Philosopher issue #366
Comments
|
Can you send us the whole log? Best, Fengchao |
|
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
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You are receiving this because you authored the thread.
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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:
- X:\Group member data folders\Kim\Maryam_Round5\20201210_5_2_D12_P.d
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_Fragger_lib\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_decoy_DB.fasta --prefix DECOY_
PhilosopherFilter [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 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.config ~~~~~~~~~
# 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
decoy_prefix = 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
001. 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
decoy_prefix = 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
001. 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
001. 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_Fragger_lib\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
- C:\Users\wysocki-lab\Documents\Kim\MSFRAGGER\MS_Fragger_lib\test\interact.pep.xml
- Building Commentz-Walter keyword tree...
- Searching the tree...
- Linking duplicate entries...
- Printing results...
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
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........118000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........119000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........120000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........121000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........122000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........123000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........124000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........125000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........126000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........127000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........128000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........129000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........130000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........131000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........132000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........133000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........134000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........135000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........136000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........137000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........138000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........139000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........140000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........141000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........142000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........143000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........144000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........145000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........146000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........147000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........148000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........149000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........150000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........151000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........152000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........153000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........154000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........155000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........156000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........157000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........158000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........159000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........160000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........161000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........162000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........163000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........164000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........165000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........166000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........167000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........168000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........169000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........170000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........171000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........172000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........173000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........174000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........175000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........176000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........177000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........178000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........179000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........180000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........181000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........182000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........183000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........184000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........185000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........186000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........187000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........188000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........189000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........190000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........191000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........192000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........193000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........194000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........195000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........196000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........197000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........198000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........199000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........200000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........201000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........202000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........203000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........204000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........205000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........206000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........207000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........208000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........209000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........210000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........211000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........212000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........213000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........214000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........215000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........216000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........217000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........218000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........219000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........220000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........221000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........222000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........223000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........224000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........225000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........226000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........227000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........228000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........229000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........230000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........231000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........232000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........233000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........234000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........235000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........236000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........237000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........238000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........239000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........240000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........241000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........242000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........243000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........244000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........245000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........246000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........247000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........248000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........249000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........250000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........251000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........252000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........253000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........254000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........255000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........256000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........257000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........258000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........259000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........260000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........261000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........262000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........263000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........264000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........265000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........266000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........267000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........268000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........269000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........270000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........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%
|
|
Hi Kim, Your log was truncated by GitHub, can you 1) zip your log and sent it to us; and 2) zip your Best, Fengchao |
|
@ykim7263 The program is complaining about a special character in one of your interact.pep.xml files. See the error:
You can pinpoint the problem by searching for the phrase |
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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,
The text was updated successfully, but these errors were encountered: