 --minions 2 --minexps 1 --psm HeLa_Triple_LOW_RES\psm.tsv --multidir . --specdir E:\20210329_HeLa_Inverted-uPAC HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML WorkspaceClean [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
    Cmd: [WorkspaceCleanInit], Work dir: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
    Cmd: [WorkspaceCleanInit], Work dir: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES]
    Cmd: [MSFragger], Work dir: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
    Cmd: [PeptideProphet], Work dir: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
    Cmd: [ProteinProphet], Work dir: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
    Cmd: [PhilosopherDbAnnotate], Work dir: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
    Cmd: [PhilosopherFilter], Work dir: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
    Cmd: [PhilosopherReport], Work dir: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
    Cmd: [IonQuant], Work dir: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
    Cmd: [WorkspaceClean], Work dir: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
    Cmd: [WorkspaceClean], Work dir: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES]

# FragPipe v15.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
crystalc.run-crystalc=false
database.db-path=E\:\\PHILOSOPHER_FASTA\\2021-03-17-decoys-reviewed-contam-UP000005640.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\MSPrograms\\fragpipe-15\\tools\\MSFragger-3.2\\MSFragger-3.2.jar
fragpipe-config.bin-philosopher=C\:\\MSPrograms\\fragpipe-15\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\Program Files\\Python39\\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.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.data_type=0
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.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.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=stricttrypsin
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=tsv_pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-50
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=50
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --picked --prot 0.01
phi-report.pep-level-summary=true
phi-report.print-decoys=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.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.diag_ions=
ptmshepherd.glyco_mode=false
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.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.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
run-diaumpire=false
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.groupby=0
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.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=E\:\\20210329_HeLa_Inverted-uPAC\\MSFragger_Default_Closed_by_RAW
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=0

WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[07:25:23] Executing Workspace v3.4.13
INFO[07:25:23] Removing workspace
WARN[07:25:23] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:25:23] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[07:25:23] Executing Workspace v3.4.13
INFO[07:25:23] Creating workspace
INFO[07:25:23] Done
WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[07:25:24] Executing Workspace v3.4.13
INFO[07:25:24] Removing workspace
WARN[07:25:24] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:25:24] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[07:25:24] Executing Workspace v3.4.13
INFO[07:25:24] Creating workspace
INFO[07:25:24] Done
MSFragger [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx108G C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\MSFragger-3.2.jar E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\fragger.params E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw MSFragger version MSFragger-3.2 Batmass-IO version 1.22.1 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 108 GB memory Checking database... Checking spectral files... E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw: Scans = 102005 ***FIRST SEARCH**** Parameters: num_threads = 48 database_name = E:\PHILOSOPHER_FASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = tsv_pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false 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 = 2 deisotope = 1 deneutralloss = true 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 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 = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.10 Da. 318543152 fragments to be searched in 1 slices (4.75 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.14 s

  1. 20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw 139.2 s | deisotoping 0.7 s [progress: 40816/40816 (100%) - 19002 spectra/s] 2.1s | postprocessing 0.2 s ***FIRST SEARCH DONE IN 3.765 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 4.07 2.39 -0.19 1.70 2.41 3.45 -0.07 3.32
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 19626 21152 22157 22662 22693 22540 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- ------- -------
Peaks 500_0 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- ------- -------
Count 22700 22685 skip rest
------- ------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 22940
------- -------
------- -------
Rm P. 1
------- -------
Count 22688
------- -------

New fragment_mass_tolerance = 20 PPM New use_topN_peaks = 500 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 0 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 3.173 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 48 database_name = E:\PHILOSOPHER_FASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas decoyprefix = rev precursor_mass_lower = -50.0 precursor_mass_upper = 50.0 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 write_calibrated_mgf = 0 isotope_error = 0/1/2/3 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = tsv_pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false 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 = 2 deisotope = 1 deneutralloss = true 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 = 500 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 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 = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.10 Da. 318543152 fragments to be searched in 1 slices (4.75 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.45 s

  1. 20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.mzBIN_calibrated 0.6 s [progress: 37923/37923 (100%) - 56099 spectra/s] 0.7s | postprocessing 2.3 s MAIN SEARCH DONE IN 0.105 MIN

