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Nesvilab / FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
http://fragpipe.nesvilab.org
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IonQuant returning nonzero exit code (MSFragger v15.0) #348

Closed ashleyjulio closed 3 years ago

ashleyjulio commented 3 years ago

I am attempting to quantify an experiment with heavy and light isotopic labels. When I run my file, I get an error that IonQuant returned a nonzero exit code. I have tried running the .raw and .mzML files and have ensured that there are no spaces in any path directories. How can I get IonQuant to run the quantification?

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK

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

LCMS files: Experiment/Group: 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1

3 commands to execute: MSFragger [Work dir: D:\NSP14JC36mzML] C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx40G C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\NSP14JC36mzML\fragger.params D:\JC36mzML\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.mzML MSFragger move pepxml C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\jre\bin\java.exe -cp C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/ajulio/Downloads/FragPipe-jre-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\JC36mzML\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML D:\NSP14JC36mzML\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML IonQuant [Work dir: D:\NSP14JC36mzML] C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\jre\bin\java.exe -Xmx40G -Dlibs.bruker.dir="C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\tools\MSFragger-3.2\ext\bruker" -Dlibs.thermo.dir="C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\tools\MSFragger-3.2\ext\thermo" -cp "C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\tools\ionquant-1.5.5.jar;C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\tools\batmass-io-1.22.1.jar" ionquant.IonQuant --threads 7 --ionmobility 0 --mbr 1 --proteinquant 2 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --light C464.28595 --heavy C470.29976 --tp 3 --minfreq 0.5 --minions 2 --minexps 1 --psm 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\psm.tsv --multidir . --specdir D:\JC36mzML 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML


Execution order:

    Cmd: [START], Work dir: [D:\NSP14JC36mzML]
    Cmd: [MSFragger], Work dir: [D:\NSP14JC36mzML]
    Cmd: [IonQuant], Work dir: [D:\NSP14JC36mzML]

# FragPipe v15.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
crystalc.correct_isotope_error=false
crystalc.isotope_number=3
crystalc.max-charge=6
crystalc.precursor_isolation_window=0.7
crystalc.precursor_mass=20
crystalc.run-crystalc=false
database.db-path=C\:\\Users\\ajulio\\Downloads\\2021-03-31-decoys-_ip2_ip2_data_kbackus_database__Uniprot__Human__contaminant_01-18-2021-correctheaders.fasta.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\Users\\ajulio\\Downloads\\FragPipe-jre-15.0\\fragpipe\\tools\\MSFragger-3.2\\MSFragger-3.2.jar
fragpipe-config.bin-philosopher=C\:\\Users\\ajulio\\Downloads\\philosopherNEW\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\ajulio\\Anaconda3\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=C470.29976
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.label=
ionquant.light=C464.28595
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=3
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.deltamass_allowed_residues=ST
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=6
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=600
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=6000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown=stricttrypsin
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-10
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=10
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=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; 57.021464,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; 410.231400,C,false,1; 406.215100,C,false,1; 406.215090,C,false,1; 464.285950,C,true,1; 470.299760,C,true,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=false
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=false
phi-report.write-mzid=false
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=false
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.diag_ions=
ptmshepherd.glyco_mode=false
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
run-diaumpire=false
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=0
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=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\NSP14JC36mzML
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=true
workflow.ram=0
workflow.threads=7

MSFragger [Work dir: D:\NSP14JC36mzML] C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx40G C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\NSP14JC36mzML\fragger.params D:\JC36mzML\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.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: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 40 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:\JC36mzML\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.mzML: Scans = 98356 ***FIRST SEARCH**** Parameters: num_threads = 7 database_name = C:\Users\ajulio\Downloads\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.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 = 600.0 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 = 6 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 6000.0 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 = 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 = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 3.00 Da. 329540120 fragments to be searched in 1 slices (4.91 GB total) Operating on slice 1 of 1: Fragment index slice generated in 4.83 s

  1. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.mzML 11.4 s [progress: 97952/97952 (100%) - 3205 spectra/s] 30.6s | postprocessing 0.9 s ***FIRST SEARCH DONE IN 1.154 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 1.02 9.56 -0.43 9.48 164.57 200.91 53.03 190.51
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- MS2 150 200 250 300 350 400
Count 0 0 0 0 0 0
------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- ------- -------
Peaks 500_0 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- ------- -------
Count 0 0 0 0 0 0 0
------- ------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 0
------- -------
------- -------
Rm P. 1
------- -------
Count 0
------- -------

New fragment_mass_tolerance = 600 PPM New use_topN_peaks = 100 New minimum_ratio = 0.010000 New intensity_transform = 1 New remove_precursor_peak = 1 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 11.739 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 = 7 database_name = C:\Users\ajulio\Downloads\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.fasta.fas decoyprefix = rev precursor_mass_lower = -10.0 precursor_mass_upper = 10.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 600.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 0 isotope_error = 0/1/2 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 = 3 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 = 6 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 6000.0 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 = 100 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 1 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_09 = 464.285950 C 1 variable_mod_10 = 470.299760 C 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 3.00 Da. 1573147060 fragments to be searched in 1 slices (23.44 GB total) Operating on slice 1 of 1: Fragment index slice generated in 32.15 s

  1. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.mzBIN_calibrated 5.3 s [progress: 97728/97728 (100%) - 2433 spectra/s] 40.2s | postprocessing 11.5 s MAIN SEARCH DONE IN 1.551 MIN

***TOTAL TIME 14.445 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\jre\bin\java.exe -cp C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/ajulio/Downloads/FragPipe-jre-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\JC36mzML\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML D:\NSP14JC36mzML\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 IonQuant [Work dir: D:\NSP14JC36mzML] C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\jre\bin\java.exe -Xmx40G -Dlibs.bruker.dir="C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\tools\MSFragger-3.2\ext\bruker" -Dlibs.thermo.dir="C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\tools\MSFragger-3.2\ext\thermo" -cp "C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\tools\ionquant-1.5.5.jar;C:\Users\ajulio\Downloads\FragPipe-jre-15.0\fragpipe\tools\batmass-io-1.22.1.jar" ionquant.IonQuant --threads 7 --ionmobility 0 --mbr 1 --proteinquant 2 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --light C464.28595 --heavy C470.29976 --tp 3 --minfreq 0.5 --minions 2 --minexps 1 --psm 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\psm.tsv --multidir . --specdir D:\JC36mzML 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML Cannot read file D:\NSP14JC36mzML\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\psm.tsv. IonQuant version IonQuant-1.5.5 Batmass-IO version 1.22.1 timsdata library version timsdata-2-7-0 (c) University of Michigan System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 40 GB memory 2021-04-06 12:32:19 [WARNING] - There are only 1 experiments. Using Top-N protein intensity calculation algorithm with min exps = 1. 2021-04-06 12:32:19 [WARNING] - proteinquant == 1 but minions > 1. Changing minions to 1.

fcyu commented 3 years ago

Although your log seems not complete, but I think the error is caused by not running PeptideProphet, ProteinProphet, and etc... For the first time running FragPipe, I suggest you loading one of the built-in workflow (LFQ-MBR in your case), specifying your spectral files, specifying fasta files, and do not change anything else. You can tweak the settings after you understand what they are later. If your sample is too special to be fitted into any workflow, could you tell us more information regarding it?

Best,

Fengchao

fcyu commented 3 years ago

And the MSFragger part in your log also seems weird. Could you briefly describe your sample?

Best,

Fengchao

ashleyjulio commented 3 years ago

Thank you for your quick response! Unfortunately, when I run ProteinProphet and PeptideProphet, I also get an error that ProteinProphet returns a nonzero exit code, and the 8 remaining tasks are cancelled. My sample is made from treating cells with either a chemical probe or vehicle, conjugating the proteins in the probe-treated cells with a isotopically light biotin tag and proteins in the vehicle-treated cells with an isotopically heavy biotin tag, combing the light/heavy pair, and enriching tagged proteins on streptavidin. Thank you again for your help.

Best, Ashley Julio

On Tue, Apr 6, 2021 at 1:20 PM Fengchao @.***> wrote:

And the MSFragger part in your log also seems weird. Could you briefly describe your sample?

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/348#issuecomment-814413304, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATSCAYY25NISSSUU327EOJ3THNUJHANCNFSM42PNJMCQ .

anesvi commented 3 years ago

MSFragger during the first optimization step did not consider those modifications. You can either turn mass calibration OFF for now, or (better option) we can build a custom version of MSFragger for you. We need to add your modifications to the ‘allowed modification’ list for the first (calibration/optimization) search Alexey

From: ashleyjulio @.> Sent: Thursday, April 8, 2021 10:33 AM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: Re: [Nesvilab/FragPipe] IonQuant returning nonzero exit code (MSFragger v15.0) (#348)

External Email - Use Caution Thank you for your quick response! Unfortunately, when I run ProteinProphet and PeptideProphet, I also get an error that ProteinProphet returns a nonzero exit code, and the 8 remaining tasks are cancelled. My sample is made from treating cells with either a chemical probe or vehicle, conjugating the proteins in the probe-treated cells with a isotopically light biotin tag and proteins in the vehicle-treated cells with an isotopically heavy biotin tag, combing the light/heavy pair, and enriching tagged proteins on streptavidin. Thank you again for your help.

Best, Ashley Julio

On Tue, Apr 6, 2021 at 1:20 PM Fengchao @.<mailto:@.>> wrote:

And the MSFragger part in your log also seems weird. Could you briefly describe your sample?

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/348#issuecomment-814413304, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATSCAYY25NISSSUU327EOJ3THNUJHANCNFSM42PNJMCQ .

