anesvi
commented
3 years ago Looks like TMT-Integrator did not like something, we will take a look
Sent from my iPhone
On Apr 7, 2021, at 7:59 PM, mwfoster @.***> wrote:
External Email - Use Caution
Hi,
I'm trying to search an MS3-TMT file. Error is below. I generated the mzml using MSConvert but perhaps incorrectly. Also using runstart IC. MS2-TMT files processed fine.
Thanks,
Matt
System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_281, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
Version info: FragPipe version 15.0 MSFragger version 3.2 Philosopher version 3.4.13 (build 1611589727)
LCMS files: Experiment/Group:
- D:\5749\ID63522_T2_FSN20560_5749_040721_F1.mzML
16 commands to execute: WorkspaceCleanInit [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: D:\5749\5749_MS3] java -jar -Dfile.encoding=UTF-8 -Xmx104G C:\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\5749\5749_MS3\fragger.params D:\5749\ID63522_T2_FSN20560_5749_040721_F1.mzML MSFragger move pepxml java -cp C:\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\5749\ID63522_T2_FSN20560_5749_040721_F1.pepXML D:\5749\5749_MS3\ID63522_T2_FSN20560_5749_040721_F1.pepXML PeptideProphet: Workspace init [Work dir: D:\5749\5749_MS3\fragpipe-ID63522_T2_FSN20560_5749_040721_F1.pepXML-temp] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: D:\5749\5749_MS3\fragpipe-ID63522_T2_FSN20560_5749_040721F1.pepXML-temp] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database Z:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH_42219.fasta.fas ..\ID63522_T2_FSN20560_5749_040721_F1.pepXML PeptideProphet: Delete temp java -cp C:\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\5749\5749_MS3\fragpipe-ID63522_T2_FSN20560_5749_040721_F1.pepXML-temp Rewrite pepxml [Work dir: D:\5749\5749_MS3] java -cp C:\FragPipe-15.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml D:\5749\ID63522_T2_FSN20560_5749_040721_F1.mzML ProteinProphet [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml PhilosopherDbAnnotate [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate Z:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH42219.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\5749\5749MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --picked --prot 0.01 --tag rev --pepxml D:\5749\5749_MS3 --protxml D:\5749\5749_MS3\combined.prot.xml FreeQuant [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir D:\5749 Quant (Isobaric) [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe labelquant --tol 20 --level 3 --plex 16 --annot D:\5749\annotation.txt --brand tmt --dir D:\5749 PhilosopherReport [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report TmtIntegrator [Work dir: D:\5749\5749_MS3] java -cp "C:\FragPipe-15.0\fragpipe\tools\tmt-integrator-2.4.0.jar" TMTIntegrator D:\5749\5749_MS3\tmt-integrator-conf.yml D:\5749\5749_MS3\psm.tsv WorkspaceClean [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
Execution order:
Cmd: [START], Work dir: [D:\5749\5749_MS3]
Cmd: [WorkspaceCleanInit], Work dir: [D:\5749\5749_MS3]
Cmd: [MSFragger], Work dir: [D:\5749\5749_MS3]
Cmd: [PeptideProphet], Work dir: [D:\5749\5749_MS3]
Cmd: [ProteinProphet], Work dir: [D:\5749\5749_MS3]
Cmd: [PhilosopherDbAnnotate], Work dir: [D:\5749\5749_MS3]
Cmd: [PhilosopherFilter], Work dir: [D:\5749\5749_MS3]
Cmd: [FreeQuant], Work dir: [D:\5749\5749_MS3]
Cmd: [Quant (Isobaric)], Work dir: [D:\5749\5749_MS3]
Cmd: [PhilosopherReport], Work dir: [D:\5749\5749_MS3]
Cmd: [TmtIntegrator], Work dir: [D:\5749\5749_MS3]
Cmd: [WorkspaceClean], Work dir: [D:\5749\5749_MS3]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 Table.editor= crystalc.run-crystalc=false database.db-path=Z\:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH42219.fasta.fas database.decoy-tag=rev fragpipe-config.bin-msfragger=C\:\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar fragpipe-config.bin-philosopher=C\:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe fragpipe-config.bin-python=C\:\Python\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=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.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.allow_multiple_variable_mods_on_residue=false 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=0.8 msfragger.fragment_mass_units=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2/3 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.01 msfragger.misc.fragger.clear-mz-hi=134.5 msfragger.misc.fragger.clear-mz-lo=125.5 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=200 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=pepXML msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.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; 304.207146,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; 304.207146,n^,true,1; 229.162930,S,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 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=false phi-report.print-decoys=false phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.9 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=false ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=false 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=false 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=noiRT speclibgen.easypqp.select-file.text= speclibgen.run-speclibgen=false speclibgen.use-easypqp=false speclibgen.use-spectrast=true tmtintegrator.add_Ref=1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=false tmtintegrator.best_psm=true tmtintegrator.channel_num=16 tmtintegrator.dont-run-fq-lq=false tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated tmtintegrator.groupby=0 tmtintegrator.labelquant=--tol 20 --level 2 tmtintegrator.max_pep_prob_thres=0.9 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=-1 tmtintegrator.psm_norm=false tmtintegrator.quant_level=3 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=true tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false workdir=D\:\5749\5749_MS3 workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.process-exps-separately=false workflow.ram=0 workflow.threads=35
