Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 0

[animesh]

Describe the bug I am running open workflow in the headless mode over a timsTOF-pro data/file and got the following error

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 0
    at edu.umich.andykong.ptmshepherd.core.FastLocator.getIndex(FastLocator.java:90)
    at edu.umich.andykong.ptmshepherd.peakpicker.PeakAnnotator.getDeltaMassMappings(PeakAnnotator.java:361)
    at edu.umich.andykong.ptmshepherd.PTMShepherd.main(PTMShepherd.java:545)
    Removed 240 peaks with insufficient PSMs
    Created summary table

Is this because of low number of spectra? The protein.tsv has 231 entries though.

If you're submitting a bug report, please attach log file

The log file can be saved from FragPipe:

• by clicking the Export Log button on the Run tab.
• or just copy text from the output console on Run tab to a text file.

System OS: Linux, Architecture: amd64
Java Info: 13.0.2, OpenJDK 64-Bit Server VM, Oracle Corporation

Version info:
FragPipe version 18.0
MSFragger version 3.5
Philosopher version 4.2.2

LCMS files:
  Experiment/Group: 
  - /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.d   DDA

15 commands to execute:
CheckCentroid
java -Xmx128G -cp /cluster/projects/nn9036k/FP18/fragpipe/lib/fragpipe-18.0.jar:/cluster/projects/nn9036k/FP18/fragpipe/tools/batmass-io-1.25.5.jar com.dmtavt.fragpipe.util.CheckCentroid /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.d 40
WorkspaceCleanInit [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher workspace --clean --nocheck
WorkspaceCleanInit [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/5d97b83e-84da-4d5a-9691-c8e08d488724
MSFragger [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
java -jar -Dfile.encoding=UTF-8 -Xmx128G /cluster/projects/nn9036k/FP18/fragpipe/tools/MSFragger-3.5/MSFragger-3.5.jar /cluster/projects/nn9036k/220614_MAthilde/FP18/fragger.params /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.d
MSFragger move pepxml
java -cp /cluster/projects/nn9036k/FP18/fragpipe/lib/fragpipe-18.0.jar:/cluster/projects/nn9036k/FP18/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.pepXML /cluster/projects/nn9036k/220614_MAthilde/FP18/220613_Mathilde_organoid2_Slot1-13_1_1964.pepXML
MSFragger move tsv
java -cp /cluster/projects/nn9036k/FP18/fragpipe/lib/fragpipe-18.0.jar:/cluster/projects/nn9036k/FP18/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.tsv /cluster/projects/nn9036k/220614_MAthilde/FP18/220613_Mathilde_organoid2_Slot1-13_1_1964.tsv
MSFragger move pin
java -cp /cluster/projects/nn9036k/FP18/fragpipe/lib/fragpipe-18.0.jar:/cluster/projects/nn9036k/FP18/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.pin /cluster/projects/nn9036k/220614_MAthilde/FP18/220613_Mathilde_organoid2_Slot1-13_1_1964.pin
PeptideProphet [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database /cluster/projects/nn9036k/220614_MAthilde/2022-06-21-decoys-reviewed-contam-UP000000589.fas --combine 220613_Mathilde_organoid2_Slot1-13_1_1964.pepXML
Rewrite pepxml [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
java -cp /cluster/projects/nn9036k/FP18/fragpipe/lib/* com.dmtavt.fragpipe.util.RewritePepxml /cluster/projects/nn9036k/220614_MAthilde/FP18/interact.pep.xml /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.d
ProteinProphet [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher proteinprophet --maxppmdiff 2000000 --output combined /cluster/projects/nn9036k/220614_MAthilde/FP18/filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher database --annotate /cluster/projects/nn9036k/220614_MAthilde/2022-06-21-decoys-reviewed-contam-UP000000589.fas --prefix rev_
PhilosopherFilter [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher filter --sequential --prot 0.01 --mapmods --tag rev_ --pepxml /cluster/projects/nn9036k/220614_MAthilde/FP18 --protxml /cluster/projects/nn9036k/220614_MAthilde/FP18/combined.prot.xml --razor
PhilosopherReport [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher report
PTMShepherd [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
java -Xmx128G -Dbatmass.io.libs.thermo.dir=/cluster/projects/nn9036k/FP18/fragpipe/tools/MSFragger-3.5/ext/thermo -cp /cluster/projects/nn9036k/FP18/fragpipe/tools/ptmshepherd-2.0.0.jar:/cluster/projects/nn9036k/FP18/fragpipe/tools/batmass-io-1.25.5.jar:/cluster/projects/nn9036k/FP18/fragpipe/tools/commons-math3-3.6.1.jar:/cluster/projects/nn9036k/FP18/fragpipe/tools/hipparchus-1.8/hipparchus-core-1.8.jar:/cluster/projects/nn9036k/FP18/fragpipe/tools/hipparchus-1.8/hipparchus-stat-1.8.jar edu.umich.andykong.ptmshepherd.PTMShepherd "/cluster/projects/nn9036k/220614_MAthilde/FP18/shepherd.config"
WorkspaceClean [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher workspace --clean --nocheck
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [/cluster/projects/nn9036k/220614_MAthilde/FP18]
    Cmd: [CheckCentroid], Work dir: [/cluster/projects/nn9036k/220614_MAthilde/FP18]
    Cmd: [WorkspaceCleanInit], Work dir: [/cluster/projects/nn9036k/220614_MAthilde/FP18]
    Cmd: [MSFragger], Work dir: [/cluster/projects/nn9036k/220614_MAthilde/FP18]
    Cmd: [PeptideProphet], Work dir: [/cluster/projects/nn9036k/220614_MAthilde/FP18]
    Cmd: [ProteinProphet], Work dir: [/cluster/projects/nn9036k/220614_MAthilde/FP18]
    Cmd: [PhilosopherDbAnnotate], Work dir: [/cluster/projects/nn9036k/220614_MAthilde/FP18]
    Cmd: [PhilosopherFilter], Work dir: [/cluster/projects/nn9036k/220614_MAthilde/FP18]
    Cmd: [PhilosopherReport], Work dir: [/cluster/projects/nn9036k/220614_MAthilde/FP18]
    Cmd: [PTMShepherd], Work dir: [/cluster/projects/nn9036k/220614_MAthilde/FP18]
    Cmd: [WorkspaceClean], Work dir: [/cluster/projects/nn9036k/220614_MAthilde/FP18]

~~~~~~~~~~~~~~~~~~~~~~