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ashleyjulio commented 3 years ago

Thank you, the quantification was successful when I turned the mass calibration off. However, my labmate is able to run the quantification of the same file on her MSFragger program with the mass calibration/optimization on. As far as I can tell we have everything configured the same way with all of the same parameters. Is there a reason why her MSFragger supports the specific isotopic modifications and mine does not? I have attached a log of the run from her account below.

Best, Ashley Julio

On Thu, Apr 8, 2021 at 7:39 AM Alexey Nesvizhskii @.***> wrote:

MSFragger during the first optimization step did not consider those modifications. You can either turn mass calibration OFF for now, or (better option) we can build a custom version of MSFragger for you. We need to add your modifications to the ‘allowed modification’ list for the first (calibration/optimization) search Alexey

From: ashleyjulio @.> Sent: Thursday, April 8, 2021 10:33 AM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: Re: [Nesvilab/FragPipe] IonQuant returning nonzero exit code (MSFragger v15.0) (#348)

External Email - Use Caution Thank you for your quick response! Unfortunately, when I run ProteinProphet and PeptideProphet, I also get an error that ProteinProphet returns a nonzero exit code, and the 8 remaining tasks are cancelled. My sample is made from treating cells with either a chemical probe or vehicle, conjugating the proteins in the probe-treated cells with a isotopically light biotin tag and proteins in the vehicle-treated cells with an isotopically heavy biotin tag, combing the light/heavy pair, and enriching tagged proteins on streptavidin. Thank you again for your help.

Best, Ashley Julio

On Tue, Apr 6, 2021 at 1:20 PM Fengchao @.<mailto:@.>> wrote:

And the MSFragger part in your log also seems weird. Could you briefly describe your sample?

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/348#issuecomment-814413304,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/ATSCAYY25NISSSUU327EOJ3THNUJHANCNFSM42PNJMCQ>

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System OS: Windows 10, Architecture: AMD64 Java Info: 14.0.2, 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: 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2

63 commands to execute: WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: D:\NSP14_isoTOP_NEW] java -jar -Dfile.encoding=UTF-8 -Xmx40G C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\NSP14_isoTOP_NEW\fragger.params C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.raw MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-JC36-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHumancontaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-CF3-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-CF3-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHumancontaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-C2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHumancontaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-JC36-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML PeptideProphet: Delete temp java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML-temp PeptideProphet: Delete temp java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML-temp PeptideProphet: Delete temp java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML-temp PeptideProphet: Delete temp java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML-temp PeptideProphet: Delete temp java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML-temp Rewrite pepxml [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pep.xml C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.raw Rewrite pepxml [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pep.xml C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.raw Rewrite pepxml [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pep.xml C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.raw Rewrite pepxml [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pep.xml C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.raw Rewrite pepxml [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pep.xml C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.raw ProteinProphet [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pep.xml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pep.xml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pep.xml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pep.xml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pep.xml PhilosopherDbAnnotate [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHumancontaminant01-18-2021-correctheaders.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHumancontaminant01-18-2021-correctheaders.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant01-18-2021-correctheaders.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHumancontaminant01-18-2021-correctheaders.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant01-18-2021-correctheaders.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant01-18-2021-correctheaders.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2 --protxml D:\NSP14_isoTOP_NEW\combined.prot.xml PhilosopherFilter [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1 --protxml D:\NSP14_isoTOP_NEW\combined.prot.xml PhilosopherFilter [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2 --protxml D:\NSP14_isoTOP_NEW\combined.prot.xml PhilosopherFilter [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1 --protxml D:\NSP14_isoTOP_NEW\combined.prot.xml PhilosopherFilter [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2 --protxml D:\NSP14_isoTOP_NEW\combined.prot.xml PhilosopherReport [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report PhilosopherAbacus [Work dir: D:\NSP14_isoTOPNEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe abacus --razor --reprint --tag rev --protein 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2 IonQuant [Work dir: D:\NSP14_isoTOP_NEW] java -Xmx40G -Dlibs.bruker.dir="C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\ext\bruker" -Dlibs.thermo.dir="C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\ext\thermo" -cp "C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\ionquant-1.5.5.jar;C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\batmass-io-1.22.1.jar" ionquant.IonQuant --threads 7 --ionmobility 0 --mbr 0 --proteinquant 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 1 --minscans 3 --writeindex 0 --light C464.28595 --heavy C470.29976 --tp 3 --minfreq 0.5 --minions 1 --minexps 1 --psm 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\psm.tsv --psm 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\psm.tsv --psm 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\psm.tsv --psm 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\psm.tsv --psm 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\psm.tsv --multidir . --specdir C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML WorkspaceClean [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [D:\NSP14_isoTOP_NEW]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-CF3-1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-JC36-1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-CF3-2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-JC36-2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\NSP14_isoTOP_NEW]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-C2]
    Cmd: [MSFragger], Work dir: [D:\NSP14_isoTOP_NEW]
    Cmd: [PeptideProphet], Work dir: [D:\NSP14_isoTOP_NEW]
    Cmd: [ProteinProphet], Work dir: [D:\NSP14_isoTOP_NEW]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\NSP14_isoTOP_NEW]
    Cmd: [PhilosopherFilter], Work dir: [D:\NSP14_isoTOP_NEW]
    Cmd: [PhilosopherReport], Work dir: [D:\NSP14_isoTOP_NEW]
    Cmd: [PhilosopherAbacus], Work dir: [D:\NSP14_isoTOP_NEW]
    Cmd: [IonQuant], Work dir: [D:\NSP14_isoTOP_NEW]
    Cmd: [WorkspaceClean], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-CF3-1]
    Cmd: [WorkspaceClean], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-JC36-1]
    Cmd: [WorkspaceClean], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-CF3-2]
    Cmd: [WorkspaceClean], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-JC36-2]
    Cmd: [WorkspaceClean], Work dir: [D:\NSP14_isoTOP_NEW]
    Cmd: [WorkspaceClean], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-C2]