WorkspaceCleanInit [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[19:46:51] Executing Workspace v3.4.13 INFO[19:46:51] Removing workspace WARN[19:46:51] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[19:46:51] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[19:46:51] Executing Workspace v3.4.13 INFO[19:46:51] Creating workspace INFO[19:46:51] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\5749\5749_MS3] java -jar -Dfile.encoding=UTF-8 -Xmx104G C:\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\5749\5749_MS3\fragger.params D:\5749\ID63522_T2_FSN20560_5749_040721_F1.mzML 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: 1.8.0_281, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 92 GB memory Checking database... Deisotoping doesn't support low resolution tandem mass spectra. Changing deisotope to 0. deisotope = 0. Changing deneutralloss to 0. Checking spectral files... D:\5749\ID63522_T2_FSN20560_5749_040721_F1.mzML: Scans = 17202 FIRST SEARCH* Parameters: num_threads = 35 database_name = Z:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH_42219.fasta.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 = 800.0 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 = 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 = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 0 deneutralloss = false 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 = 125.5 clear_mz_range_high = 134.5 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 variable_mod_06 = 304.207146 n^ 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 = 304.207146 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 4.00 Da. 543889032 fragments to be searched in 1 slices (8.10 GB total) Operating on slice 1 of 1: Fragment index slice generated in 4.62 s
- ID63522_T2_FSN20560_5749_040721_F1.mzML 1.6 s [progress: 16510/16510 (100%) - 4015 spectra/s] 4.1s | postprocessing 0.2 s *FIRST SEARCH DONE IN 0.359 MIN
| **MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- | --------------- | --------------- | --------------- | --------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) |
|---|---|---|---|---|---|---|---|---|
| Run | Median MAD | Median MAD | Median MAD | Median MAD |
001 0.54 0.70 -0.05 0.88 32.14 113.51 -13.49 132.60 Finding the optimal parameters:
MS2 150 200 250 300
Count 1964 2134 2839 2895
Peaks 500_0 300_0 200_0 175_0
Count 2425 2758 3192 3194
Int. 1
Count 3158
Rm P. 1
Count 3173
New fragment_mass_tolerance = 400 PPM New use_topN_peaks = 175 New minimum_ratio = 0.000000 New intensity_transform = 0 New remove_precursor_peak = 0 ***MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 1.128 MIN
MAIN SEARCH Checking database... Deisotoping doesn't support low resolution tandem mass spectra. Changing deisotope to 0. deisotope = 0. Changing deneutralloss to 0. Parameters: num_threads = 35 database_name = Z:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH_42219.fasta.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 = 400.0 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 = 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 = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 0 deneutralloss = false 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 = 175 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 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 variable_mod_06 = 304.207146 n^ 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 = 304.207146 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 2.00 Da. 543889032 fragments to be searched in 1 slices (8.10 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.84 s
- ID63522_T2_FSN20560_5749_040721_F1.mzBIN_calibrated 0.5 s [progress: 16059/16059 (100%) - 17012 spectra/s] 0.9s | postprocessing 1.8 s MAIN SEARCH DONE IN 0.110 MIN
TOTAL TIME 1.597 MIN* Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp C:\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\5749\ID63522_T2_FSN20560_5749_040721_F1.pepXML D:\5749\5749_MS3\ID63522_T2_FSN20560_5749_040721_F1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\5749\5749_MS3\fragpipe-ID63522_T2_FSN20560_5749_040721_F1.pepXML-temp] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'PeptideProphet: Workspace init' finished, exit code: 0 INFO[19:48:32] Executing Workspace v3.4.13 INFO[19:48:32] Creating workspace INFO[19:48:32] Done PeptideProphet [Work dir: D:\5749\5749_MS3\fragpipe-ID63522_T2_FSN20560_5749_040721F1.pepXML-temp] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database Z:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH_42219.fasta.fas ..\ID63522_T2_FSN20560_5749_040721_F1.pepXML INFO[19:48:32] Executing PeptideProphet v3.4.13 file 1: D:\5749\5749_MS3\ID63522_T2_FSN20560_5749_040721_F1.pepXML processed altogether 14669 results INFO: Results written to file: D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml
- D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml
- Building Commentz-Walter keyword tree...