~~~~~~Sample of /cluster/projects/nn9036k/220614_MAthilde/2022-06-21-decoys-reviewed-contam-UP000000589.fas~~~~~~~
>contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries GN=KRT15 PE=2 SV=1
>rev_sp|O88569|ROA2_MOUSE Heterogeneous nuclear ribonucleoproteins A2/B1 OS=Mus musculus OX=10090 GN=Hnrnpa2b1 PE=1 SV=2
>rev_sp|P41155|TNFC_MOUSE Lymphotoxin-beta OS=Mus musculus OX=10090 GN=Ltb PE=2 SV=1
>rev_sp|Q07104|GDF3_MOUSE Growth/differentiation factor 3 OS=Mus musculus OX=10090 GN=Gdf3 PE=1 SV=2
>rev_sp|Q60773|CDN2D_MOUSE Cyclin-dependent kinase 4 inhibitor D OS=Mus musculus OX=10090 GN=Cdkn2d PE=1 SV=2
>rev_sp|Q7TMM9|TBB2A_MOUSE Tubulin beta-2A chain OS=Mus musculus OX=10090 GN=Tubb2a PE=1 SV=1
>rev_sp|Q8BX09|RBBP5_MOUSE Retinoblastoma-binding protein 5 OS=Mus musculus OX=10090 GN=Rbbp5 PE=1 SV=2
>rev_sp|Q8R3S6|EXOC1_MOUSE Exocyst complex component 1 OS=Mus musculus OX=10090 GN=Exoc1 PE=1 SV=4
>rev_sp|Q9CPV7|ZDHC6_MOUSE Palmitoyltransferase ZDHHC6 OS=Mus musculus OX=10090 GN=Zdhhc6 PE=1 SV=1
>rev_sp|Q9EP93|V1R53_MOUSE Vomeronasal type-1 receptor 53 OS=Mus musculus OX=10090 GN=Vmn1r53 PE=2 SV=1
>rev_sp|Q9Z2I8|SUCB2_MOUSE Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial OS=Mus musculus OX=10090 GN=Suclg2 PE=1 SV=3
>sp|O88721|V2R_MOUSE Vasopressin V2 receptor OS=Mus musculus OX=10090 GN=Avpr2 PE=2 SV=1
>sp|P42567|EPS15_MOUSE Epidermal growth factor receptor substrate 15 OS=Mus musculus OX=10090 GN=Eps15 PE=1 SV=1
>sp|Q08369|GATA4_MOUSE Transcription factor GATA-4 OS=Mus musculus OX=10090 GN=Gata4 PE=1 SV=4
>sp|Q60867|NDF1_MOUSE Neurogenic differentiation factor 1 OS=Mus musculus OX=10090 GN=Neurod1 PE=1 SV=2
>sp|Q7TNC9|I5P1_MOUSE Inositol polyphosphate-5-phosphatase A OS=Mus musculus OX=10090 GN=Inpp5a PE=1 SV=1
>sp|Q8BXQ2|PIGT_MOUSE GPI transamidase component PIG-T OS=Mus musculus OX=10090 GN=Pigt PE=1 SV=2
>sp|Q8R4H2|ARHGC_MOUSE Rho guanine nucleotide exchange factor 12 OS=Mus musculus OX=10090 GN=Arhgef12 PE=1 SV=2
>sp|Q9CQ25|MZT2_MOUSE Mitotic-spindle organizing protein 2 OS=Mus musculus OX=10090 GN=Mzt2 PE=1 SV=1
>sp|Q9EPU0|RENT1_MOUSE Regulator of nonsense transcripts 1 OS=Mus musculus OX=10090 GN=Upf1 PE=1 SV=2
>sp|Q9Z2Z9|GFPT2_MOUSE Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 2 OS=Mus musculus OX=10090 GN=Gfpt2 PE=1 SV=3
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v18.0ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=/cluster/projects/nn9036k/220614_MAthilde/2022-06-21-decoys-reviewed-contam-UP000000589.fas