# FragPipe v15.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
crystalc.run-crystalc=false
database.db-path=C\:\\Users\\fshikwana\\Box\\Backus_Lab\\Ashley\\2021-03-31-decoys-_ip2_ip2_data_kbackus_database__Uniprot__Human__contaminant_01-18-2021-correctheaders.fasta.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\Users\\fshikwana\\AppData\\Local\\Temp\\FragPipe-15.0\\fragpipe\\tools\\MSFragger-3.2\\MSFragger-3.2.jar
fragpipe-config.bin-philosopher=C\:\\Users\\fshikwana\\AppData\\Local\\Temp\\FragPipe-15.0\\fragpipe\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3LOCAL\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=C470.29976
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=C464.28595
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=1
ionquant.minisotopes=1
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage=3
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=6
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=600
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=6000
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=-10
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=10
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=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; 57.021464,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; 410.231400,C,false,1; 406.215100,C,false,1; 406.215090,C,false,1; 464.285950,C,true,1; 470.299760,C,true,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 --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
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=--keepold --static --em 1 --nions b --mods STY\:79.966331,M\:15.9949 --minprob 0.5
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=all
ptmshepherd.localization_background=4
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
run-diaumpire=false
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.groupby=0
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\NSP14_isoTOP_NEW
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=7

WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:33:38] Executing Workspace v3.4.13
INFO[14:33:38] Removing workspace
WARN[14:33:38] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:33:38] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:33:38] Executing Workspace v3.4.13
INFO[14:33:38] Creating workspace
INFO[14:33:38] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:33:39] Executing Workspace v3.4.13
INFO[14:33:39] Removing workspace
WARN[14:33:39] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:33:39] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:33:39] Executing Workspace v3.4.13
INFO[14:33:39] Creating workspace
INFO[14:33:39] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:33:40] Executing Workspace v3.4.13
INFO[14:33:40] Removing workspace
WARN[14:33:40] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:33:40] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:33:41] Executing Workspace v3.4.13
INFO[14:33:41] Creating workspace
INFO[14:33:41] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:33:42] Executing Workspace v3.4.13
INFO[14:33:42] Removing workspace
WARN[14:33:42] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:33:42] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:33:42] Executing Workspace v3.4.13
INFO[14:33:42] Creating workspace
INFO[14:33:42] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:33:43] Executing Workspace v3.4.13
INFO[14:33:43] Removing workspace
WARN[14:33:43] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:33:43] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:33:44] Executing Workspace v3.4.13
INFO[14:33:44] Creating workspace
INFO[14:33:44] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:33:45] Executing Workspace v3.4.13
INFO[14:33:45] Removing workspace
WARN[14:33:45] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:33:45] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:33:46] Executing Workspace v3.4.13
INFO[14:33:46] Creating workspace
INFO[14:33:46] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\NSP14_isoTOP_NEW] java -jar -Dfile.encoding=UTF-8 -Xmx40G C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\NSP14_isoTOP_NEW\fragger.params C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.raw MSFragger version MSFragger-3.2 Batmass-IO version 1.22.1 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 14.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 40 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... C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.raw: Scans = 72046 C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.raw: Scans = 82045 C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.raw: Scans = 97520 C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.raw: Scans = 98484 C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.raw: Scans = 101291 ***FIRST SEARCH**** Parameters: num_threads = 7 database_name = C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.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 = 600.0 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 = 6 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 6000.0 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 = 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 = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 3.00 Da. 329540120 fragments to be searched in 1 slices (4.91 GB total) Operating on slice 1 of 1: Fragment index slice generated in 5.26 s