- Searching the tree...
- Linking duplicate entries...
- Printing results...
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+, 10483 2+, 3223 3+, 729 4+, 181 5+, 53 6+, and 0 7+ spectra. Found 4547 Decoys, and 10122 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 26 iterations INFO[19:49:06] Done Process 'PeptideProphet' finished, exit code: 0 PeptideProphet: Delete temp java -cp C:\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\5749\5749_MS3\fragpipe-ID63522_T2_FSN20560_5749_040721_F1.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 Rewrite pepxml [Work dir: D:\5749\5749_MS3] java -cp C:\FragPipe-15.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml D:\5749\ID63522_T2_FSN20560_5749_040721_F1.mzML Fixing pepxml: D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml Writing output to: D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml8485112526112677135.temp-rewrite Deleting file: D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml Moving rewritten file to original location: [D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml8485112526112677135.temp-rewrite] -> [D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml INFO[19:49:08] 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 D:/5749/5749_MS3/interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml... ...read in 0 1+, 2728 2+, 1288 3+, 165 4+, 7 5+, 0 6+, 0 7+ spectra with min prob 0.9
Initializing 3070 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database z:/proteomics/Databases/Modified Databases/2021-04-07-decoys-SP_mouse_cas_ADH_42219.fasta.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 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.......WARNING: Found the following zero-mass residues in protein entry sp|Q99MD6|TRXR3_MOUSE : U MEKPPSPPPPPRAQTSPGLGKVGVLPNRRLGAVRGGLMSSPPGRRARLASPGTSRPSSEAREELRRRLRDLIEGNRVMIFSKSYCPHSTRVKELFSSLGVVYNILELDQVDDGASVQEVLTEISNQKTVPNIFVNKVHVGGCDRTFQAHQNGLLQKLLQDDSAHDYDLIIIGGGSGGLSCAKEAANLGKKVMVLDFVVPSPQGTTWGLGGTCVNVGCIPKKLMHQAALLGHALQDAKKYGWEYNQQVKHNWEAMTEAIQSHIGSLNWGYRVTLREKGVTYVNSFGEFVDLHKIKATNKKGQETFYTASKFVIATGERPRYLGIQGDKEYCITSDDLFSLPYCPGCTLVVGASYVGLECAGFLAGLGLDVTVMVRSVLLRGFDQEMAEKVGSYLEQQGVKFQRKFTPILVQQLEKGLPGKLKVVAKSTEGPETVEGIYNTVLLAIGRDSCTRKIGLEKIGVKINEKNGKIPVNDVEQTNVPHVYAIGDILDGKPELTPVAIQAGKLLARRLFGVSLEKCDYINIPTTVFTPLEYGCCGLSEEKAIEMYKKENLEVYHTLFWPLEWTVAGRDNNTCYAKIICNKFDNERVVGFHLLGPNAGEITQGFAAAMKCGLTKQLLDDTIGIHPTCGEVFTTLEITKSSGLDITQKGCUG ..:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry sp|Q9JLT4|TRXR2_MOUSE : U MVAAMVAALRGPSRRFRPRTRALTRGTRGAASAAGGQQSFDLLVIGGGSGGLACAKEAAQLGKKVAVADYVEPSPRGTKWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAHHYGWEVAQPVQHNWKTMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVRGVDKGGKATLLSAEHIVIATGGRPRYPTQVKGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTVMMRSIPLRGFDQQMSSLVTEHMESHGTQFLKGCVPSHIKKLPTNQLQVTWEDHASGKEDTGTFDTVLWAIGRVPETRTLNLEKAGISTNPKNQKIIVDAQEATSVPHIYAIGDVAEGRPELTPTAIKAGKLLAQRLFGKSSTLMDYSNVPTTVFTPLEYGCVGLSEEEAVALHGQEHVEVYHAYYKPLEFTVADRDASQCYIKMVCMREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMQTVGIHPTCSEEVVKLHISKRSGLEPTVTGCUG ........