Table.editor=*
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.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=0.01
diann.unrelated-runs=false
diann.use-predicted-spectra=false
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=/cluster/projects/nn9036k/FP18/fragpipe/tools/IonQuant-1.8.0.jar
fragpipe-config.bin-msfragger=/cluster/projects/nn9036k/FP18/fragpipe/tools/MSFragger-3.5/MSFragger-3.5.jar
fragpipe-config.bin-philosopher=/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher
fragpipe-config.bin-python=/cluster/projects/nn9036k/MC3/bin/python3
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=true
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.label=
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100000
ionquant.medium=
ionquant.minexps=1
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.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=false
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=false
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
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.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=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=true
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.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=-150
msfragger.precursor_mass_mode=corrected
msfragger.precursor_mass_units=0
msfragger.precursor_mass_upper=500
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=stricttrypsin
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=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
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=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=false
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 0.01 --mapmods
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.run-report=true
phi-report.write-mzid=false
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.assign_glycans=true
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=25
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=12.5
ptmshepherd.diagmine_fragMinSpecDiff=25
ptmshepherd.diagmine_minIons=25
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
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=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
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=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=true
ptmshepherd.spectra_maxfragcharge=1
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-psm-validation=true
run-validation-tab=true
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
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
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=10
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=-1
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=-1
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=pool
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=/cluster/projects/nn9036k/220614_MAthilde/FP18
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.process-exps-separately=false
workflow.ram=128
workflow.threads=40

