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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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batchcoverage' is not recognized as an internal or external command, operable program or batch file #1100

Closed ht-lau closed 1 year ago

ht-lau commented 1 year ago

Hello, Thank you for this great tool. I ran into this error that prevent ProteinPropeht from finishing the task. Do you have any idea how to resolve this?

System OS: Windows 10, Architecture: AMD64 Java Info: 19, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation .NET Core Info: 6.0.401

Version info: FragPipe version 19.1 MSFragger version 3.7 IonQuant version 1.8.10 Philosopher version 4.8.1

LCMS files: Experiment/Group:

22 commands to execute: CheckCentroid java -Xmx40G -cp "E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar;E:\MStools\FragPipe-19.1\tools\batmass-io-1.28.9.jar" com.dmtavt.fragpipe.util.CheckCentroid E:\MSdata\k562\K562_grad2_1_1_2076.d 7 WorkspaceCleanInit [Work dir: E:\MSdata\k562\output] E:\MStools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\MSdata\k562\output] E:\MStools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\LABSTA~1\AppData\Local\Temp\cfd2dbcb-1489-4563-8e25-6c19b2deae8d MSFragger [Work dir: E:\MSdata\k562\output] java -jar -Dfile.encoding=UTF-8 -Xmx40G E:\MStools\MSFragger-3.7\MSFragger-3.7.jar E:\MSdata\k562\output\fragger.params E:\MSdata\k562\K562_grad2_1_1_2076.d E:\MSdata\k562\K562_grad2_1_1_2077.d MSFragger move pepxml java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar;/E:/MStools/FragPipe-19.1/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err E:\MSdata\k562\K562_grad2_1_1_2076.pepXML E:\MSdata\k562\output\K562_grad2_1_1_2076.pepXML MSFragger move pin java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar;/E:/MStools/FragPipe-19.1/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err E:\MSdata\k562\K562_grad2_1_1_2076.pin E:\MSdata\k562\output\K562_grad2_1_1_2076.pin MSFragger move pepxml java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar;/E:/MStools/FragPipe-19.1/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err E:\MSdata\k562\K562_grad2_1_1_2077.pepXML E:\MSdata\k562\output\K562_grad2_1_1_2077.pepXML MSFragger move pin java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar;/E:/MStools/FragPipe-19.1/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err E:\MSdata\k562\K562_grad2_1_1_2077.pin E:\MSdata\k562\output\K562_grad2_1_1_2077.pin MSBooster [Work dir: E:\MSdata\k562\output] java -Xmx40G -cp "E:\MStools\FragPipe-19.1\tools\msbooster-1.1.11.jar;E:\MStools\FragPipe-19.1\tools\batmass-io-1.28.9.jar" Features.MainClass --paramsList E:\MSdata\k562\output\msbooster_params.txt Percolator [Work dir: E:\MSdata\k562\output] E:\MStools\FragPipe-19.1\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms K562_grad2_1_1_2077_percolator_target_psms.tsv --decoy-results-psms K562_grad2_1_1_2077_percolator_decoy_psms.tsv K562_grad2_1_1_2077_edited.pin Percolator [Work dir: E:\MSdata\k562\output] E:\MStools\FragPipe-19.1\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms K562_grad2_1_1_2076_percolator_target_psms.tsv --decoy-results-psms K562_grad2_1_1_2076_percolator_decoy_psms.tsv K562_grad2_1_1_2076_edited.pin Percolator: Convert to pepxml [Work dir: E:\MSdata\k562\output] java -cp E:\MStools\FragPipe-19.1\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML K562_grad2_1_1_2077.pin K562_grad2_1_1_2077 K562_grad2_1_1_2077_percolator_target_psms.tsv K562_grad2_1_1_2077_percolator_decoy_psms.tsv interact-K562_grad2_1_1_2077 DDA 0.5 Percolator: Delete temp java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete E:\MSdata\k562\output\K562_grad2_1_1_2077_percolator_target_psms.tsv Percolator: Delete temp java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete E:\MSdata\k562\output\K562_grad2_1_1_2077_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\MSdata\k562\output] java -cp E:\MStools\FragPipe-19.1\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML K562_grad2_1_1_2076.pin K562_grad2_1_1_2076 K562_grad2_1_1_2076_percolator_target_psms.tsv K562_grad2_1_1_2076_percolator_decoy_psms.tsv interact-K562_grad2_1_1_2076 DDA 0.5 Percolator: Delete temp java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete E:\MSdata\k562\output\K562_grad2_1_1_2076_percolator_target_psms.tsv Percolator: Delete temp java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete E:\MSdata\k562\output\K562_grad2_1_1_2076_percolator_decoy_psms.tsv ProteinProphet [Work dir: E:\MSdata\k562\output] E:\MStools\philosopher_v4.8.1_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\MSdata\k562\output\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: E:\MSdata\k562\output] E:\MStools\philosopher_v4.8.1_windowsamd64\philosopher.exe database --annotate E:\MSdata\k562\2023-05-04-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherFilter [Work dir: E:\MSdata\k562\output] E:\MStools\philosopher_v4.8.1_windowsamd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml E:\MSdata\k562\output --protxml E:\MSdata\k562\output\combined.prot.xml --razor PhilosopherReport [Work dir: E:\MSdata\k562\output] E:\MStools\philosopher_v4.8.1_windows_amd64\philosopher.exe report WorkspaceClean [Work dir: E:\MSdata\k562\output] E:\MStools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [E:\MSdata\k562\output]
    Cmd: [CheckCentroid], Work dir: [E:\MSdata\k562\output]
    Cmd: [WorkspaceCleanInit], Work dir: [E:\MSdata\k562\output]
    Cmd: [MSFragger], Work dir: [E:\MSdata\k562\output]
    Cmd: [MSBooster], Work dir: [E:\MSdata\k562\output]
    Cmd: [Percolator], Work dir: [E:\MSdata\k562\output]
    Cmd: [ProteinProphet], Work dir: [E:\MSdata\k562\output]
    Cmd: [PhilosopherDbAnnotate], Work dir: [E:\MSdata\k562\output]
    Cmd: [PhilosopherFilter], Work dir: [E:\MSdata\k562\output]
    Cmd: [PhilosopherReport], Work dir: [E:\MSdata\k562\output]
    Cmd: [WorkspaceClean], Work dir: [E:\MSdata\k562\output]

>contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries OX=9940 GN=KRT15 PE=2 SV=1
>rev_sp|O43542|XRCC3_HUMAN DNA repair protein XRCC3 OS=Homo sapiens OX=9606 GN=XRCC3 PE=1 SV=1
>rev_sp|P0DMR3|AT8OS_HUMAN Putative protein ATXN8OS OS=Homo sapiens OX=9606 GN=ATXN8OS PE=5 SV=1
>rev_sp|P49746|TSP3_HUMAN Thrombospondin-3 OS=Homo sapiens OX=9606 GN=THBS3 PE=1 SV=1
>rev_sp|Q14160|SCRIB_HUMAN Protein scribble homolog OS=Homo sapiens OX=9606 GN=SCRIB PE=1 SV=5
>rev_sp|Q68DY9|ZN772_HUMAN Zinc finger protein 772 OS=Homo sapiens OX=9606 GN=ZNF772 PE=1 SV=2
>rev_sp|Q8IWF2|FXRD2_HUMAN FAD-dependent oxidoreductase domain-containing protein 2 OS=Homo sapiens OX=9606 GN=FOXRED2 PE=1 SV=1
>rev_sp|Q8WVL7|ANR49_HUMAN Ankyrin repeat domain-containing protein 49 OS=Homo sapiens OX=9606 GN=ANKRD49 PE=1 SV=1
>rev_sp|Q9BRG2|SH23A_HUMAN SH2 domain-containing protein 3A OS=Homo sapiens OX=9606 GN=SH2D3A PE=1 SV=1
>rev_sp|Q9NUQ3|TXLNG_HUMAN Gamma-taxilin OS=Homo sapiens OX=9606 GN=TXLNG PE=1 SV=2
>rev_sp|Q9Y6N5|SQOR_HUMAN Sulfide:quinone oxidoreductase, mitochondrial OS=Homo sapiens OX=9606 GN=SQOR PE=1 SV=1
>sp|O43680|TCF21_HUMAN Transcription factor 21 OS=Homo sapiens OX=9606 GN=TCF21 PE=1 SV=2
>sp|P0DP24|CALM2_HUMAN Calmodulin-2 OS=Homo sapiens OX=9606 GN=CALM2 PE=1 SV=1
>sp|P49910|ZN165_HUMAN Zinc finger protein 165 OS=Homo sapiens OX=9606 GN=ZNF165 PE=1 SV=1
>sp|Q14314|FGL2_HUMAN Fibroleukin OS=Homo sapiens OX=9606 GN=FGL2 PE=1 SV=1
>sp|Q6BAA4|FCRLB_HUMAN Fc receptor-like B OS=Homo sapiens OX=9606 GN=FCRLB PE=1 SV=1
>sp|Q8IWZ6|BBS7_HUMAN Bardet-Biedl syndrome 7 protein OS=Homo sapiens OX=9606 GN=BBS7 PE=1 SV=2
>sp|Q8WWC4|MAIP1_HUMAN m-AAA protease-interacting protein 1, mitochondrial OS=Homo sapiens OX=9606 GN=MAIP1 PE=1 SV=1
>sp|Q9BRX5|PSF3_HUMAN DNA replication complex GINS protein PSF3 OS=Homo sapiens OX=9606 GN=GINS3 PE=1 SV=1
>sp|Q9NVF7|FBX28_HUMAN F-box only protein 28 OS=Homo sapiens OX=9606 GN=FBXO28 PE=1 SV=1
>sp|Q9Y6Z5|AFDDT_HUMAN Putative uncharacterized protein AFDN-DT OS=Homo sapiens OX=9606 GN=AFDN-DT PE=5 SV=1
# FragPipe v19.1ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=E\:\\MSdata\\k562\\2023-05-04-decoys-reviewed-contam-UP000005640.fas

crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=3
diann.run-dia-nn=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=true
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fragpipe-config.bin-ionquant=E\:\\MStools\\IonQuant-1.8.10\\IonQuant-1.8.10.jar
fragpipe-config.bin-msfragger=E\:\\MStools\\MSFragger-3.7\\MSFragger-3.7.jar
fragpipe-config.bin-philosopher=E\:\\MStools\\philosopher_v4.8.1_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\LabStation\\AppData\\Local\\Programs\\Python\\Python39\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=true
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2/3
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
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_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mzml=false
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.glyco_db=
opair.max_glycans=4
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=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.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=00.2
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=00.1
ptmshepherd.diagmine_fragMinSpecDiff=00.1
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=00.2
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
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.max_adducts=0
ptmshepherd.n_glyco=true
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.print_decoys=false
ptmshepherd.prob_dhexOx=2,0.5,0.1
ptmshepherd.prob_dhexY=2,0.5
ptmshepherd.prob_neuacOx=2,0.05,0.2
ptmshepherd.prob_neugcOx=2,0.05,0.2
ptmshepherd.prob_phosphoOx=2,0.05,0.2
ptmshepherd.prob_regY=5,0.5
ptmshepherd.prob_sulfoOx=2,0.05,0.2
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
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.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=E\:\\MSdata\\k562\\output
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.ram=40
workflow.threads=7

CheckCentroid java -Xmx40G -cp "E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar;E:\MStools\FragPipe-19.1\tools\batmass-io-1.28.9.jar" com.dmtavt.fragpipe.util.CheckCentroid E:\MSdata\k562\K562_grad2_1_1_2076.d 7 Done in 0 ms. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\MSdata\k562\output] E:\MStools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[22:25:23] Executing Workspace v4.8.1
INFO[22:25:23] Removing workspace
WARN[22:25:23] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[22:25:23] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\MSdata\k562\output] E:\MStools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\LABSTA~1\AppData\Local\Temp\cfd2dbcb-1489-4563-8e25-6c19b2deae8d INFO[22:25:27] Executing Workspace v4.8.1
INFO[22:25:27] Creating workspace
INFO[22:25:27] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: E:\MSdata\k562\output] java -jar -Dfile.encoding=UTF-8 -Xmx40G E:\MStools\MSFragger-3.7\MSFragger-3.7.jar E:\MSdata\k562\output\fragger.params E:\MSdata\k562\K562_grad2_1_1_2076.d E:\MSdata\k562\K562_grad2_1_1_2077.d MSFragger version MSFragger-3.7 Batmass-IO version 1.28.9 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 19, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 40 GB memory Checking database... Checking spectral files... E:\MSdata\k562\K562_grad2_1_1_2076.d: Scans = 14816 E:\MSdata\k562\K562_grad2_1_1_2077.d: Scans = 10693 ***FIRST SEARCH**** Parameters: num_threads = 7 database_name = E:\MSdata\k562\2023-05-04-decoys-reviewed-contam-UP000005640.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mzml = 0 write_uncalibrated_mgf = false isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 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_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_types = all 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 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 290084 of length 8: 281126 of length 9: 280410 of length 10: 264679 of length 11: 251294 of length 12: 240461 of length 13: 234327 of length 14: 219655 of length 15: 208312 of length 16: 194629 of length 17: 182067 of length 18: 174864 of length 19: 171615 of length 20: 153722 of length 21: 146973 of length 22: 137911 of length 23: 128652 of length 24: 121986 of length 25: 114698 of length 26: 106858 of length 27: 101786 of length 28: 97203 of length 29: 88394 of length 30: 83875 of length 31: 78620 of length 32: 74477 of length 33: 69673 of length 34: 65282 of length 35: 59125 of length 36: 57556 of length 37: 52295 of length 38: 49253 of length 39: 44394 of length 40: 42241 of length 41: 39335 of length 42: 36335 of length 43: 30456 of length 44: 24668 of length 45: 18984 of length 46: 12394 of length 47: 7817 of length 48: 4495 of length 49: 2436 of length 50: 1486 In total 5046903 peptides. Generated 7932326 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 323465482 fragments to be searched in 1 slices (4.82 GB total) Operating on slice 1 of 1: Fragment index slice generated in 5.15 s