  1. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.raw 68.7 s [progress: 81456/81456 (100%) - 3823 spectra/s] 21.3s | postprocessing 0.8 s
  2. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.raw 58.9 s [progress: 71451/71451 (100%) - 4434 spectra/s] 16.1s | postprocessing 0.4 s
  3. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.raw 92.6 s [progress: 97108/97108 (100%) - 3530 spectra/s] 27.5s | postprocessing 0.6 s
  4. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.raw 93.8 s [progress: 97952/97952 (100%) - 3541 spectra/s] 27.7s | postprocessing 0.6 s
  5. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.raw 94.3 s [progress: 100765/100765 (100%) - 3519 spectra/s] 28.6s | postprocessing 0.6 s ***FIRST SEARCH DONE IN 16.276 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 0.17 11.22 0.37 11.14 142.87 235.24 44.93 229.34
002 0.52 11.66 0.05 11.68 91.73 273.69 27.32 269.30
003 1.22 2.92 0.02 2.81 156.65 125.58 28.04 121.54
004 1.02 9.56 -0.48 9.51 164.57 200.91 53.03 190.51
005 0.39 11.15 -0.23 11.59 171.16 216.11 49.87 204.99
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- MS2 150 200 250 300 350 400
Count 0 0 0 0 0 0
------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- ------- -------
Peaks 500_0 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- ------- -------
Count 0 0 0 0 0 0 0
------- ------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 0
------- -------
------- -------
Rm P. 1
------- -------
Count 0
------- -------

New fragment_mass_tolerance = 600 PPM New use_topN_peaks = 100 New minimum_ratio = 0.010000 New intensity_transform = 1 New remove_precursor_peak = 1 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 27.630 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 = 7 database_name = C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.fasta.fas decoyprefix = rev precursor_mass_lower = -10.0 precursor_mass_upper = 10.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 600.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 0 isotope_error = 0/1/2 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 = 3 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 = 6 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 6000.0 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 = 100 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 1 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_09 = 464.285950 C 1 variable_mod_10 = 470.299760 C 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 3.00 Da. 1573147060 fragments to be searched in 1 slices (23.44 GB total) Operating on slice 1 of 1: Fragment index slice generated in 34.40 s

  1. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.mzBIN_calibrated 11.4 s [progress: 81189/81189 (100%) - 2932 spectra/s] 27.7s | postprocessing 9.4 s
  2. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.mzBIN_calibrated 9.6 s [progress: 71346/71346 (100%) - 3043 spectra/s] 23.4s | postprocessing 7.2 s
  3. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.mzBIN_calibrated 20.7 s [progress: 96895/96895 (100%) - 2375 spectra/s] 40.8s | postprocessing 12.1 s
  4. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.mzBIN_calibrated 21.2 s [progress: 97728/97728 (100%) - 2393 spectra/s] 40.8s | postprocessing 11.3 s
  5. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.mzBIN_calibrated 21.7 s [progress: 100437/100437 (100%) - 2336 spectra/s] 43.0s | postprocessing 12.8 s MAIN SEARCH DONE IN 6.032 MIN

***TOTAL TIME 49.938 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[15:23:51] Executing Workspace v3.4.13
INFO[15:23:51] Creating workspace
INFO[15:23:51] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[15:23:51] Executing Workspace v3.4.13
INFO[15:23:51] Creating workspace
INFO[15:23:51] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[15:23:52] Executing Workspace v3.4.13
INFO[15:23:52] Creating workspace
INFO[15:23:52] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[15:23:53] Executing Workspace v3.4.13
INFO[15:23:53] Creating workspace
INFO[15:23:53] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[15:23:54] Executing Workspace v3.4.13
INFO[15:23:54] Creating workspace
INFO[15:23:54] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-CF3-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-JC36-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-C2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-de

anesvi commented 3 years ago

Her log shows the same issue. It did not crash, yes, but the calibration/optimization results are still suboptimal Her searches may benefit from turning calibration off, I am not sure

From: ashleyjulio @.> Sent: Thursday, April 8, 2021 1:33 PM To: Nesvilab/FragPipe @.> Cc: Nesvizhskii, Alexey @.>; Comment @.> Subject: Re: [Nesvilab/FragPipe] IonQuant returning nonzero exit code (MSFragger v15.0) (#348)

External Email - Use Caution Thank you, the quantification was successful when I turned the mass calibration off. However, my labmate is able to run the quantification of the same file on her MSFragger program with the mass calibration/optimization on. As far as I can tell we have everything configured the same way with all of the same parameters. Is there a reason why her MSFragger supports the specific isotopic modifications and mine does not? I have attached a log of the run from her account below.