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:. Total: 34914 Computing degenerate peptides for 1576 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 1663 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 1663 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 1663 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 1663 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 1425 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... INFO: mu=1.023e-06, db_size=39608687 Computing MU for 1663 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Finished. INFO[19:49:11] Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate Z:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH42219.fasta.fas --prefix rev INFO[19:49:11] Executing Database v3.4.13 INFO[19:49:11] Processing database Process 'PhilosopherDbAnnotate' finished, exit code: 0 INFO[19:49:14] Done PhilosopherFilter [Work dir: D:\5749\5749MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --picked --prot 0.01 --tag rev --pepxml D:\5749\5749_MS3 --protxml D:\5749\5749_MS3\combined.prot.xml INFO[19:49:14] Executing Filter v3.4.13 INFO[19:49:14] Processing peptide identification files INFO[19:49:15] 1+ Charge profile decoy=0 target=0 INFO[19:49:15] 2+ Charge profile decoy=192 target=3437 INFO[19:49:15] 3+ Charge profile decoy=39 target=1466 INFO[19:49:15] 4+ Charge profile decoy=6 target=209 INFO[19:49:15] 5+ Charge profile decoy=0 target=15 INFO[19:49:15] 6+ Charge profile decoy=0 target=0 INFO[19:49:15] Database search results ions=3852 peptides=3349 psms=5364 INFO[19:49:15] Converged to 1.00 % FDR with 4255 PSMs decoy=42 threshold=0.8738 total=4297 INFO[19:49:15] Converged to 0.99 % FDR with 2713 Peptides decoy=27 threshold=0.8652 total=2740 INFO[19:49:15] Converged to 0.99 % FDR with 3202 Ions decoy=31 threshold=0.8295 total=3233 INFO[19:49:15] Protein inference results decoy=39 target=1386 INFO[19:49:15] Converged to 1.05 % FDR with 1234 Proteins decoy=13 threshold=0.9269 total=1247 INFO[19:49:15] Applying sequential FDR estimation ions=3030 peptides=2608 psms=4192 INFO[19:49:15] Converged to 0.62 % FDR with 4166 PSMs decoy=26 threshold=0.8738 total=4192 INFO[19:49:15] Converged to 0.50 % FDR with 2595 Peptides decoy=13 threshold=0.9001 total=2608 INFO[19:49:15] Converged to 0.46 % FDR with 3016 Ions decoy=14 threshold=0.8765 total=3030 INFO[19:49:16] Post processing identifications INFO[19:49:16] Mapping modifications INFO[19:49:17] Processing protein inference INFO[19:49:19] Assigning protein identifications to layers INFO[19:49:20] Updating razor PSM assignment to proteins INFO[19:49:20] Calculating spectral counts INFO[19:49:20] Saving INFO[19:49:20] Done Process 'PhilosopherFilter' finished, exit code: 0 FreeQuant [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir D:\5749 INFO[19:49:20] Executing Label-free quantification v3.4.13 INFO[19:49:21] Indexing PSM information INFO[19:49:21] Reading spectra and tracing peaks INFO[19:49:21] Processing ID63522_T2_FSN20560_5749_040721_F1 INFO[19:49:57] Assigning intensities to data layers INFO[19:49:57] Done Process 'FreeQuant' finished, exit code: 0 Quant (Isobaric) [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe labelquant --tol 20 --level 3 --plex 16 --annot D:\5749\annotation.txt --brand tmt --dir D:\5749 INFO[19:49:58] Executing Isobaric-label quantification v3.4.13 INFO[19:49:58] Calculating intensities and ion interference INFO[19:49:58] Processing ID63522_T2_FSN20560_5749_040721_F1 INFO[19:50:37] Filtering spectra for label quantification INFO[19:50:37] Removing 0 PSMs from isobaric quantification INFO[19:50:37] Calculating normalized protein levels INFO[19:50:37] Saving Process 'Quant (Isobaric)' finished, exit code: 0 