  1. K562_grad2_1_1_2076.d loading 99%408.6 s | deisotoping 1.9 s [progress: 95840/95840 (100%) - 12243 spectra/s] 7.8s | postprocessing 0.8 s
  2. K562_grad2_1_1_2077.d loading 99%317.5 s | deisotoping 1.1 s [progress: 76428/76428 (100%) - 13582 spectra/s] 5.6s | postprocessing 0.3 s ***FIRST SEARCH DONE IN 12.666 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 -0.15 2.03 0.05 1.92 -1.51 5.84 -0.17 5.82
002 -0.61 1.95 0.07 1.89 -1.93 5.84 -0.25 5.82
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count skip skip skip 56948 56879 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- -------
Peaks 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- -------
Count 57103 57051 skip rest
------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 57123
------- -------
------- -------
Rm P. 0
------- -------
Count 56957
------- -------

New fragment_mass_tolerance = 15 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 1.862 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 7 database_name = E:\MSdata\k562\2023-05-04-decoys-reviewed-contam-UP000005640.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mzml = 0 write_uncalibrated_mgf = false isotope_error = 0/1/2/3 mass_offsets = 0.0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 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_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = true override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all 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 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 290084 of length 8: 281126 of length 9: 280410 of length 10: 264679 of length 11: 251294 of length 12: 240461 of length 13: 234327 of length 14: 219655 of length 15: 208312 of length 16: 194629 of length 17: 182067 of length 18: 174864 of length 19: 171615 of length 20: 153722 of length 21: 146973 of length 22: 137911 of length 23: 128652 of length 24: 121986 of length 25: 114698 of length 26: 106858 of length 27: 101786 of length 28: 97203 of length 29: 88394 of length 30: 83875 of length 31: 78620 of length 32: 74477 of length 33: 69673 of length 34: 65282 of length 35: 59125 of length 36: 57556 of length 37: 52295 of length 38: 49253 of length 39: 44394 of length 40: 42241 of length 41: 39335 of length 42: 36335 of length 43: 30456 of length 44: 24668 of length 45: 18984 of length 46: 12394 of length 47: 7817 of length 48: 4495 of length 49: 2436 of length 50: 1486 In total 5046903 peptides. Generated 7932326 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.08 Da. 323465482 fragments to be searched in 1 slices (4.82 GB total) Operating on slice 1 of 1: Fragment index slice generated in 4.82 s

  1. K562_grad2_1_1_2076.mzBIN_calibrated 1.6 s [progress: 95584/95584 (100%) - 6848 spectra/s] 14.0s | remapping alternative proteins and postprocessing 10.2 s
  2. K562_grad2_1_1_2077.mzBIN_calibrated 1.4 s [progress: 76252/76252 (100%) - 6911 spectra/s] 11.0s | remapping alternative proteins and postprocessing 7.0 s MAIN SEARCH DONE IN 0.984 MIN

***TOTAL TIME 15.513 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar;/E:/MStools/FragPipe-19.1/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err E:\MSdata\k562\K562_grad2_1_1_2076.pepXML E:\MSdata\k562\output\K562_grad2_1_1_2076.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar;/E:/MStools/FragPipe-19.1/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err E:\MSdata\k562\K562_grad2_1_1_2076.pin E:\MSdata\k562\output\K562_grad2_1_1_2076.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar;/E:/MStools/FragPipe-19.1/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err E:\MSdata\k562\K562_grad2_1_1_2077.pepXML E:\MSdata\k562\output\K562_grad2_1_1_2077.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar;/E:/MStools/FragPipe-19.1/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err E:\MSdata\k562\K562_grad2_1_1_2077.pin E:\MSdata\k562\output\K562_grad2_1_1_2077.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: E:\MSdata\k562\output] java -Xmx40G -cp "E:\MStools\FragPipe-19.1\tools\msbooster-1.1.11.jar;E:\MStools\FragPipe-19.1\tools\batmass-io-1.28.9.jar" Features.MainClass --paramsList E:\MSdata\k562\output\msbooster_params.txt MSBooster v1.1.11 Using 7 threads Generating input file for DIA-NN 58884 unique peptides from 138939 PSMs Writing DIA-NN input file Diann input file generation took 1133 milliseconds Input file at E:\MSdata\k562\output\spectraRT.tsv 58884 unique peptides from 138939 PSMs createFull input file generation took 504 milliseconds Input file at E:\MSdata\k562\output\spectraRT_full.tsv Generating DIA-NN predictions E:\MStools\FragPipe-19.1\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib E:\MSdata\k562\output\spectraRT.tsv --predict --threads 7 --strip-unknown-mods --mod TMT,229.1629 --predict-n-frag 100 DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks) Compiled on Sep 15 2022 18:28:57 Current date and time: Thu May 4 22:41:03 2023 CPU: GenuineIntel Intel(R) Xeon(R) W-2123 CPU @ 3.60GHz SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 Logical CPU cores: 8 Predicted spectra will be saved in a binary format Thread number set to 7 DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option Modification TMT with mass delta 229.163 added to the list of recognised modifications for spectral library-based search Deep learning predictor will predict 100 fragments Cannot find a UniMod modification match for TMT: 73.0618 minimal mass discrepancy; using the original modificaiton name