Best, Ashley Julio

On Thu, Apr 8, 2021 at 7:39 AM Alexey Nesvizhskii @.<mailto:@.>> wrote:

MSFragger during the first optimization step did not consider those modifications. You can either turn mass calibration OFF for now, or (better option) we can build a custom version of MSFragger for you. We need to add your modifications to the ‘allowed modification’ list for the first (calibration/optimization) search Alexey

From: ashleyjulio @.<mailto:@.>> Sent: Thursday, April 8, 2021 10:33 AM To: Nesvilab/FragPipe @.<mailto:@.>> Cc: Subscribed @.<mailto:@.>> Subject: Re: [Nesvilab/FragPipe] IonQuant returning nonzero exit code (MSFragger v15.0) (#348)

External Email - Use Caution Thank you for your quick response! Unfortunately, when I run ProteinProphet and PeptideProphet, I also get an error that ProteinProphet returns a nonzero exit code, and the 8 remaining tasks are cancelled. My sample is made from treating cells with either a chemical probe or vehicle, conjugating the proteins in the probe-treated cells with a isotopically light biotin tag and proteins in the vehicle-treated cells with an isotopically heavy biotin tag, combing the light/heavy pair, and enriching tagged proteins on streptavidin. Thank you again for your help.

Best, Ashley Julio

On Tue, Apr 6, 2021 at 1:20 PM Fengchao @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> wrote:

And the MSFragger part in your log also seems weird. Could you briefly describe your sample?

Best,

Fengchao

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System OS: Windows 10, Architecture: AMD64 Java Info: 14.0.2, 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: 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2

63 commands to execute: WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: D:\NSP14_isoTOP_NEW] java -jar -Dfile.encoding=UTF-8 -Xmx40G C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\NSP14_isoTOP_NEW\fragger.params C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.raw MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-JC36-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHumancontaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-CF3-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-CF3-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHumancontaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-C2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHumancontaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-JC36-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML PeptideProphet: Delete temp java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML-temp PeptideProphet: Delete temp java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML-temp PeptideProphet: Delete temp java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML-temp PeptideProphet: Delete temp java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML-temp PeptideProphet: Delete temp java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML-temp Rewrite pepxml [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pep.xml C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.raw Rewrite pepxml [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pep.xml C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.raw Rewrite pepxml [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pep.xml C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.raw Rewrite pepxml [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pep.xml C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.raw Rewrite pepxml [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pep.xml C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.raw ProteinProphet [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pep.xml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pep.xml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pep.xml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pep.xml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\interact-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pep.xml PhilosopherDbAnnotate [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHumancontaminant01-18-2021-correctheaders.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHumancontaminant01-18-2021-correctheaders.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant01-18-2021-correctheaders.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHumancontaminant01-18-2021-correctheaders.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant01-18-2021-correctheaders.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant01-18-2021-correctheaders.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2 --protxml D:\NSP14_isoTOP_NEW\combined.prot.xml PhilosopherFilter [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1 --protxml D:\NSP14_isoTOP_NEW\combined.prot.xml PhilosopherFilter [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2 --protxml D:\NSP14_isoTOP_NEW\combined.prot.xml PhilosopherFilter [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1 --protxml D:\NSP14_isoTOP_NEW\combined.prot.xml PhilosopherFilter [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2 --protxml D:\NSP14_isoTOP_NEW\combined.prot.xml PhilosopherReport [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report PhilosopherAbacus [Work dir: D:\NSP14_isoTOPNEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe abacus --razor --reprint --tag rev --protein 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2 IonQuant [Work dir: D:\NSP14_isoTOP_NEW] java -Xmx40G -Dlibs.bruker.dir="C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\ext\bruker" -Dlibs.thermo.dir="C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\ext\thermo" -cp "C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\ionquant-1.5.5.jar;C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\batmass-io-1.22.1.jar" ionquant.IonQuant --threads 7 --ionmobility 0 --mbr 0 --proteinquant 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 1 --minscans 3 --writeindex 0 --light C464.28595 --heavy C470.29976 --tp 3 --minfreq 0.5 --minions 1 --minexps 1 --psm 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\psm.tsv --psm 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\psm.tsv --psm 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\psm.tsv --psm 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\psm.tsv --psm 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\psm.tsv --multidir . --specdir C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML WorkspaceClean [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck


Execution order:

Cmd: [START], Work dir: [D:\NSP14_isoTOP_NEW]
Cmd: [WorkspaceCleanInit], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-CF3-1]
Cmd: [WorkspaceCleanInit], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-JC36-1]
Cmd: [WorkspaceCleanInit], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-CF3-2]
Cmd: [WorkspaceCleanInit], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-JC36-2]
Cmd: [WorkspaceCleanInit], Work dir: [D:\NSP14_isoTOP_NEW]
Cmd: [WorkspaceCleanInit], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-C2]
Cmd: [MSFragger], Work dir: [D:\NSP14_isoTOP_NEW]
Cmd: [PeptideProphet], Work dir: [D:\NSP14_isoTOP_NEW]
Cmd: [ProteinProphet], Work dir: [D:\NSP14_isoTOP_NEW]
Cmd: [PhilosopherDbAnnotate], Work dir: [D:\NSP14_isoTOP_NEW]
Cmd: [PhilosopherFilter], Work dir: [D:\NSP14_isoTOP_NEW]
Cmd: [PhilosopherReport], Work dir: [D:\NSP14_isoTOP_NEW]
Cmd: [PhilosopherAbacus], Work dir: [D:\NSP14_isoTOP_NEW]
Cmd: [IonQuant], Work dir: [D:\NSP14_isoTOP_NEW]
Cmd: [WorkspaceClean], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-CF3-1]
Cmd: [WorkspaceClean], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-JC36-1]
Cmd: [WorkspaceClean], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-CF3-2]
Cmd: [WorkspaceClean], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-JC36-2]
Cmd: [WorkspaceClean], Work dir: [D:\NSP14_isoTOP_NEW]
Cmd: [WorkspaceClean], Work dir: [D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron_3cv_-35_-34_-55_AJ-C2]