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx128G -cp /cluster/projects/nn9036k/FP18/fragpipe/lib/fragpipe-18.0.jar:/cluster/projects/nn9036k/FP18/fragpipe/tools/batmass-io-1.25.5.jar com.dmtavt.fragpipe.util.CheckCentroid /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.d 40
Process 'CheckCentroid' finished, exit code: 0
Done in 0 ms.
WorkspaceCleanInit [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher workspace --clean --nocheck
time="12:14:27" level=info msg="Executing Workspace  v4.2.2"
time="12:14:27" level=info msg="Removing workspace"
time="12:14:27" level=warning msg="Cannot read file. open .meta/meta.bin: no such file or directory"
time="12:14:27" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/5d97b83e-84da-4d5a-9691-c8e08d488724
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFraggertime="12:14:28" level=info msg="Executing Workspace  v4.2.2"
time="12:14:28" level=info msg="Creating workspace"
time="12:14:28" level=info msg=Done
 [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
java -jar -Dfile.encoding=UTF-8 -Xmx128G /cluster/projects/nn9036k/FP18/fragpipe/tools/MSFragger-3.5/MSFragger-3.5.jar /cluster/projects/nn9036k/220614_MAthilde/FP18/fragger.params /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.d
MSFragger version MSFragger-3.5
Batmass-IO version 1.25.5
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: Linux, Architecture: amd64
Java Info: 13.0.2, OpenJDK 64-Bit Server VM, Oracle Corporation
JVM started with 128 GB memory
Checking database...
Checking spectral files...
/cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.d: Scans = 37770
precursor_mass_mode = CORRECTED does not support specified spectral files. Using SELECTED instead.
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 40
database_name = /cluster/projects/nn9036k/220614_MAthilde/2022-06-21-decoys-reviewed-contam-UP000000589.fas
decoy_prefix = 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_mgf = 0
isotope_error = 0/1
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_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 = 15.994900 M 3
variable_mod_02 = 42.010600 [^ 1
add_A_alanine = 0.000000
add_B_user_amino_acid = 0.000000
add_C_cysteine = 57.021460
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.000000
add_E_glutamic_acid = 0.000000
add_F_phenylalanine = 0.000000
add_G_glycine = 0.000000
add_H_histidine = 0.000000
add_I_isoleucine = 0.000000
add_J_user_amino_acid = 0.000000
add_K_lysine = 0.000000
add_L_leucine = 0.000000
add_M_methionine = 0.000000
add_N_asparagine = 0.000000
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.000000  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.000000
add_Q_glutamine = 0.000000
add_R_arginine = 0.000000
add_S_serine = 0.000000
add_T_threonine = 0.000000
add_U_user_amino_acid = 0.000000  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.000000
add_W_tryptophan = 0.000000
add_X_user_amino_acid = 0.000000
add_Y_tyrosine = 0.000000
add_Z_user_amino_acid = 0.000000
Number of unique peptides
    of length 7: 250996
    of length 8: 244278
    of length 9: 237557
    of length 10: 225602
    of length 11: 217621
    of length 12: 205827
    of length 13: 198732
    of length 14: 187892
    of length 15: 177836
    of length 16: 167859
    of length 17: 156695
    of length 18: 150069
    of length 19: 143794
    of length 20: 133532
    of length 21: 127365
    of length 22: 118113
    of length 23: 111204
    of length 24: 106504
    of length 25: 99260
    of length 26: 93677
    of length 27: 88955
    of length 28: 83414
    of length 29: 76954
    of length 30: 73090
    of length 31: 68970
    of length 32: 64909
    of length 33: 61595
    of length 34: 57271
    of length 35: 52527
    of length 36: 50378
    of length 37: 46331
    of length 38: 43332
    of length 39: 39149
    of length 40: 37022
    of length 41: 34379
    of length 42: 31697
    of length 43: 27479
    of length 44: 21910
    of length 45: 16561
    of length 46: 10808
    of length 47: 6547
    of length 48: 3659
    of length 49: 2091
    of length 50: 1183
In total 4354624 peptides.
Generated 6840793 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.10 Da.
280767676 fragments to be searched in 1 slices (4.18 GB total)
Operating on slice 1 of 1: 
    Fragment index slice generated in 2.29 s
    001. 220613_Mathilde_organoid2_Slot1-13_1_1964.d ​
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    001. 220613_Mathilde_organoid2_Slot1-13_1_1964.d loading 98%​
    001. 220613_Mathilde_organoid2_Slot1-13_1_1964.d loading 99%606.4 s | deisotoping 2.0 s
        [progress: 29247/29247 (100%) - 5406 spectra/s] 5.4s | postprocessing 0.2 s
***************************FIRST SEARCH DONE IN 10.793 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |  -4.63   1.75 |  -0.02   1.75 |  -4.72   5.36 |  -0.48   4.47  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count | skip  | skip  |    215|    221|    217| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |    181|    181|    177| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |    171
-------|-------
-------|-------
 Rm P. |    0  
-------|-------
 Count |    170
-------|-------
New fragment_mass_tolerance = 15 PPM
New use_topN_peaks = 200
New minimum_ratio = 0.000000
New intensity_transform = 0
New remove_precursor_peak = 1
New precursor_true_tolerance = 9.000000 PPM (tie breaker)
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.672 MIN*********