INFO[19:50:37] Done PhilosopherReport [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report INFO[19:50:37] Executing Report v3.4.13 INFO[19:50:38] Creating reports INFO[19:50:38] Done Process 'PhilosopherReport' finished, exit code: 0 TmtIntegrator [Work dir: D:\5749\5749_MS3] java -cp "C:\FragPipe-15.0\fragpipe\tools\tmt-integrator-2.4.0.jar" TMTIntegrator D:\5749\5749_MS3\tmt-integrator-conf.yml D:\5749\5749_MS3\psm.tsv Exception in thread "main" java.lang.NumberFormatException: For input string: "N-term(304.2072)" at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source) at sun.misc.FloatingDecimal.parseDouble(Unknown Source) at java.lang.Double.parseDouble(Unknown Source) at TMTIntegrator.UpdateColumns(TMTIntegrator.java:516) at TMTIntegrator.main(TMTIntegrator.java:43) Process 'TmtIntegrator' finished, exit code: 1 Process returned non-zero exit code, stopping
Cancelling 2 remaining tasks 19:50:39 ERROR: Error writing log to file java.nio.channels.ClosedByInterruptException: null at java.nio.channels.spi.AbstractInterruptibleChannel.end(Unknown Source) at sun.nio.ch.FileChannelImpl.write(Unknown Source) at java.nio.channels.Channels.writeFullyImpl(Unknown Source) at java.nio.channels.Channels.writeFully(Unknown Source) at java.nio.channels.Channels.access$000(Unknown Source) at java.nio.channels.Channels$1.write(Unknown Source) at sun.nio.cs.StreamEncoder.writeBytes(Unknown Source) at sun.nio.cs.StreamEncoder.implWrite(Unknown Source) at sun.nio.cs.StreamEncoder.write(Unknown Source) at java.io.OutputStreamWriter.write(Unknown Source) at java.io.BufferedWriter.flushBuffer(Unknown Source) at java.io.BufferedWriter.write(Unknown Source) at java.io.Writer.write(Unknown Source) at com.dmtavt.fragpipe.tabs.TabRun.saveLogToFile(TabRun.java:354) at com.dmtavt.fragpipe.tabs.TabRun.on(TabRun.java:309) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:510) at org.greenrobot.eventbus.EventBus.postToSubscription(EventBus.java:447) at org.greenrobot.eventbus.EventBus.postSingleEventForEventType(EventBus.java:414) at org.greenrobot.eventbus.EventBus.postSingleEvent(EventBus.java:387) at org.greenrobot.eventbus.EventBus.post(EventBus.java:268) at com.dmtavt.fragpipe.api.Bus.post(Bus.java:51) at com.dmtavt.fragpipe.cmd.ProcessBuilderInfo.lambda$toRunnable$0(ProcessBuilderInfo.java:96) at java.util.concurrent.CompletableFuture$AsyncRun.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Suppressed: java.nio.channels.ClosedChannelException: null at sun.nio.ch.FileChannelImpl.ensureOpen(Unknown Source) at sun.nio.ch.FileChannelImpl.write(Unknown Source) at java.nio.channels.Channels.writeFullyImpl(Unknown Source) at java.nio.channels.Channels.writeFully(Unknown Source) at java.nio.channels.Channels.access$000(Unknown Source) at java.nio.channels.Channels$1.write(Unknown Source) at sun.nio.cs.StreamEncoder.writeBytes(Unknown Source) at sun.nio.cs.StreamEncoder.implClose(Unknown Source) at sun.nio.cs.StreamEncoder.close(Unknown Source) at java.io.OutputStreamWriter.close(Unknown Source) at java.io.BufferedWriter.close(Unknown Source) at com.dmtavt.fragpipe.tabs.TabRun.saveLogToFile(TabRun.java:355) ... 16 common frames omitted
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mwfoster
huiyinc
fcyu
Hi,
I'm trying to search an MS3-TMT file. Error is below. I generated the mzml using MSConvert but perhaps incorrectly. Also using runstart IC. MS2-TMT files processed fine.