# FragPipe v15.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
crystalc.run-crystalc=false
database.db-path=C\:\\Users\\fshikwana\\Box\\Backus_Lab\\Ashley\\2021-03-31-decoys-_ip2_ip2_data_kbackus_database__Uniprot__Human__contaminant_01-18-2021-correctheaders.fasta.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\Users\\fshikwana\\AppData\\Local\\Temp\\FragPipe-15.0\\fragpipe\\tools\\MSFragger-3.2\\MSFragger-3.2.jar
fragpipe-config.bin-philosopher=C\:\\Users\\fshikwana\\AppData\\Local\\Temp\\FragPipe-15.0\\fragpipe\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3LOCAL\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=C470.29976
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=C464.28595
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=1
ionquant.minisotopes=1
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage=3
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=6
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=600
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=6000
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=-10
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=10
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=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; 57.021464,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; 410.231400,C,false,1; 406.215100,C,false,1; 406.215090,C,false,1; 464.285950,C,true,1; 470.299760,C,true,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 --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
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=--keepold --static --em 1 --nions b --mods STY\:79.966331,M\:15.9949 --minprob 0.5
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=all
ptmshepherd.localization_background=4
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
run-diaumpire=false
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.groupby=0
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\NSP14_isoTOP_NEW
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=7

WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:33:38] Executing Workspace v3.4.13 INFO[14:33:38] Removing workspace WARN[14:33:38] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:33:38] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:33:38] Executing Workspace v3.4.13 INFO[14:33:38] Creating workspace INFO[14:33:38] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:33:39] Executing Workspace v3.4.13 INFO[14:33:39] Removing workspace WARN[14:33:39] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:33:39] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:33:39] Executing Workspace v3.4.13 INFO[14:33:39] Creating workspace INFO[14:33:39] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:33:40] Executing Workspace v3.4.13 INFO[14:33:40] Removing workspace WARN[14:33:40] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:33:40] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:33:41] Executing Workspace v3.4.13 INFO[14:33:41] Creating workspace INFO[14:33:41] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:33:42] Executing Workspace v3.4.13 INFO[14:33:42] Removing workspace WARN[14:33:42] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:33:42] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:33:42] Executing Workspace v3.4.13 INFO[14:33:42] Creating workspace INFO[14:33:42] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:33:43] Executing Workspace v3.4.13 INFO[14:33:43] Removing workspace WARN[14:33:43] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:33:43] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:33:44] Executing Workspace v3.4.13 INFO[14:33:44] Creating workspace INFO[14:33:44] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:33:45] Executing Workspace v3.4.13 INFO[14:33:45] Removing workspace WARN[14:33:45] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:33:45] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:33:46] Executing Workspace v3.4.13 INFO[14:33:46] Creating workspace INFO[14:33:46] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\NSP14_isoTOP_NEW] java -jar -Dfile.encoding=UTF-8 -Xmx40G C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\NSP14_isoTOP_NEW\fragger.params C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.raw C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.raw MSFragger version MSFragger-3.2 Batmass-IO version 1.22.1 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 14.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 40 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... C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.raw: Scans = 72046 C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.raw: Scans = 82045 C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.raw: Scans = 97520 C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.raw: Scans = 98484 C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.raw: Scans = 101291 ***FIRST SEARCH**** Parameters: num_threads = 7 database_name = C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.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 = 600.0 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 = 6 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 6000.0 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 = 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 = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 3.00 Da. 329540120 fragments to be searched in 1 slices (4.91 GB total) Operating on slice 1 of 1: Fragment index slice generated in 5.26 s