************************************MAIN SEARCH************************************
Checking database...
Parameters:
num_threads = 40
database_name = /cluster/projects/nn9036k/220614_MAthilde/2022-06-21-decoys-reviewed-contam-UP000000589.fas
decoy_prefix = rev_
precursor_mass_lower = -150.0
precursor_mass_upper = 500.0
precursor_mass_units = 0
data_type = 0
precursor_true_tolerance = 9.0
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_mgf = 0
isotope_error = 0
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = true
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = 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 = 200
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.0
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 = 15.994900 M 3
variable_mod_02 = 42.010600 [^ 1
add_A_alanine = 0.000000
add_B_user_amino_acid = 0.000000
add_C_cysteine = 57.021460
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.000000
add_E_glutamic_acid = 0.000000
add_F_phenylalanine = 0.000000
add_G_glycine = 0.000000
add_H_histidine = 0.000000
add_I_isoleucine = 0.000000
add_J_user_amino_acid = 0.000000
add_K_lysine = 0.000000
add_L_leucine = 0.000000
add_M_methionine = 0.000000
add_N_asparagine = 0.000000
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.000000  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.000000
add_Q_glutamine = 0.000000
add_R_arginine = 0.000000
add_S_serine = 0.000000
add_T_threonine = 0.000000
add_U_user_amino_acid = 0.000000  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.000000
add_W_tryptophan = 0.000000
add_X_user_amino_acid = 0.000000
add_Y_tyrosine = 0.000000
add_Z_user_amino_acid = 0.000000
Number of unique peptides
    of length 7: 250996
    of length 8: 244278
    of length 9: 237557
    of length 10: 225602
    of length 11: 217621
    of length 12: 205827
    of length 13: 198732
    of length 14: 187892
    of length 15: 177836
    of length 16: 167859
    of length 17: 156695
    of length 18: 150069
    of length 19: 143794
    of length 20: 133532
    of length 21: 127365
    of length 22: 118113
    of length 23: 111204
    of length 24: 106504
    of length 25: 99260
    of length 26: 93677
    of length 27: 88955
    of length 28: 83414
    of length 29: 76954
    of length 30: 73090
    of length 31: 68970
    of length 32: 64909
    of length 33: 61595
    of length 34: 57271
    of length 35: 52527
    of length 36: 50378
    of length 37: 46331
    of length 38: 43332
    of length 39: 39149
    of length 40: 37022
    of length 41: 34379
    of length 42: 31697
    of length 43: 27479
    of length 44: 21910
    of length 45: 16561
    of length 46: 10808
    of length 47: 6547
    of length 48: 3659
    of length 49: 2091
    of length 50: 1183
In total 4354624 peptides.
Generated 6840793 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.01 Da.
561535352 fragments to be searched in 1 slices (8.37 GB total)
Operating on slice 1 of 1: 
    Fragment index slice generated in 4.62 s
    001. 220613_Mathilde_organoid2_Slot1-13_1_1964.mzBIN_calibrated 1.3 s
        [progress: 1599/27436 (6%) - 160 spectra/s]​
        [progress: 16861/27436 (61%) - 841 spectra/s]​
        [progress: 24386/27436 (89%) - 811 spectra/s]​
        [progress: 27436/27436 (100%) - 702 spectra/s] 39.1s | ramaping alternative proteins and postprocessing 4.5 s
***************************MAIN SEARCH DONE IN 0.921 MIN***************************

