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A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Philosopher issue #366

Closed ykim7263 closed 3 years ago

ykim7263 commented 3 years ago

Dear all,

I am trying to analyze tims tof pro data with Open search and I ran into this error described below. INFO[01:07:14] Executing Filter v3.4.13
INFO[01:07:14] Processing peptide identification files
FATA[01:07:14] Cannot decode packed binary. XML syntax error on line 134207: invalid character entity &EALdomains (no semicolon) Process 'PhilosopherFilter' finished, exit code: 1 Process returned non-zero exit code, stoppingPhilosopherReport [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe report

It would be great, if you can let me know how to solve this probelm

Best,

fcyu commented 3 years ago

Can you send us the whole log?

Best,

Fengchao

ykim7263 commented 3 years ago

Hi,

I have attached the log file,

Best, Kim

On Sat, May 1, 2021 at 10:08 AM Fengchao @.***> wrote:

Can you send us the whole log?

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/366#issuecomment-830638872, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMSQ7M3SHDKYH3LTZK3Z5ZDTLQDOTANCNFSM436K5RYQ .

System OS: Windows 10, Architecture: AMD64 Java Info: 15.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 14.0 MSFragger version 3.2 Philosopher version 3.4.13 (build 1611589727)

LCMS files: Experiment/Group:

12 commands to execute: WorkspaceCleanInit [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] java -jar -Dfile.encoding=UTF-8 -Xmx51G C:\Users\wysocki-lab\Downloads\MSFragger-3.2\MSFragger-3.2.jar C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\fragger.params X:\Group member data folders\Kim\Maryam_Round5\20201210_5_2_D12_P.d MsFragger move pepxml java -cp C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove X:\Group member data folders\Kim\Maryam_Round5\20201210_5_2_D12_P.pepXML C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\20201210_5_2_D12_P.pepXML MsFragger move tsv java -cp C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove --no-err X:\Group member data folders\Kim\Maryam_Round5\20201210_5_2_D12_P.tsv C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\20201210_5_2_D12_P.tsv PeptideProphet [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fraggerlib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy DECOY --database C:\Users\wysocki-lab\Documents\Kim\Proteomics_DB\20201023_Proteomics_DB_Salmonella_rev_decoy_DB.fasta --combine 20201210_5_2_D12_P.pepXML Rewrite pepxml [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] java -cp C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\interact.pep.xml X:\Group member data folders\Kim\Maryam_Round5\20201210_5_2_D12_P.d ProteinProphet [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\interact.pep.xml PhilosopherDbAnnotate [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\Users\wysocki-lab\Documents\Kim\Proteomics_DB\20201023_Proteomics_DB_Salmonella_rev_decoyDB.fasta --prefix DECOY PhilosopherFilter [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fraggerlib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag DECOY --pepxml C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test --protxml C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\combined.prot.xml PhilosopherReport [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe report WorkspaceClean [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test]
    Cmd: [MsFragger], Work dir: [C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test]
    Cmd: [PeptideProphet], Work dir: [C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test]
    Cmd: [ProteinProphet], Work dir: [C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test]
    Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test]
    Cmd: [PhilosopherFilter], Work dir: [C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test]
    Cmd: [PhilosopherReport], Work dir: [C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test]
    Cmd: [WorkspaceClean], Work dir: [C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test]

# FragPipe v14.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.1
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.MS1PPM=10
SE.MS2PPM=10
SE.MS2SN=1.1
SE.MaxCurveRTRange=2
SE.MaxNoPeakCluster=4
SE.MinFrag=10
SE.MinMSIntensity=1
SE.MinMSMSIntensity=1
SE.MinNoPeakCluster=2
SE.NoMissedScan=1
SE.SN=1.1
WindowSize=26
crystalc.run-crystalc=true
database.db-path=C\:\\Users\\wysocki-lab\\Documents\\Kim\\Proteomics_DB\\20201023_Proteomics_DB_Salmonella_rev_decoy_DB.fasta
database.decoy-tag=DECOY_
diaumpire_se.params=
fragpipe-config.bin-msfragger=C\:\\Users\\wysocki-lab\\Downloads\\MSFragger-3.2\\MSFragger-3.2.jar
fragpipe-config.bin-philosopher=C\:\\Users\\wysocki-lab\\Documents\\Kim\\fragpipe\\lib\\..\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\wysocki-lab\\anaconda3\\python.exe
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=0
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.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.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
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
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=true
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.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=trypsin
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
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-150
msfragger.precursor_mass_mode=corrected
msfragger.precursor_mass_units=0
msfragger.precursor_mass_upper=1500
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=P
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=trypsin
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; 0.000000,site_06,false,1; 0.000000,site_07,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 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
path.textfield.msconvert=C\:\\Program Files (x86)\\ProteoWizard 3.0.1908 64-bit\\msconvert.exe
peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01 --mapmods
phi-report.pep-level-summary=false
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-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=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_background=4
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
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.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=false
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tmtintegrator.add_Ref=-1
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=10
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=-1
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=-1
tmtintegrator.psm_norm=false
tmtintegrator.ref_tag=pool
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=C\:\\Users\\wysocki-lab\\Documents\\Kim\\MSFRAGGER\\MS_Fragger_lib\\test
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=7

WorkspaceCleanInit [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[09:50:13] Executing Workspace v3.4.13
INFO[09:50:13] Removing workspace
INFO[09:50:13] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[09:50:13] Executing Workspace v3.4.13
INFO[09:50:13] Creating workspace
INFO[09:50:13] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MsFragger [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] java -jar -Dfile.encoding=UTF-8 -Xmx51G C:\Users\wysocki-lab\Downloads\MSFragger-3.2\MSFragger-3.2.jar C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\fragger.params X:\Group member data folders\Kim\Maryam_Round5\20201210_5_2_D12_P.d MSFragger version MSFragger-3.2 Batmass-IO version 1.22.1 Parameter 'data_type' was not supplied. Using default value: 0 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: 15.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 51 GB memory Checking database... Parameter 'deneutralloss' was not supplied. Using default value: 1 Checking spectral files... X:\Group member data folders\Kim\Maryam_Round5\20201210_5_2_D12_P.d: Scans = 55020 precursor_mass_mode = CORRECTED does not support specified spectral files. Using SELECTED instead. There is a mzBIN file from X:\Group member data folders\Kim\Maryam_Round5\20201210_5_2_D12_P.d converted with timsdata-2-7-0. Will use this mzBIN file. ***FIRST SEARCH**** Parameters: num_threads = 7 database_name = C:\Users\wysocki-lab\Documents\Kim\Proteomics_DB\20201023_Proteomics_DB_Salmonella_rev_decoy_DB.fasta decoyprefix = DECOY 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 = trypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = P 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 = 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 Number of unique peptides of length 7: 1054699 of length 8: 1063985 of length 9: 1030353 of length 10: 1003312 of length 11: 981771 of length 12: 940757 of length 13: 899022 of length 14: 869353 of length 15: 828096 of length 16: 792630 of length 17: 753310 of length 18: 723969 of length 19: 686566 of length 20: 655367 of length 21: 629787 of length 22: 600466 of length 23: 566598 of length 24: 539198 of length 25: 509443 of length 26: 486967 of length 27: 454725 of length 28: 431155 of length 29: 403281 of length 30: 380827 of length 31: 355500 of length 32: 334499 of length 33: 313258 of length 34: 293604 of length 35: 270811 of length 36: 255051 of length 37: 235720 of length 38: 218911 of length 39: 203155 of length 40: 188922 of length 41: 175487 of length 42: 161310 of length 43: 140204 of length 44: 111866 of length 45: 82779 of length 46: 54147 of length 47: 32744 of length 48: 17432 of length 49: 8425 of length 50: 3979 In total 20743441 peptides. Generated 38111856 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 1660962780 fragments to be searched in 1 slices (24.75 GB total) Operating on slice 1 of 1: Fragment index slice generated in 21.45 s

  1. 20201210_5_2_D12_P.mzBIN 144.8 s | deisotoping 2.9 s [progress: 127903/127903 (100%) - 7056 spectra/s] 18.1s | postprocessing 0.7 s ***FIRST SEARCH DONE IN 4.308 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 1.10 2.08 0.03 2.00 -0.01 4.74 -0.14 4.62
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 26161 28531 30185 30682 30680 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- ------- -------
Peaks 500_0 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- ------- -------
Count 31413 31420 31231 30982 skip rest
------- ------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 31719
------- -------
------- -------
Rm P. 1
------- -------
Count Parameter 'data_type' was not supplied. Using default value: 0 31703

New fragment_mass_tolerance = 15 PPM New use_topN_peaks = 200 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 0 New precursor_true_tolerance = 11.000000 PPM (tie breaker) ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 10.676 MIN*****