0 files will be processed [0:00] Loading spectral library E:\MSdata\k562\output\spectraRT.tsv [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 58884 precursors in 55743 elution groups. [0:00] Encoding peptides for spectra and RTs prediction [0:00] Predicting spectra and IMs [0:25] Predicting RTs [0:34] Decoding predicted spectra and IMs [0:35] Decoding RTs [0:35] Saving the list of predictions to E:\MSdata\k562\output\spectraRT.predicted.bin Finished Done generating DIA-NN predictions Model running took 37222 milliseconds Generating edited pin with following features: [unweightedSpectralEntropy, deltaRTLOESS] Loading predicted spectra Processing K562_grad2_1_1_2076_uncalibrated.mzML RT regression using 5000 PSMs Edited pin file at E:\MSdata\k562\output\K562_grad2_1_1_2076_edited.pin Processing K562_grad2_1_1_2077_uncalibrated.mzML RT regression using 5000 PSMs Edited pin file at E:\MSdata\k562\output\K562_grad2_1_1_2077_edited.pin Done in 29596 ms Process 'MSBooster' finished, exit code: 0 Percolator [Work dir: E:\MSdata\k562\output] E:\MStools\FragPipe-19.1\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms K562_grad2_1_1_2077_percolator_target_psms.tsv --decoy-results-psms K562_grad2_1_1_2077_percolator_decoy_psms.tsv K562_grad2_1_1_2077_edited.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: E:\MStools\FragPipe-19.1\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms K562_grad2_1_1_2077_percolator_target_psms.tsv --decoy-results-psms K562_grad2_1_1_2077_percolator_decoy_psms.tsv K562_grad2_1_1_2077_edited.pin Started Thu May 4 22:42:19 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile K562_grad2_1_1_2077_edited.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more 15.9949M unweighted_spectral_entropy delta_RT_loess Found 62180 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 55966 positives and 6214 negatives, size ratio=9.00644 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 23 as initial direction. Could separate 32056 training set positives with q<0.01 in that direction. Split 2: Selected feature 23 as initial direction. Could separate 31965 training set positives with q<0.01 in that direction. Split 3: Selected feature 23 as initial direction. Could separate 31949 training set positives with q<0.01 in that direction. Found 47975 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 1.704 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 49921 PSMs with q<0.01 Iteration 2: Estimated 50037 PSMs with q<0.01 Iteration 3: Estimated 50029 PSMs with q<0.01 Iteration 4: Estimated 50028 PSMs with q<0.01 Iteration 5: Estimated 50031 PSMs with q<0.01 Iteration 6: Estimated 50038 PSMs with q<0.01 Iteration 7: Estimated 50038 PSMs with q<0.01 Iteration 8: Estimated 50041 PSMs with q<0.01 Iteration 9: Estimated 50043 PSMs with q<0.01 Iteration 10: Estimated 50044 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.1563 0.0969 0.1482 retentiontime 0.0000 0.0000 0.0000 rank -0.0702 -0.0799 -0.0456 abs_ppm -0.1390 -0.1160 -0.1340 isotope_errors -0.7877 -0.8348 -1.2058 log10_evalue 1.2975 1.4301 1.5517 hyperscore 0.7202 0.6713 0.6493 delta_hyperscore -0.3748 -0.2815 -0.5444 matched_ion_num -0.6052 -0.7265 -0.6748 complementary_ions -0.0797 -0.1585 -0.0638 ion_series -0.0473 -0.0954 -0.0377 weighted_average_abs_fragment_ppm 0.4994 0.4107 0.4846 peptide_length 0.0000 0.0000 0.0000 ntt -0.2886 -0.3238 -0.3557 nmc 0.0151 -0.0066 0.0070 charge_1 0.1371 0.0995 0.1224 charge_2 -0.0996 -0.0618 -0.0742 charge_3 -0.0945 -0.0868 -0.1089 charge_4 -0.0582 -0.0394 -0.0728 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more -0.1014 -0.1237 -0.1253 15.9949M 0.9085 0.8137 0.8944 unweighted_spectral_entropy -0.6459 -0.6178 -0.6505 delta_RT_loess 2.2189 2.2904 2.5831 m0 Found 50036 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 55966 target PSMs and 6214 decoy PSMs. Calculating q values. Final list yields 50040 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 15.13 cpu seconds or 16 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\MSdata\k562\output] E:\MStools\FragPipe-19.1\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms K562_grad2_1_1_2076_percolator_target_psms.tsv --decoy-results-psms K562_grad2_1_1_2076_percolator_decoy_psms.tsv K562_grad2_1_1_2076_edited.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: E:\MStools\FragPipe-19.1\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms K562_grad2_1_1_2076_percolator_target_psms.tsv --decoy-results-psms K562_grad2_1_1_2076_percolator_decoy_psms.tsv K562_grad2_1_1_2076_edited.pin Started Thu May 4 22:42:36 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile K562_grad2_1_1_2076_edited.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more 15.9949M unweighted_spectral_entropy delta_RT_loess Found 76759 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 68689 positives and 8070 negatives, size ratio=8.51165 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 23 as initial direction. Could separate 39016 training set positives with q<0.01 in that direction. Split 2: Selected feature 23 as initial direction. Could separate 39006 training set positives with q<0.01 in that direction. Split 3: Selected feature 23 as initial direction. Could separate 38980 training set positives with q<0.01 in that direction. Found 58486 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 1.585 cpu seconds or 2 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 60955 PSMs with q<0.01 Iteration 2: Estimated 61089 PSMs with q<0.01 Iteration 3: Estimated 61124 PSMs with q<0.01 Iteration 4: Estimated 61136 PSMs with q<0.01 Iteration 5: Estimated 61136 PSMs with q<0.01 Iteration 6: Estimated 61135 PSMs with q<0.01 Iteration 7: Estimated 61135 PSMs with q<0.01 Iteration 8: Estimated 61135 PSMs with q<0.01 Iteration 9: Estimated 61135 PSMs with q<0.01 Iteration 10: Estimated 61132 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.3149 0.2679 0.2320 retentiontime 0.0000 0.0000 0.0000 rank -0.1047 -0.1073 -0.0886 abs_ppm -0.1322 -0.1205 -0.1110 isotope_errors -1.3041 -1.2850 -0.8783 log10_evalue 1.4212 1.0606 1.2545 hyperscore 0.6020 0.6487 0.5956 delta_hyperscore -0.5069 -0.2149 -0.2589 matched_ion_num -0.7153 -0.7025 -0.6836 complementary_ions -0.0651 0.0813 -0.0395 ion_series -0.0487 -0.0465 -0.0179 weighted_average_abs_fragment_ppm 