***TOTAL TIME 7.043 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar;/C:/MSPrograms/fragpipe-15/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move tsv C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar;/C:/MSPrograms/fragpipe-15/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.tsv E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.tsv Process 'MSFragger move tsv' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML-temp] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'PeptideProphet: Workspace init' finished, exit code: 0 INFO[07:32:31] Executing Workspace v3.4.13
INFO[07:32:31] Creating workspace
INFO[07:32:31] Done
PeptideProphet [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWERRES.pepXML-temp] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database E:\PHILOSOPHER_FASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas ..\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML INFO[07:32:32] Executing PeptideProphet v3.4.13
Unknown file type. No file loaded.E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES/20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw Unknown file type. No file loaded.E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES/20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw file 1: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML processed altogether 29614 results INFO: Results written to file: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using search_offsets in ACCMASS mixture distr: 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+, 13434 2+, 12029 3+, 3402 4+, 656 5+, 93 6+, and 0 7+ spectra. Found 2702 Decoys, and 26912 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 (7+). model complete after 26 iterations INFO[07:33:37] Done
Process 'PeptideProphet' finished, exit code: 0 PeptideProphet: Delete temp C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 Rewrite pepxml [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib/* com.dmtavt.fragpipe.util.RewritePepxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw Fixing pepxml: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml Writing output to: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml12015410115015550458.temp-rewrite Deleting file: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml Moving rewritten file to original location: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml12015410115015550458.temp-rewrite] -> [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml INFO[07:33:39] Executing ProteinProphet v3.4.13
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) (no FPKM) (using degen pep info) Reading in E:/20210329_HeLa_Inverted-uPAC/MSFragger_Default_Closed_by_RAW/HeLa_Triple_LOW_RES/interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml... ...read in 0 1+, 10257 2+, 9316 3+, 2556 4+, 422 5+, 49 6+, 0 7+ spectra with min prob 0.05

Initializing 12499 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database e:/PHILOSOPHER_FASTA/2021-03-17-decoys-reviewed-contam-UP000005640.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:......WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG ...:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|Q9NNW7|TRXR2_HUMAN : U MAAMAVALRGLGGRFRWRTQAVAGGVRGAARGAAAGQRDYDLLVVGGGSGGLACAKEAAQLGRKVAVVDYVEPSPQGTRWGLGGTCVNVGCIPKKLMHQAALLGGLIQDAPNYGWEVAQPVPHDWRKMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVCGVAKGGKEILLSADHIIIATGGRPRYPTHIEGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTIMMRSIPLRGFDQQMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTVLWAIGRVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEGRPELTPIAIMAGRLLVQRLFGGSSDLMDYDNVPTTVFTPLEYGCVGLSEEEAVARHGQEHVEVYHAHYKPLEFTVAGRDASQCYVKMVCLREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG ......:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........:...... Total: 40860 Computing degenerate peptides for 3246 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 3358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 3010 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... INFO: mu=7.33977e-06, db_size=45499165 Computing MU for 3358 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%

