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Nesvilab / MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
https://msfragger.nesvilab.org
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MSFragger 3.1.1 on Linux couldn't find optimal parameters after mass calibration #103

Closed merbllab closed 4 years ago

merbllab commented 4 years ago
Hi, I run MSFragger 3.1.1 on linux system with calibrate_mass = 2. it calibrate the masses but didn't find any optimal parameters. when I run MSFragger through FragPipe on the same database with same params it successfully allocate optimal parameters. this is how it looks in FragPipe: **MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 5.00 2.40 -0.01 2.00 1.77 2.85 -0.08 3.25
002 4.55 1.67 0.11 1.39 1.67 3.30 -0.07 3.61
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- MS2 7 10 15 20 25 30
Count 2245 947 skip rest
------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- -------
Peaks 300_0 200_0 150_1 100_1
------- ------- ------- ------- -------
Count 2245 2929 2677 skip rest
------- ------- ------- ------- -------
------- -------
Int. 0
------- -------
Count 2736
------- -------
------- -------
Rm P. 0
------- -------
Count 2946
------- -------

New fragment_mass_tolerance = 7 PPM New use_topN_peaks = 200 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 0 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 9.483 MIN*****

this is how it looks like in stand alone MSFragger in linux: ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 5.03 2.56 0.11 1.94 1.73 2.88 -0.15 3.24
002 4.51 1.67 0.25 1.33 1.66 3.27 -0.18 3.61
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- MS2 7 10 15 20 25 30
Count 0 0 0 0 0 0
------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- -------
Peaks 300_0 200_0 150_1 100_1
------- ------- ------- ------- -------
Count 0 0 0 1
------- ------- ------- ------- -------
------- -------
Int. 0
------- -------
Count 0
------- -------
------- -------
Rm P. 0
------- -------
Count 1
------- -------

New fragment_mass_tolerance = 20 PPM New use_topN_peaks = 100 New minimum_ratio = 0.010000 New intensity_transform = 1 New remove_precursor_peak = 0

full log file is attached. LOG-MSFragger_mass_calib-346894.txt

fcyu commented 4 years ago

I think your two searches have different parameters because the calibration measures are different.

-----|---------------|---------------|---------------|---------------
| MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New)
-----|---------------|---------------|---------------|---------------
Run | Median MAD | Median MAD | Median MAD | Median MAD
001 | 5.00 2.40 | -0.01 2.00 | 1.77 2.85 | -0.08 3.25

vs

-----|---------------|---------------|---------------|---------------
| MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New)
-----|---------------|---------------|---------------|---------------
Run | Median MAD | Median MAD | Median MAD | Median MAD
001 | 5.03 2.56 | 0.11 1.94 | 1.73 2.88 | -0.15 3.24

Could you send me both logs?

Thanks,

Fengchao

merbllab commented 4 years ago

Hi

Attached is the log of FragPipe.

The stand-alone MSFragger log was attached in the previous mail

Thanks

Assaf

From: Fengchao notifications@github.com Sent: Saturday, October 10, 2020 3:25 PM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: merbllab assafkacen@gmail.com; Author author@noreply.github.com Subject: Re: [Nesvilab/MSFragger] MSFragger 3.1.1 on Linux couldn't find optimal parameters after mass calibration (#103)

I think your two searches have different parameters because the calibration measures are different.

----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 5.00 2.40 -0.01 2.00 1.77 2.85 -0.08 3.25

vs

----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 5.03 2.56 0.11 1.94 1.73 2.88 -0.15 3.24

Could you send me both logs?