0.4397 0.5090 0.4365 peptide_length 0.0000 0.0000 0.0000 ntt -0.3212 -0.3149 -0.2707 nmc -0.0213 0.0036 0.0536 charge_1 0.1657 0.1625 0.1370 charge_2 -0.1322 -0.1165 -0.1074 charge_3 -0.0844 -0.0977 -0.0808 charge_4 -0.0143 -0.0873 -0.0703 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more -0.1248 -0.1539 -0.1028 15.9949M 1.0253 1.0590 0.9986 unweighted_spectral_entropy -0.5346 -0.5153 -0.4129 delta_RT_loess 2.6330 2.4624 1.6717 m0 Found 61116 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 68689 target PSMs and 8070 decoy PSMs. Calculating q values. Final list yields 61116 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 30.43 cpu seconds or 30 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\MSdata\k562\output] java -cp E:\MStools\FragPipe-19.1\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML K562_grad2_1_1_2077.pin K562_grad2_1_1_2077 K562_grad2_1_1_2077_percolator_target_psms.tsv K562_grad2_1_1_2077_percolator_decoy_psms.tsv interact-K562_grad2_1_1_2077 DDA 0.5 Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete E:\MSdata\k562\output\K562_grad2_1_1_2077_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete E:\MSdata\k562\output\K562_grad2_1_1_2077_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\MSdata\k562\output] java -cp E:\MStools\FragPipe-19.1\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML K562_grad2_1_1_2076.pin K562_grad2_1_1_2076 K562_grad2_1_1_2076_percolator_target_psms.tsv K562_grad2_1_1_2076_percolator_decoy_psms.tsv interact-K562_grad2_1_1_2076 DDA 0.5 Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete E:\MSdata\k562\output\K562_grad2_1_1_2076_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp E:\MStools\FragPipe-19.1\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete E:\MSdata\k562\output\K562_grad2_1_1_2076_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: E:\MSdata\k562\output] E:\MStools\philosopher_v4.8.1_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\MSdata\k562\output\filelist_proteinprophet.txt INFO[22:43:20] Executing ProteinProphet v4.8.1
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64)) (no FPKM) (no groups) (using degen pep info) Reading in E:\MSdata\k562\output\interact-K562_grad2_1_1_2076.pep.xml... ...read in 47 1+, 43820 2+, 14859 3+, 2107 4+, 165 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in E:\MSdata\k562\output\interact-K562_grad2_1_1_2077.pep.xml... ...read in 40 1+, 38399 2+, 9979 3+, 1387 4+, 131 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 33296 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database E:\MSdata\k562\2023-05-04-decoys-reviewed-contam-UP000005640.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|O60613|SEP15_HUMAN : U MVAMAAGPSGCLVPAFGLRLLLATVLQAVSAFGAEFSSEACRELGFSSNLLCSSCDLLGQFNLLQLDPDCRGCCQEEAQFETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEELSILKWNTDSVEEFLSEKLERI .........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|P22352|GPX3_HUMAN : U MARLLQASCLLSLLLAGFVSQSRGQEKSKMDCHGGISGTIYEYGALTIDGEEYIPFKQYAGKYVLFVNVASYUGLTGQYIELNALQEELAPFGLVILGFPCNQFGKQEPGENSEILPTLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTSELLGTSDRLFWEPMKVHDIRWNFEKFLVGPDGIPIMRWHHRTTVSNVKMDILSYMRRQAALGVKRK ...:.........:.........:.........:.........:.........:.........26000 .....WARNING: Found the following zero-mass residues in protein entry sp|P36969|GPX4_HUMAN : U MSLGRLCRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF ....:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.....WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG ....:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .WARNING: Found the following zero-mass residues in protein entry sp|Q9BVL4|SELO_HUMAN : U MAVYRAALGASLAAARLLPLGRCSPSPAPRSTLSGAAMEPAPRWLAGLRFDNRALRALPVEAPPPGPEGAPSAPRPVPGACFTRVQPTPLRQPRLVALSEPALALLGLGAPPAREAEAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTATGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGVPTTRAGACVTSESTVVRDVFYDGNPKYEQCTVVLRVASTFIRFGSFEIFKSADEHTGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASDSVQRNAAFFREVTRRTARMVAEWQCVGFCHGVLNTDNMSILGLTIDYGPFGFLDRYDPDHVCNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLELGEAILAEEFDAEFQRHYLQKMRRKLGLVQVELEEDGALVSKLLETMHLTGADFTNTFYLLSSFPVELESPGLAEFLARLMEQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSAAELQSRNQGHWADWLQAYRARLDKDLEGAGDAAAWQAEHVRVMHANNPKYVLRNYIAQNAIEAAERGDFSEVRRVLKLLETPYHCEAGAATDAEATEADGADGRQRSYSSKPPLWAAELCVTUSS ........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry sp|Q9C0D9|EPT1_HUMAN : U MAGYEYVSPEQLAGFDKYKYSAVDTNPLSLYVMHPFWNTIVKVFPTWLAPNLITFSGFLLVVFNFLLMAYFDPDFYASAPGHKHVPDWVWIVVGILNFVAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKYNTGILFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKNNTLKLNSVYEAMVPLFSPCLLFILSTAWILWSPSDILELHPRVFYFMVGTAFANSTCQLIVCQMSSTRCPTLNWLLVPLFLVVLVVNLGVASYVESILLYTLTTAFTLAHIHYGVRVVKQLSSHFQIYPFSLRKPNSDULGMEEKNIGL .......:.........:.........:.........:.........:.........38000 .........:.........:.........:........WARNING: Found the following zero-mass residues in protein entry sp|Q9NNW7|TRXR2_HUMAN : U MAAMAVALRGLGGRFRWRTQAVAGGVRGAARGAAAGQRDYDLLVVGGGSGGLACAKEAAQLGRKVAVVDYVEPSPQGTRWGLGGTCVNVGCIPKKLMHQAALLGGLIQDAPNYGWEVAQPVPHDWRKMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVCGVAKGGKEILLSADHIIIATGGRPRYPTHIEGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTIMMRSIPLRGFDQQMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTVLWAIGRVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEGRPELTPIAIMAGRLLVQRLFGGSSDLMDYDNVPTTVFTPLEYGCVGLSEEEAVARHGQEHVEVYHAHYKPLEFTVAGRDASQCYVKMVCLREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG .:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........:.........:. Total: 40910 Computing degenerate peptides for 6255 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 6392 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6392 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6392 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6392 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... 'C:\Users\LABSTA~1\AppData\Local\Temp\cfd2dbcb-1489-4563-8e25-6c19b2deae8d/batchcoverage' is not recognized as an internal or external command, operable program or batch file. panic: Cannot execute program. there was an error with ProteinProphet, please check your parameters and input files