Finished. INFO[07:33:52] Done
Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe database --annotate E:\PHILOSOPHERFASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[07:33:52] Executing Database v3.4.13
INFO[07:33:52] Processing database
INFO[07:33:56] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe database --annotate E:\PHILOSOPHERFASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[07:33:56] Executing Database v3.4.13
INFO[07:33:56] Processing database
INFO[07:33:59] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOWRES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe filter --sequential --razor --picked --prot 0.01 --tag rev --pepxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES --protxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\combined.prot.xml INFO[07:33:59] Executing Filter v3.4.13
INFO[07:33:59] Processing peptide identification files
INFO[07:34:02] 1+ Charge profile decoy=0 target=0 INFO[07:34:02] 2+ Charge profile decoy=70 target=10187 INFO[07:34:02] 3+ Charge profile decoy=43 target=9273 INFO[07:34:02] 4+ Charge profile decoy=12 target=2544 INFO[07:34:02] 5+ Charge profile decoy=2 target=420 INFO[07:34:02] 6+ Charge profile decoy=0 target=49 INFO[07:34:02] Database search results ions=12482 peptides=10743 psms=22600 INFO[07:34:02] Converged to 0.56 % FDR with 22473 PSMs decoy=127 threshold=0.0503 total=22600 INFO[07:34:02] Converged to 1.00 % FDR with 10622 Peptides decoy=107 threshold=0.0573 total=10729 INFO[07:34:02] Converged to 0.91 % FDR with 12369 Ions decoy=113 threshold=0.0504 total=12482 INFO[07:34:03] Protein inference results decoy=143 target=2867 INFO[07:34:03] Converged to 1.02 % FDR with 2449 Proteins decoy=25 threshold=0.8943 total=2474 INFO[07:34:04] Applying sequential FDR estimation ions=12267 peptides=10529 psms=22360 INFO[07:34:04] Converged to 0.12 % FDR with 22332 PSMs decoy=28 threshold=0.0503 total=22360 INFO[07:34:04] Converged to 0.20 % FDR with 10507 Peptides decoy=22 threshold=0.0511 total=10529 INFO[07:34:05] Converged to 0.18 % FDR with 12245 Ions decoy=22 threshold=0.0511 total=12267 INFO[07:34:05] Post processing identifications
INFO[07:34:06] Mapping modifications
INFO[07:34:10] Processing protein inference
INFO[07:34:14] Assigning protein identifications to layers
INFO[07:34:15] Updating razor PSM assignment to proteins
INFO[07:34:15] Calculating spectral counts
INFO[07:34:15] Saving
INFO[07:34:17] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe report INFO[07:34:17] Executing Report v3.4.13
INFO[07:34:19] Creating reports
INFO[07:34:20] Done
Process 'PhilosopherReport' finished, exit code: 0 IonQuant [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\jre\bin\java.exe -Xmx108G -Dlibs.bruker.dir="C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\ext\bruker" -Dlibs.thermo.dir="C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\ext\thermo" -cp "C:\MSPrograms\fragpipe-15\tools\ionquant-1.5.5.jar;C:\MSPrograms\fragpipe-15\tools\batmass-io-1.22.1.jar" ionquant.IonQuant --threads 0 --ionmobility 0 --mbr 1 --proteinquant 2 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 3 --minfreq 0.5 --minions 2 --minexps 1 --psm HeLa_Triple_LOW_RES\psm.tsv --multidir . --specdir E:\20210329_HeLa_Inverted-uPAC HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML IonQuant version IonQuant-1.5.5 Batmass-IO version 1.22.1 timsdata library version timsdata-2-7-0 (c) University of Michigan System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 108 GB memory 2021-03-30 07:34:21 [WARNING] - There are only 1 experiments. Using Top-N protein intensity calculation algorithm with min exps = 1. 2021-03-30 07:34:21 [WARNING] - proteinquant == 1 but minions > 1. Changing minions to 1. 2021-03-30 07:34:21 [INFO] - Parameters: 2021-03-30 07:34:21 [INFO] - threads = 48 2021-03-30 07:34:21 [INFO] - mztol = 10.0 2021-03-30 07:34:21 [INFO] - rttol = 0.4 2021-03-30 07:34:21 [INFO] - imtol = 0.05 2021-03-30 07:34:21 [INFO] - seedmz = 0 2021-03-30 07:34:21 [INFO] - minisotopes = 2 2021-03-30 07:34:21 [INFO] - minscans = 3 2021-03-30 07:34:21 [INFO] - psm = E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\psm.tsv 2021-03-30 07:34:21 [INFO] - multidir = E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW.\ 2021-03-30 07:34:21 [INFO] - excludemods = 2021-03-30 07:34:21 [INFO] - minions = 1 2021-03-30 07:34:21 [INFO] - proteinquant = 1 2021-03-30 07:34:21 [INFO] - normalization = 1 2021-03-30 07:34:21 [INFO] - minexps = 1 2021-03-30 07:34:21 [INFO] - minfreq = 0.5 2021-03-30 07:34:21 [INFO] - tp = 3 2021-03-30 07:34:21 [INFO] - mbr = 1 2021-03-30 07:34:21 [INFO] - mbrrttol = 1.0 2021-03-30 07:34:21 [INFO] - mbrimtol = 0.05 2021-03-30 07:34:21 [INFO] - mbrtoprun = 10 2021-03-30 07:34:21 [INFO] - mbrmincorr = 0.0 2021-03-30 07:34:21 [INFO] - ionmobility = 0 2021-03-30 07:34:21 [INFO] - ionfdr = 0.01 2021-03-30 07:34:21 [INFO] - peptidefdr = 1.0 2021-03-30 07:34:21 [INFO] - proteinfdr = 1.0 2021-03-30 07:34:21 [INFO] - light = 2021-03-30 07:34:21 [INFO] - medium = 2021-03-30 07:34:21 [INFO] - heavy = 2021-03-30 07:34:21 [INFO] - requantify = 0 2021-03-30 07:34:21 [INFO] - writeindex = 0 2021-03-30 07:34:21 [INFO] - specdir = E:\20210329_HeLa_Inverted-uPAC 2021-03-30 07:34:21 [INFO] - E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML 2021-03-30 07:34:21 [INFO] - Checking E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw... 2021-03-30 07:34:24 [INFO] - Loading E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw... 2021-03-30 07:36:45 [INFO] - 20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES has 3 compensation voltages: -70.0, -43.0, -30.0 2021-03-30 07:36:45 [INFO] - Building index... 2021-03-30 07:36:46 [INFO] - Writing index to E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.quantindex 2021-03-30 07:36:46 [INFO] - Loading E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML... 2021-03-30 07:36:47 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2021-03-30 07:36:47 [INFO] - Quantifying... 2021-03-30 07:36:49 [INFO] - Updating Philosopher's tables... 2021-03-30 07:36:51 [INFO] - Matching-between-runs: 20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES... 2021-03-30 07:36:51 [INFO] - Calculating correlations between all other runs... 2021-03-30 07:36:51 [WARNING] - There is no run passing the minimum correlation threshold 0.0 2021-03-30 07:36:51 [WARNING] - Run 20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES got nothing matched. 2021-03-30 07:36:51 [INFO] - Estimating match-between-runs FDR... 2021-03-30 07:36:51 [WARNING] - There is no mbr file for run E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES. May be because it failed in MBR. 2021-03-30 07:36:51 [WARNING] - There is no MBR result. 2021-03-30 07:36:51 [INFO] - Combining experiments and estimating protein intensity... java.lang.Exception: The intensity columns don't match the experiments. at l.a(Unknown Source) at l.(Unknown Source) at ionquant.IonQuant.main(Unknown Source) 2021-03-30 07:36:52 [ERROR] - The intensity columns don't match the experiments. Process 'IonQuant' finished, exit code: 1 Process returned non-zero exit code, stopping


Cancelling 3 remaining tasks
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fcyu commented 3 years ago

Thanks for your feedback and suggestion. I will fix this in the next version.

Best,

Fengchao

fcyu commented 3 years ago

Fixed in version 1.7.5.