Thanks,
Matt
System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_281, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
Version info: FragPipe version 15.0 MSFragger version 3.2 Philosopher version 3.4.13 (build 1611589727)
LCMS files: Experiment/Group:
16 commands to execute: WorkspaceCleanInit [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: D:\5749\5749_MS3] java -jar -Dfile.encoding=UTF-8 -Xmx104G C:\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\5749\5749_MS3\fragger.params D:\5749\ID63522_T2_FSN20560_5749_040721_F1.mzML MSFragger move pepxml java -cp C:\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\5749\ID63522_T2_FSN20560_5749_040721_F1.pepXML D:\5749\5749_MS3\ID63522_T2_FSN20560_5749_040721_F1.pepXML PeptideProphet: Workspace init [Work dir: D:\5749\5749_MS3\fragpipe-ID63522_T2_FSN20560_5749_040721_F1.pepXML-temp] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: D:\5749\5749_MS3\fragpipe-ID63522_T2_FSN20560_5749_040721F1.pepXML-temp] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database Z:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH_42219.fasta.fas ..\ID63522_T2_FSN20560_5749_040721_F1.pepXML PeptideProphet: Delete temp java -cp C:\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\5749\5749_MS3\fragpipe-ID63522_T2_FSN20560_5749_040721_F1.pepXML-temp Rewrite pepxml [Work dir: D:\5749\5749_MS3] java -cp C:\FragPipe-15.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml D:\5749\ID63522_T2_FSN20560_5749_040721_F1.mzML ProteinProphet [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml PhilosopherDbAnnotate [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate Z:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH42219.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\5749\5749MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --picked --prot 0.01 --tag rev --pepxml D:\5749\5749_MS3 --protxml D:\5749\5749_MS3\combined.prot.xml FreeQuant [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir D:\5749 Quant (Isobaric) [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe labelquant --tol 20 --level 3 --plex 16 --annot D:\5749\annotation.txt --brand tmt --dir D:\5749 PhilosopherReport [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report TmtIntegrator [Work dir: D:\5749\5749_MS3] java -cp "C:\FragPipe-15.0\fragpipe\tools\tmt-integrator-2.4.0.jar" TMTIntegrator D:\5749\5749_MS3\tmt-integrator-conf.yml D:\5749\5749_MS3\psm.tsv WorkspaceClean [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[19:46:51] Executing Workspace v3.4.13
INFO[19:46:51] Removing workspace
WARN[19:46:51] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[19:46:51] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[19:46:51] Executing Workspace v3.4.13
INFO[19:46:51] Creating workspace
INFO[19:46:51] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\5749\5749_MS3] java -jar -Dfile.encoding=UTF-8 -Xmx104G C:\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\5749\5749_MS3\fragger.params D:\5749\ID63522_T2_FSN20560_5749_040721_F1.mzML 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: 1.8.0_281, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 92 GB memory Checking database... Deisotoping doesn't support low resolution tandem mass spectra. Changing deisotope to 0. deisotope = 0. Changing deneutralloss to 0. Checking spectral files... D:\5749\ID63522_T2_FSN20560_5749_040721_F1.mzML: Scans = 17202 ***FIRST SEARCH**** Parameters: num_threads = 35 database_name = Z:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH_42219.fasta.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 = 800.0 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 = 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 = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 0 deneutralloss = false 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 = 125.5 clear_mz_range_high = 134.5 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 variable_mod_06 = 304.207146 n^ 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 = 304.207146 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 4.00 Da. 543889032 fragments to be searched in 1 slices (8.10 GB total) Operating on slice 1 of 1: Fragment index slice generated in 4.62 s
New fragment_mass_tolerance = 400 PPM New use_topN_peaks = 175 New minimum_ratio = 0.000000 New intensity_transform = 0 New remove_precursor_peak = 0 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 1.128 MIN*****