  1. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.raw 68.7 s [progress: 81456/81456 (100%) - 3823 spectra/s] 21.3s | postprocessing 0.8 s
  2. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.raw 58.9 s [progress: 71451/71451 (100%) - 4434 spectra/s] 16.1s | postprocessing 0.4 s
  3. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.raw 92.6 s [progress: 97108/97108 (100%) - 3530 spectra/s] 27.5s | postprocessing 0.6 s
  4. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.raw 93.8 s [progress: 97952/97952 (100%) - 3541 spectra/s] 27.7s | postprocessing 0.6 s
  5. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.raw 94.3 s [progress: 100765/100765 (100%) - 3519 spectra/s] 28.6s | postprocessing 0.6 s ***FIRST SEARCH DONE IN 16.276 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 0.17 11.22 0.37 11.14 142.87 235.24 44.93 229.34
002 0.52 11.66 0.05 11.68 91.73 273.69 27.32 269.30
003 1.22 2.92 0.02 2.81 156.65 125.58 28.04 121.54
004 1.02 9.56 -0.48 9.51 164.57 200.91 53.03 190.51
005 0.39 11.15 -0.23 11.59 171.16 216.11 49.87 204.99
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- MS2 150 200 250 300 350 400
Count 0 0 0 0 0 0
------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- ------- -------
Peaks 500_0 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- ------- -------
Count 0 0 0 0 0 0 0
------- ------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 0
------- -------
------- -------
Rm P. 1
------- -------
Count 0
------- -------

New fragment_mass_tolerance = 600 PPM New use_topN_peaks = 100 New minimum_ratio = 0.010000 New intensity_transform = 1 New remove_precursor_peak = 1 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 27.630 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 = 7 database_name = C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.fasta.fas decoyprefix = rev precursor_mass_lower = -10.0 precursor_mass_upper = 10.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 600.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 0 isotope_error = 0/1/2 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 = 3 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 = 6 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 6000.0 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 = 100 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 1 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_09 = 464.285950 C 1 variable_mod_10 = 470.299760 C 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 3.00 Da. 1573147060 fragments to be searched in 1 slices (23.44 GB total) Operating on slice 1 of 1: Fragment index slice generated in 34.40 s

  1. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.mzBIN_calibrated 11.4 s [progress: 81189/81189 (100%) - 2932 spectra/s] 27.7s | postprocessing 9.4 s
  2. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.mzBIN_calibrated 9.6 s [progress: 71346/71346 (100%) - 3043 spectra/s] 23.4s | postprocessing 7.2 s
  3. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.mzBIN_calibrated 20.7 s [progress: 96895/96895 (100%) - 2375 spectra/s] 40.8s | postprocessing 12.1 s
  4. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.mzBIN_calibrated 21.2 s [progress: 97728/97728 (100%) - 2393 spectra/s] 40.8s | postprocessing 11.3 s
  5. 2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.mzBIN_calibrated 21.7 s [progress: 100437/100437 (100%) - 2336 spectra/s] 43.0s | postprocessing 12.8 s MAIN SEARCH DONE IN 6.032 MIN

***TOTAL TIME 49.938 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Users/fshikwana/AppData/Local/Temp/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\fshikwana\Box\Backus_Lab\MS_data_raw\2021_03\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[15:23:51] Executing Workspace v3.4.13 INFO[15:23:51] Creating workspace INFO[15:23:51] Done Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[15:23:51] Executing Workspace v3.4.13 INFO[15:23:51] Creating workspace INFO[15:23:51] Done Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[15:23:52] Executing Workspace v3.4.13 INFO[15:23:52] Creating workspace INFO[15:23:52] Done Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[15:23:53] Executing Workspace v3.4.13 INFO[15:23:53] Creating workspace INFO[15:23:53] Done Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[15:23:54] Executing Workspace v3.4.13 INFO[15:23:54] Creating workspace INFO[15:23:54] Done Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-CF3-2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-CF3-2.pepXML PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-JC36-1.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-decoys-_ip2_ip2_data_kbackus_databaseUniprotHuman__contaminant_01-18-2021-correctheaders.fasta.fas ..\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-JC36-1.pepXML PeptideProphet [Work dir: D:\NSP14_isoTOP_NEW\2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55_AJ-C2\fragpipe-2021-03-05-kb-70min_FAIMS_100micron3cv-35-34-55AJ-C2.pepXML-temp] C:\Users\fshikwana\AppData\Local\Temp\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\fshikwana\Box\Backus_Lab\Ashley\2021-03-31-de

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fcyu commented 3 years ago

To be clear, the reason of your first error is due to "not running PeptideProphet, ProteinProphet, and etc...". Mass calibration was performed successfully but there was not many IDs according to the parameter optimization table following that. So, it would be good to turn off mass calibration in the future. But, not matter if you turn it off or not, the search and quantification should be able to finish successfully without any error.

Best,

Fengchao

ashleyjulio commented 3 years ago

Great, I will turn off the mass calibration for future analyses. Thank you so much for your help, I greatly appreciate it!

Best, Ashley Julio

On Thu, Apr 8, 2021 at 10:41 AM Fengchao @.***> wrote:

To be clear, the reason of your first error is due to "not running PeptideProphet, ProteinProphet, and etc...". Mass calibration was performed successfully but there was not many IDs according to the parameter optimization table following that. So, it would be good to turn off mass calibration in the future. But, not matter if you turn it off or not, the search and quantification should be able to finish successfully without any error.

Best,

Fengchao

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fcyu commented 3 years ago

You are welcome.

Best,

Fengchao