*******************************TOTAL TIME 12.387 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
java -cp /cluster/projects/nn9036k/FP18/fragpipe/lib/fragpipe-18.0.jar:/cluster/projects/nn9036k/FP18/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.pepXML /cluster/projects/nn9036k/220614_MAthilde/FP18/220613_Mathilde_organoid2_Slot1-13_1_1964.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move tsv
java -cp /cluster/projects/nn9036k/FP18/fragpipe/lib/fragpipe-18.0.jar:/cluster/projects/nn9036k/FP18/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.tsv /cluster/projects/nn9036k/220614_MAthilde/FP18/220613_Mathilde_organoid2_Slot1-13_1_1964.tsv
Process 'MSFragger move tsv' finished, exit code: 0
MSFragger move pin
java -cp /cluster/projects/nn9036k/FP18/fragpipe/lib/fragpipe-18.0.jar:/cluster/projects/nn9036k/FP18/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.pin /cluster/projects/nn9036k/220614_MAthilde/FP18/220613_Mathilde_organoid2_Slot1-13_1_1964.pin
Process 'MSFragger move pin' finished, exit code: 0
PeptideProphet [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database /cluster/projects/nn9036k/220614_MAthilde/2022-06-21-decoys-reviewed-contam-UP000000589.fas --combine 220613_Mathilde_organoid2_Slot1-13_1_1964.pepXML
time="12:26:55" level=info msg="Executing PeptideProphet  v4.2.2"
Unknown file type. No file loaded./cluster/projects/nn9036k/220614_MAthilde/FP18/220613_Mathilde_organoid2_Slot1-13_1_1964.d
Unknown file type. No file loaded./cluster/projects/nn9036k/220614_MAthilde/FP18/220613_Mathilde_organoid2_Slot1-13_1_1964.d
 file 1: /cluster/projects/nn9036k/220614_MAthilde/FP18/220613_Mathilde_organoid2_Slot1-13_1_1964.pepXML
 processed altogether 15451 results
INFO: Results written to file: /cluster/projects/nn9036k/220614_MAthilde/FP18/interact.pep.xml