****MAIN SEARCH**** Checking database... Deisotoping doesn't support low resolution tandem mass spectra. Changing deisotope to 0. deisotope = 0. Changing deneutralloss to 0. Parameters: num_threads = 35 database_name = Z:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH_42219.fasta.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 = 400.0 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 = 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 = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 0 deneutralloss = false 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 = 175 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 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 variable_mod_06 = 304.207146 n^ 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 = 304.207146 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 2.00 Da. 543889032 fragments to be searched in 1 slices (8.10 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.84 s
***TOTAL TIME 1.597 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp C:\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\5749\ID63522_T2_FSN20560_5749_040721_F1.pepXML D:\5749\5749_MS3\ID63522_T2_FSN20560_5749_040721_F1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\5749\5749_MS3\fragpipe-ID63522_T2_FSN20560_5749_040721_F1.pepXML-temp] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'PeptideProphet: Workspace init' finished, exit code: 0 INFO[19:48:32] Executing Workspace v3.4.13
INFO[19:48:32] Creating workspace
INFO[19:48:32] Done
PeptideProphet [Work dir: D:\5749\5749_MS3\fragpipe-ID63522_T2_FSN20560_5749_040721F1.pepXML-temp] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database Z:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH_42219.fasta.fas ..\ID63522_T2_FSN20560_5749_040721_F1.pepXML INFO[19:48:32] Executing PeptideProphet v3.4.13
file 1: D:\5749\5749_MS3\ID63522_T2_FSN20560_5749_040721_F1.pepXML processed altogether 14669 results INFO: Results written to file: D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.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+, 10483 2+, 3223 3+, 729 4+, 181 5+, 53 6+, and 0 7+ spectra. Found 4547 Decoys, and 10122 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 26 iterations INFO[19:49:06] Done
Process 'PeptideProphet' finished, exit code: 0 PeptideProphet: Delete temp java -cp C:\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\5749\5749_MS3\fragpipe-ID63522_T2_FSN20560_5749_040721_F1.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 Rewrite pepxml [Work dir: D:\5749\5749_MS3] java -cp C:\FragPipe-15.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml D:\5749\ID63522_T2_FSN20560_5749_040721_F1.mzML Fixing pepxml: D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml Writing output to: D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml8485112526112677135.temp-rewrite Deleting file: D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml Moving rewritten file to original location: [D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml8485112526112677135.temp-rewrite] -> [D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined D:\5749\5749_MS3\interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml INFO[19:49:08] 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 D:/5749/5749_MS3/interact-ID63522_T2_FSN20560_5749_040721_F1.pep.xml... ...read in 0 1+, 2728 2+, 1288 3+, 165 4+, 7 5+, 0 6+, 0 7+ spectra with min prob 0.9
Initializing 3070 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database z:/proteomics/Databases/Modified Databases/2021-04-07-decoys-SP_mouse_cas_ADH_42219.fasta.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 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.......WARNING: Found the following zero-mass residues in protein entry sp|Q99MD6|TRXR3_MOUSE : U MEKPPSPPPPPRAQTSPGLGKVGVLPNRRLGAVRGGLMSSPPGRRARLASPGTSRPSSEAREELRRRLRDLIEGNRVMIFSKSYCPHSTRVKELFSSLGVVYNILELDQVDDGASVQEVLTEISNQKTVPNIFVNKVHVGGCDRTFQAHQNGLLQKLLQDDSAHDYDLIIIGGGSGGLSCAKEAANLGKKVMVLDFVVPSPQGTTWGLGGTCVNVGCIPKKLMHQAALLGHALQDAKKYGWEYNQQVKHNWEAMTEAIQSHIGSLNWGYRVTLREKGVTYVNSFGEFVDLHKIKATNKKGQETFYTASKFVIATGERPRYLGIQGDKEYCITSDDLFSLPYCPGCTLVVGASYVGLECAGFLAGLGLDVTVMVRSVLLRGFDQEMAEKVGSYLEQQGVKFQRKFTPILVQQLEKGLPGKLKVVAKSTEGPETVEGIYNTVLLAIGRDSCTRKIGLEKIGVKINEKNGKIPVNDVEQTNVPHVYAIGDILDGKPELTPVAIQAGKLLARRLFGVSLEKCDYINIPTTVFTPLEYGCCGLSEEKAIEMYKKENLEVYHTLFWPLEWTVAGRDNNTCYAKIICNKFDNERVVGFHLLGPNAGEITQGFAAAMKCGLTKQLLDDTIGIHPTCGEVFTTLEITKSSGLDITQKGCUG ..:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry sp|Q9JLT4|TRXR2_MOUSE : U MVAAMVAALRGPSRRFRPRTRALTRGTRGAASAAGGQQSFDLLVIGGGSGGLACAKEAAQLGKKVAVADYVEPSPRGTKWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAHHYGWEVAQPVQHNWKTMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVRGVDKGGKATLLSAEHIVIATGGRPRYPTQVKGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTVMMRSIPLRGFDQQMSSLVTEHMESHGTQFLKGCVPSHIKKLPTNQLQVTWEDHASGKEDTGTFDTVLWAIGRVPETRTLNLEKAGISTNPKNQKIIVDAQEATSVPHIYAIGDVAEGRPELTPTAIKAGKLLAQRLFGKSSTLMDYSNVPTTVFTPLEYGCVGLSEEEAVALHGQEHVEVYHAYYKPLEFTVADRDASQCYIKMVCMREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMQTVGIHPTCSEEVVKLHISKRSGLEPTVTGCUG ........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:. Total: 34914 Computing degenerate peptides for 1576 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 1663 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 1663 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 1663 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 1663 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 1425 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... INFO: mu=1.023e-06, db_size=39608687 Computing MU for 1663 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Finished. INFO[19:49:11] Done
Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate Z:\proteomics\Databases\Modified Databases\2021-04-07-decoys-SP_mouse_cas_ADH42219.fasta.fas --prefix rev INFO[19:49:11] Executing Database v3.4.13
INFO[19:49:11] Processing database
Process 'PhilosopherDbAnnotate' finished, exit code: 0 INFO[19:49:14] Done
PhilosopherFilter [Work dir: D:\5749\5749MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --picked --prot 0.01 --tag rev --pepxml D:\5749\5749_MS3 --protxml D:\5749\5749_MS3\combined.prot.xml INFO[19:49:14] Executing Filter v3.4.13
INFO[19:49:14] Processing peptide identification files
INFO[19:49:15] 1+ Charge profile decoy=0 target=0 INFO[19:49:15] 2+ Charge profile decoy=192 target=3437 INFO[19:49:15] 3+ Charge profile decoy=39 target=1466 INFO[19:49:15] 4+ Charge profile decoy=6 target=209 INFO[19:49:15] 5+ Charge profile decoy=0 target=15 INFO[19:49:15] 6+ Charge profile decoy=0 target=0 INFO[19:49:15] Database search results ions=3852 peptides=3349 psms=5364 INFO[19:49:15] Converged to 1.00 % FDR with 4255 PSMs decoy=42 threshold=0.8738 total=4297 INFO[19:49:15] Converged to 0.99 % FDR with 2713 Peptides decoy=27 threshold=0.8652 total=2740 INFO[19:49:15] Converged to 0.99 % FDR with 3202 Ions decoy=31 threshold=0.8295 total=3233 INFO[19:49:15] Protein inference results decoy=39 target=1386 INFO[19:49:15] Converged to 1.05 % FDR with 1234 Proteins decoy=13 threshold=0.9269 total=1247 INFO[19:49:15] Applying sequential FDR estimation ions=3030 peptides=2608 psms=4192 INFO[19:49:15] Converged to 0.62 % FDR with 4166 PSMs decoy=26 threshold=0.8738 total=4192 INFO[19:49:15] Converged to 0.50 % FDR with 2595 Peptides decoy=13 threshold=0.9001 total=2608 INFO[19:49:15] Converged to 0.46 % FDR with 3016 Ions decoy=14 threshold=0.8765 total=3030 INFO[19:49:16] Post processing identifications
INFO[19:49:16] Mapping modifications
INFO[19:49:17] Processing protein inference
INFO[19:49:19] Assigning protein identifications to layers
INFO[19:49:20] Updating razor PSM assignment to proteins
INFO[19:49:20] Calculating spectral counts
INFO[19:49:20] Saving
INFO[19:49:20] Done
Process 'PhilosopherFilter' finished, exit code: 0 FreeQuant [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir D:\5749 INFO[19:49:20] Executing Label-free quantification v3.4.13 INFO[19:49:21] Indexing PSM information
INFO[19:49:21] Reading spectra and tracing peaks
INFO[19:49:21] Processing ID63522_T2_FSN20560_5749_040721_F1 INFO[19:49:57] Assigning intensities to data layers
INFO[19:49:57] Done
Process 'FreeQuant' finished, exit code: 0 Quant (Isobaric) [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe labelquant --tol 20 --level 3 --plex 16 --annot D:\5749\annotation.txt --brand tmt --dir D:\5749 INFO[19:49:58] Executing Isobaric-label quantification v3.4.13 INFO[19:49:58] Calculating intensities and ion interference INFO[19:49:58] Processing ID63522_T2_FSN20560_5749_040721_F1 INFO[19:50:37] Filtering spectra for label quantification
INFO[19:50:37] Removing 0 PSMs from isobaric quantification INFO[19:50:37] Calculating normalized protein levels
INFO[19:50:37] Saving
Process 'Quant (Isobaric)' finished, exit code: 0 INFO[19:50:37] Done
PhilosopherReport [Work dir: D:\5749\5749_MS3] C:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report INFO[19:50:37] Executing Report v3.4.13
INFO[19:50:38] Creating reports
INFO[19:50:38] Done
Process 'PhilosopherReport' finished, exit code: 0 TmtIntegrator [Work dir: D:\5749\5749_MS3] java -cp "C:\FragPipe-15.0\fragpipe\tools\tmt-integrator-2.4.0.jar" TMTIntegrator D:\5749\5749_MS3\tmt-integrator-conf.yml D:\5749\5749_MS3\psm.tsv Exception in thread "main" java.lang.NumberFormatException: For input string: "N-term(304.2072)" at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source) at sun.misc.FloatingDecimal.parseDouble(Unknown Source) at java.lang.Double.parseDouble(Unknown Source) at TMTIntegrator.UpdateColumns(TMTIntegrator.java:516) at TMTIntegrator.main(TMTIntegrator.java:43) Process 'TmtIntegrator' finished, exit code: 1 Process returned non-zero exit code, stopping