****MAIN SEARCH**** Checking database... Parameter 'deneutralloss' was not supplied. Using default value: 1 Parameters: num_threads = 7 database_name = C:\Users\wysocki-lab\Documents\Kim\Proteomics_DB\20201023_Proteomics_DB_Salmonella_rev_decoy_DB.fasta decoyprefix = DECOY precursor_mass_lower = -150.0 precursor_mass_upper = 1500.0 precursor_mass_units = 0 data_type = 0 precursor_true_tolerance = 11.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 0 isotope_error = 0 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = true delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = trypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = P 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 = pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = true 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 = 200 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 Number of unique peptides of length 7: 1054699 of length 8: 1063985 of length 9: 1030353 of length 10: 1003312 of length 11: 981771 of length 12: 940757 of length 13: 899022 of length 14: 869353 of length 15: 828096 of length 16: 792630 of length 17: 753310 of length 18: 723969 of length 19: 686566 of length 20: 655367 of length 21: 629787 of length 22: 600466 of length 23: 566598 of length 24: 539198 of length 25: 509443 of length 26: 486967 of length 27: 454725 of length 28: 431155 of length 29: 403281 of length 30: 380827 of length 31: 355500 of length 32: 334499 of length 33: 313258 of length 34: 293604 of length 35: 270811 of length 36: 255051 of length 37: 235720 of length 38: 218911 of length 39: 203155 of length 40: 188922 of length 41: 175487 of length 42: 161310 of length 43: 140204 of length 44: 111866 of length 45: 82779 of length 46: 54147 of length 47: 32744 of length 48: 17432 of length 49: 8425 of length 50: 3979 In total 20743441 peptides. Generated 38111856 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.01 Da. 3321925560 fragments to be searched in 2 slices (49.50 GB total) Operating on slice 1 of 2: Fragment index slice generated in 30.75 s

  1. 20201210_5_2_D12_P.mzBIN_calibrated 6.6 s [progress: 127365/127365 (100%) - 9 spectra/s] 14013.6s Operating on slice 2 of 2: Fragment index slice generated in 40.20 s
  2. 20201210_5_2_D12_P.mzBIN_calibrated 13.6 s [progress: 127365/127365 (100%) - 55 spectra/s] 2303.2s | postprocessing 123.5 s MAIN SEARCH DONE IN 279.010 MIN

***TOTAL TIME 293.994 MIN**** Process 'MsFragger' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove X:\Group member data folders\Kim\Maryam_Round5\20201210_5_2_D12_P.pepXML C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\20201210_5_2_D12_P.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move tsv java -cp C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove --no-err X:\Group member data folders\Kim\Maryam_Round5\20201210_5_2_D12_P.tsv C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\20201210_5_2_D12_P.tsv Process 'MsFragger move tsv' finished, exit code: 0 PeptideProphet [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fraggerlib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy DECOY --database C:\Users\wysocki-lab\Documents\Kim\Proteomics_DB\20201023_Proteomics_DB_Salmonella_rev_decoy_DB.fasta --combine 20201210_5_2_D12_P.pepXML INFO[14:44:19] Executing PeptideProphet v3.4.13
Unknown file type. No file loaded.C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test/20201210_5_2_D12_P.d WARNING: cannot open data file C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test/20201210_5_2_D12_P.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test/20201210_5_2_D12_P.mzML in msms_run_summary tag... Unknown file type. No file loaded.C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test/20201210_5_2_D12_P.d WARNING: cannot open data file C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test/20201210_5_2_D12_P.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test/20201210_5_2_D12_P.mzML in msms_run_summary tag... file 1: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\20201210_5_2_D12_P.pepXML processed altogether 125654 results INFO: Results written to file: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\interact.pep.xml

Using Decoy Label "DECOY_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) using search_offsets in mass mixture distr: 0 init with X! Tandem trypsin PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 1774 1+, 79423 2+, 39372 3+, 4911 4+, 174 5+, 0 6+, and 0 7+ spectra. Found 34073 Decoys, and 91581 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 (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations INFO[14:47:23] Done
Process 'PeptideProphet' finished, exit code: 0 Rewrite pepxml [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] java -cp C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\interact.pep.xml X:\Group member data folders\Kim\Maryam_Round5\20201210_5_2_D12_P.d Fixing pepxml: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\interact.pep.xml Writing output to: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\interact.pep.xml17762008828448040351.temp-rewrite Deleting file: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\interact.pep.xml Moving rewritten file to original location: [C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\interact.pep.xml17762008828448040351.temp-rewrite] -> [C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\interact.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test] C:\Users\wysocki-lab\Documents\Kim\fragpipe\lib..\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\interact.pep.xml INFO[14:47:27] 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 C:/Users/wysocki-lab/Documents/Kim/MSFRAGGER/MS_Fragger_lib/test/interact.pep.xml... ...read in 0 1+, 50388 2+, 22014 3+, 2110 4+, 64 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 38594 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database c:/Users/wysocki-lab/Documents/Kim/Proteomics_DB/20201023_Proteomics_DB_Salmonella_rev_decoy_DB.fasta .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:........WARNING: Found the following zero-mass residues in protein entry sp|O70325|GPX4_MOUSE : U MSWGRLSRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVCLDKYRGFVCIVTNVASQUGKTDVNYTQLVDLHARYAECGLRILAFPCNQFGRQEPGSNQEIKEFAAGYNVKFDMYSKICVNGDDAHPLWKWMKVQPKGRGMLGNAIKWNFTKFLIDKNGCVVKRYGPMEEPQVIEKDLPCYL .:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|Q9DBC0|SELO_MOUSE : U MASVRAAVGASLAVARTRPRCVGLALPSSAPRSAWAAAMEPTPRWLAGLRFDNRALRELPVETPPPGPEDSLATPRPVPGACFSRARPAPLRRPRLVALSEPALALLGLEASEEAEVEAEAALFFSGNALLPGTEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTAAGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGIPTTRAGACVTSESTVMRDVFYDGNPKYEKCTVVLRIAPTFIRFGSFEIFKPPDEHTGRAGPSVGRDDIRVQLLDYVISSFYPEIQAAHTCDTDNIQRNAAFFREVTQRTARMVAEWQCVGFCHGVLNTDNMSIVGLTIDYGPFGFLDRYDPDHICNASDNAGRYTYSKQPQVCKWNLQKLAEALEPELPLALAEAILKEEFDTEFQRHYLQKMRKKLGLIRVEKEEDGTLVAKLLETMHLTGADFTNTFCVLSSFPADLSDSAEFLSRLTSQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALIGTQANVTKELERVEHQSRLEQLSPSDLQRKNRDHWEAWLQEYRDRLDKEKEGVGDTAAWQAERVRVMRANNPKYVLRNYIAQKAIEAAENGDFSEVRRVLKLLESPYHSEEEATGPEAVARSTEEQSSYSNRPPLWAAELCVTUSS ...:.........:.........:.........:.........:.........:.........:.........41000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000 .........:.........:........WARNING: Found the following zero-mass residues in protein entry sp|Q9JMH6|TRXR1_MOUSE : U MPVDDCWLYFPASRGRTFVQTVWVAPTCPNCCWFPGFLPPVPRPPHVPRVLLRGPRGAVLPASRPSKTLPSSSQTPCPTDPCICPPPSTPDSRQEKNTQSELPNKKGQLQKLPTMNGSKDPPGSYDFDLIIIGGGSGGLAAAKEAAKFDKKVLVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALKDSRNYGWKVEDTVKHDWEKMTESVQSHIGSLNWGYRVALREKKVVYENAYGRFIGPHRIVATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPTKIEQIEAGTPGRLRVTAQSTNSEETIEGEFNTVLLAVGRDSCTRTIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSNVKCDYDNVPTTVFTPLEYGCCGLSEEKAVEKFGEENIEVYHSFFWPLEWTVPSRDNNKCYAKIICNLKDDERVVGFHVLGPNAGEVTQGFAAALKCGLTKQQLDSTIGIHPVCAEIFTTLSVTKRSGGDILQSGCUG .:.........:.........:.........:.........:.........:.........:.........43000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........44000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........45000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........46000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........47000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........48000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........49000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........50000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........51000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........52000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........53000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........54000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........55000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........56000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........57000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........58000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........59000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........60000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........61000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........62000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........63000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........64000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........65000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........66000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........67000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........68000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........78000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........82000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........85000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........86000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........87000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........88000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........89000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........90000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........91000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........92000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........93000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........94000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........95000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........96000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........97000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........98000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........99000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........100000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........101000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........102000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........103000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........104000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........105000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........106000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........107000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........108000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........109000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........110000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........111000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........112000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........113000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........114000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........115000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........116000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........117000 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.........:.........:.........:.........:.........:.........:.........:.........:.........:.........271000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........272000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........273000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........274000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........275000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........276000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........277000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........278000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........279000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........280000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........281000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........282000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........283000 .........: Total: 283102 Computing degenerate peptides for 31404 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 34094 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 34094 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 34094 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 34094 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 34094 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 34094 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 34094 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 34094 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 34094 proteins. Loop 1: 0%

fcyu commented 3 years ago

Hi Kim,

Your log was truncated by GitHub, can you 1) zip your log and sent it to us; and 2) zip your C:\Users\wysocki-lab\Documents\Kim\Proteomics_DB\20201023_Proteomics_DB_Salmonella_rev_decoy_DB.fasta and sent it to us?

Best,

Fengchao

prvst commented 3 years ago

@ykim7263 The program is complaining about a special character in one of your interact.pep.xml files. See the error:

&EALdomains (no semicolon)

You can pinpoint the problem by searching for the phrase &EALdomains in your files, or share them with us, and I'll take a look for you.