goroutine 1 [running]: philosopher/lib/msg.callLogrus({0xc000306070, 0x6c}, {0xaa0dbc, 0x1?}) /workspace/philosopher/lib/msg/msg.go:319 +0x354 philosopher/lib/msg.ExecutingBinary({0xc19600?, 0xc00017a0e0?}, {0xaa0dbc, 0x5}) /workspace/philosopher/lib/msg/msg.go:209 +0x6e philosopher/lib/ext/proteinprophet.ProteinProphet.Execute({{0xc000086240, 0x5b}, {0xc0000862a0, 0x5c}, {0xc000086300, 0x5c}, {0xc000086240, 0x5b}, {0xc0000862a0, 0x5c}, ...}, ...) /workspace/philosopher/lib/ext/proteinprophet/proteinprophet.go:110 +0x7d2 philosopher/lib/ext/proteinprophet.Run({{0xc0000c24e0, 0x24}, {0xc0000a28d0, 0x15}, {0xc0000a4550, 0x49}, {0xc0000c2510, 0x24}, {0xc00009a660, 0x1b}, ...}, ...) /workspace/philosopher/lib/ext/proteinprophet/proteinprophet.go:62 +0x3b3 philosopher/cmd.glob..func14(0x269b740?, {0xc00006a0f0, 0x1, 0x5}) /workspace/philosopher/cmd/proproph.go:26 +0xb4 github.com/spf13/cobra.(Command).execute(0x269b740, {0xc00006a0a0, 0x5, 0x5}) /home/prvst/go/pkg/mod/github.com/spf13/cobra@v1.6.1/command.go:920 +0x847 github.com/spf13/cobra.(Command).ExecuteC(0x269c2c0) /home/prvst/go/pkg/mod/github.com/spf13/cobra@v1.6.1/command.go:1044 +0x3bd github.com/spf13/cobra.(*Command).Execute(...) /home/prvst/go/pkg/mod/github.com/spf13/cobra@v1.6.1/command.go:968 philosopher/cmd.Execute() /workspace/philosopher/cmd/root.go:35 +0x25 main.main() /workspace/philosopher/main.go:25 +0x90