  - /cluster/projects/nn9036k/220614_MAthilde/FP18/interact.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
using search_offsets in mass mixture distr: 0
init with X! Tandem stricttrypsin 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906251008-exported (Linux-x86_64)) AKeller@ISB
 read in 1941 1+, 9988 2+, 2266 3+, 929 4+, 327 5+, 0 6+, and 0 7+ spectra.
Found 7320 Decoys, and 8131 Non-Decoys
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...
Iterations: .........10.........20.......
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (2+).
WARNING: Mixture model quality test failed for charge (3+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 28 iterations
Process 'PeptideProphet' finished, exit code: 0
time="12:27:11" level=info msg=Done
Rewrite pepxml [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
java -cp /cluster/projects/nn9036k/FP18/fragpipe/lib/* com.dmtavt.fragpipe.util.RewritePepxml /cluster/projects/nn9036k/220614_MAthilde/FP18/interact.pep.xml /cluster/projects/nn9036k/220614_MAthilde/220613_Mathilde_organoid2_Slot1-13_1_1964.d
Fixing pepxml: /cluster/projects/nn9036k/220614_MAthilde/FP18/interact.pep.xml
Writing output to: /cluster/projects/nn9036k/220614_MAthilde/FP18/interact.pep.xml17832510730922153471.temp-rewrite
Deleting file: /cluster/projects/nn9036k/220614_MAthilde/FP18/interact.pep.xml
Moving rewritten file to original location: [/cluster/projects/nn9036k/220614_MAthilde/FP18/interact.pep.xml17832510730922153471.temp-rewrite] -> [/cluster/projects/nn9036k/220614_MAthilde/FP18/interact.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
ProteinProphet [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher proteinprophet --maxppmdiff 2000000 --output combined /cluster/projects/nn9036k/220614_MAthilde/FP18/filelist_proteinprophet.txt
time="12:27:14" level=info msg="Executing ProteinProphet  v4.2.2"
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105021430-exported (Linux-x86_64))
 (no FPKM) (no groups) (using degen pep info)
Reading in /cluster/projects/nn9036k/220614_MAthilde/FP18/interact.pep.xml...
...read in 0 1+, 0 2+, 0 3+, 730 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 717 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database /cluster/projects/nn9036k/220614_MAthilde/2022-06-21-decoys-reviewed-contam-UP000000589.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:......  Total: 34460
Computing degenerate peptides for 710 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 717 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 717 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=6.29639e-06, db_size=38941855
Computing MU for 717 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
time="12:27:15" level=info msg=Done
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher database --annotate /cluster/projects/nn9036k/220614_MAthilde/2022-06-21-decoys-reviewed-contam-UP000000589.fas --prefix rev_
time="12:27:15" level=info msg="Executing Database  v4.2.2"
time="12:27:15" level=info msg="Annotating the database"
time="12:27:18" level=info msg=Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher filter --sequential --prot 0.01 --mapmods --tag rev_ --pepxml /cluster/projects/nn9036k/220614_MAthilde/FP18 --protxml /cluster/projects/nn9036k/220614_MAthilde/FP18/combined.prot.xml --razor
time="12:27:18" level=info msg="Executing Filter  v4.2.2"
time="12:27:18" level=info msg="Processing peptide identification files"
time="12:27:18" level=info msg="Parsing /cluster/projects/nn9036k/220614_MAthilde/FP18/interact.pep.xml"
time="12:27:19" level=info msg="1+ Charge profile" decoy=0 target=0
time="12:27:19" level=info msg="2+ Charge profile" decoy=0 target=0
time="12:27:19" level=info msg="3+ Charge profile" decoy=0 target=0
time="12:27:19" level=info msg="4+ Charge profile" decoy=240 target=490
time="12:27:19" level=info msg="5+ Charge profile" decoy=0 target=0
time="12:27:19" level=info msg="6+ Charge profile" decoy=0 target=0
time="12:27:19" level=info msg="Database search results" ions=717 peptides=716 psms=730
time="12:27:19" level=info msg="Converged to 0.82 % FDR with 242 PSMs" decoy=2 threshold=0.8097 total=244
time="12:27:19" level=info msg="Converged to 0.84 % FDR with 237 Peptides" decoy=2 threshold=0.8097 total=239
time="12:27:19" level=info msg="Converged to 0.84 % FDR with 237 Ions" decoy=2 threshold=0.8097 total=239
time="12:27:19" level=info msg="Protein inference results" decoy=232 target=469
time="12:27:19" level=info msg="Converged to 1.30 % FDR with 231 Proteins" decoy=3 threshold=0.8059 total=234
time="12:27:19" level=info msg="Applying sequential FDR estimation" ions=239 peptides=239 psms=244
time="12:27:19" level=info msg="Converged to 0.82 % FDR with 242 PSMs" decoy=2 threshold=0.8097 total=244
time="12:27:19" level=info msg="Converged to 0.84 % FDR with 237 Peptides" decoy=2 threshold=0.8097 total=239
time="12:27:19" level=info msg="Converged to 0.84 % FDR with 237 Ions" decoy=2 threshold=0.8097 total=239
time="12:27:19" level=info msg="Post processing identifications"
time="12:27:19" level=info msg="Mapping modifications"
time="12:27:19" level=info msg="Assigning protein identifications to layers"
time="12:27:19" level=info msg="Processing protein inference"
time="12:27:20" level=info msg="Synchronizing PSMs and proteins"
time="12:27:20" level=info msg="Total report numbers after FDR filtering, and post-processing" ions=237 peptides=237 proteins=231 psms=242
time="12:27:20" level=info msg=Saving
time="12:27:20" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
/cluster/projects/nn9036k/FP18/fragpipe/tools/philosopher_v4.2.2_linux_amd64/philosopher report
time="12:27:20" level=info msg="Executing Report  v4.2.2"
time="12:27:20" level=info msg="Creating reports"
time="12:27:20" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PTMShepherd [Work dir: /cluster/projects/nn9036k/220614_MAthilde/FP18]
java -Xmx128G -Dbatmass.io.libs.thermo.dir=/cluster/projects/nn9036k/FP18/fragpipe/tools/MSFragger-3.5/ext/thermo -cp /cluster/projects/nn9036k/FP18/fragpipe/tools/ptmshepherd-2.0.0.jar:/cluster/projects/nn9036k/FP18/fragpipe/tools/batmass-io-1.25.5.jar:/cluster/projects/nn9036k/FP18/fragpipe/tools/commons-math3-3.6.1.jar:/cluster/projects/nn9036k/FP18/fragpipe/tools/hipparchus-1.8/hipparchus-core-1.8.jar:/cluster/projects/nn9036k/FP18/fragpipe/tools/hipparchus-1.8/hipparchus-stat-1.8.jar edu.umich.andykong.ptmshepherd.PTMShepherd "/cluster/projects/nn9036k/220614_MAthilde/FP18/shepherd.config"

PTM-Shepherd version 2.0.0
(c) 2022 University of Michigan

Using Java 13.0.2 on 131072MB memory

Finding spectral data
    Indexing data from dataset01
Done finding spectral data

peaks.tsv
/cluster/projects/nn9036k/220614_MAthilde/FP18/peaks.tsv
peaksummary.annotated.tsv
/cluster/projects/nn9036k/220614_MAthilde/FP18/peaksummary.annotated.tsv
peaksummary.tsv
/cluster/projects/nn9036k/220614_MAthilde/FP18/peaksummary.tsv
combined.tsv
/cluster/projects/nn9036k/220614_MAthilde/FP18/combined.tsv

Caching spectral data
    Caching data from dataset01
        220613_Mathilde_organoid2_Slot1-13_1_1964 - 242 (3405 ms, 130 ms)
    Done caching data from dataset01
Done caching spectral data

Counting MS2 scans for dataset dataset01
    242 MS2 scans present in dataset dataset01
Done counting MS2 scans for dataset dataset01

Creating combined histogram
    Generated histogram file for dataset dataset01 [-154 - 502]
Done creating combined histogram

Running peak picking
    Picked top 240 peaks
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 0
    at edu.umich.andykong.ptmshepherd.core.FastLocator.getIndex(FastLocator.java:90)
    at edu.umich.andykong.ptmshepherd.peakpicker.PeakAnnotator.getDeltaMassMappings(PeakAnnotator.java:361)
    at edu.umich.andykong.ptmshepherd.PTMShepherd.main(PTMShepherd.java:545)
    Removed 240 peaks with insufficient PSMs
    Created summary table
Done running peak picking

Annotated summary table

Mapping modifications back into PSM lists

[danielgeiszler]

You have zero MS1 peaks that passed PTM-Shepherd's minimum PSM cutoff, which is why this happened. If you think your data is fine then you can reduce PTM-Shepherd's minimum PSMs to 1, but I don't think your data is fine.

There are quite a few strange things here...

WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+).

Only charge state 4 peptides passed filtering.

You have 242 PSMs and 231 proteins out of 29000 spectra, so less than 1% recovery.

Please check your parameters.

[fcyu]

Hi @danielgeiszler ,

Can you make PTM-S give a more informative message in this case?

Thanks,

Fengchao

[danielgeiszler]

@fcyu Yes, PTM-Shepherd should crash more gracefully here and I can fix that. But datasets with <1% of spectra identified should probably be throwing errors or warnings much earlier.

[animesh]

Thanks @danielgeiszler for looking into this. I ran MaxQuant before and it has even worse IDs <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

MS | MS/MS | MS/MS identified -- | -- | -- 25564 | 37770 | 112 25564 | 37770 | 112

so i thought may be open-search will discover what could be the reason. Is there some other way to discover what the other ~99% spectra representing then?

[danielgeiszler]

Check that you’re searching the right database. Is your data mouse? Does it have any modifications you should be including, like TMT?

On Jun 22, 2022, at 03:50, Ani @.***> wrote:

 Thanks @danielgeiszler for looking into this. I ran MaxQuant before and it has even worse IDs

MS MS/MS MS/MS identified 25564 37770 112 25564 37770 112 so i thought may be open-search will discover what could be the reason. Is there some other way to discover what the other ~99% spectra representing then?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

[animesh]

AFAIK, it is mouse sample with no labels 👍

But if this is information is incorrect, my understanding is that open-search should be able to find the labels if they lie between -100-+500 Da. I see this with for example SILAC, open search gets it right but probably i misunderstand how open-search is working? Also, if i run this data against the whole uniprot, will that pick up the species correctly in case we have contamination or given the number of possible matches, FDR will too high/signal gets drowned?

[fcyu]

Hi @animesh ,

You also need to check our enzyme and species.

Best,

Fengchao

[animesh]

Trypsin protease, Species Mouse AFAIK @fcyu 👍

[danielgeiszler]

If you have labels on both termini (which is common for TMT) open searches will struggle to find any IDs. It still requires some fragment ions to be in their expected positions, either unshifted or shifted by the peptide’s delta mass (if localization is on in MSFragger). You need to include the labels as variable mods when you do this.

But as Fengchao said, there are other problems that it might be.

On Jun 23, 2022, at 09:35, Fengchao @.***> wrote:

 Hi @animesh ,

You also need to check our enzyme and species.

Best,

Fengchao

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

[fcyu]

Hi @animesh ,

I think it is already beyond the scope of the GitHub issue. We normally only answer questions regarding using our tools. As to the general research questions, please discuss with your supervisor. I will close this issue if there is no more question about our tools.

Best,

Fengchao