command "C:\Users\LABSTA~1\AppData\Local\Temp\cfd2dbcb-1489-4563-8e25-6c19b2deae8d/batchcoverage "E:\MSdata\k562\2023-05-04-decoys-reviewed-contam-UP000005640.fas" "C:/Users/LABSTA~1/AppData/Local/Temp/cfd2dbcb-1489-4563-8e25-6c19b2deae8d/combined.prot.xml.covinfo" "C:/Users/LABSTA~1/AppData/Local/Temp/cfd2dbcb-1489-4563-8e25-6c19b2deae8d/combined.prot.xml.cov"" failed: Operation not permitted command "C:\Users\LABSTA~1\AppData\Local\Temp\cfd2dbcb-1489-4563-8e25-6c19b2deae8d/batchcoverage "E:\MSdata\k562\2023-05-04-decoys-reviewed-contam-UP000005640.fas" "C:/Users/LABSTA~1/AppData/Local/Temp/cfd2dbcb-1489-4563-8e25-6c19b2deae8d/combined.prot.xml.covinfo" "C:/Users/LABSTA~1/AppData/Local/Temp/cfd2dbcb-1489-4563-8e25-6c19b2deae8d/combined.prot.xml.cov"" failed with exit code 1 ERRO[22:43:33] Cannot execute program. there was an error with ProteinProphet, please check your parameters and input files Process 'ProteinProphet' finished, exit code: 2 Process returned non-zero exit code, stopping


Cancelling 5 remaining tasks
fcyu commented 1 year ago

We never see this error before. Maybe something was wrong with the temp folder. Could you re-run from ProteinProphet again?

Thanks,

Fengchao

ht-lau commented 1 year ago

It is my antivirus suddenly flagging batchcoverage.exe It is resolved now. Thank you

fcyu commented 1 year ago

No problem.

Best,

Fengchao