Thanks,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/103#issuecomment-706541141 , or unsubscribe https://github.com/notifications/unsubscribe-auth/APGKVN56RHRV4AYDPP6AOV3SKBHALANCNFSM4SLAPPDA . https://github.com/notifications/beacon/APGKVNYLFKZBOYLVUQU3XZ3SKBHALA5CNFSM4SLAPPDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOFIOPMVI.gif

System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_144, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 14.1-build2 MSFragger version 3.1.1 Philosopher version 3.3.11 (build 1601497354)

LCMS files: Experiment/Group: U-87

23 commands to execute: WorkspaceCleanInit [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\PXD003790-fragpipe_test\analysis_6] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\PXD003790-fragpipe_test\analysis_6] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --init --nocheck MsFragger [Work dir: D:\PXD003790-fragpipe_test\analysis_6] C:\ProgramData\Anaconda3\python.exe D:\FragPipe-14.1-build2\fragpipe\tools\msfragger_pep_split.py 4 "java -jar -Dfile.encoding=UTF-8 -Xmx21G" X:\assafk\Pipeline_30\external_software\MSFragger-3.1.1\MSFragger-3.1.1.jar D:\PXD003790-fragpipe_test\analysis_6\fragger.params D:\PXD003790-fragpipe_test\Seq44762_QE2.mzML D:\PXD003790-fragpipe_test\Seq44763_QE2.mzML MsFragger move pepxml java -cp D:\FragPipe-14.1-build2\fragpipe\lib\fragpipe-14.1-build2.jar com.github.chhh.utils.FileMove D:\PXD003790-fragpipe_test\Seq44762_QE2.pepXML D:\PXD003790-fragpipe_test\analysis_6\U-87\Seq44762_QE2.pepXML MsFragger move pepxml java -cp D:\FragPipe-14.1-build2\fragpipe\lib\fragpipe-14.1-build2.jar com.github.chhh.utils.FileMove D:\PXD003790-fragpipe_test\Seq44763_QE2.pepXML D:\PXD003790-fragpipe_test\analysis_6\U-87\Seq44763_QE2.pepXML PeptideProphet: Workspace init [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87\fragpipe-Seq44763_QE2.pepXML-temp] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87\fragpipe-Seq44762_QE2.pepXML-temp] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87\fragpipe-Seq44763_QE2.pepXML-temp] D:\FragPipe-14.0\philosopher_v3.3.11_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --decoy rev --database X:\assafk\database\2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas ..\Seq44763_QE2.pepXML PeptideProphet [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87\fragpipe-Seq44762_QE2.pepXML-temp] D:\FragPipe-14.0\philosopher_v3.3.11_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --decoy rev --database X:\assafk\database\2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas ..\Seq44762_QE2.pepXML PeptideProphet: Delete temp java -cp D:\FragPipe-14.1-build2\fragpipe\lib\fragpipe-14.1-build2.jar com.github.chhh.utils.FileDelete D:\PXD003790-fragpipe_test\analysis_6\U-87\fragpipe-Seq44763_QE2.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-14.1-build2\fragpipe\lib\fragpipe-14.1-build2.jar com.github.chhh.utils.FileDelete D:\PXD003790-fragpipe_test\analysis_6\U-87\fragpipe-Seq44762_QE2.pepXML-temp Rewrite pepxml [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87] java -cp D:\FragPipe-14.1-build2\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44762_QE2.pep.xml D:\PXD003790-fragpipe_test\Seq44762_QE2.mzML Rewrite pepxml [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87] java -cp D:\FragPipe-14.1-build2\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44763_QE2.pep.xml D:\PXD003790-fragpipe_test\Seq44763_QE2.mzML ProteinProphet [Work dir: D:\PXD003790-fragpipe_test\analysis_6] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44763_QE2.pep.xml D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44762_QE2.pep.xml PhilosopherDbAnnotate [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe database --annotate X:\assafk\database\2020-10-07-decoys-contam-Human_SP27042020.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\PXD003790-fragpipe_test\analysis_6] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe database --annotate X:\assafk\database\2020-10-07-decoys-contam-Human_SP27042020.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87] D:\FragPipe-14.0\philosopher_v3.3.11_windowsamd64\philosopher.exe filter --sequential --razor --prot 1 --tag rev --pepxml D:\PXD003790-fragpipe_test\analysis_6\U-87 --protxml D:\PXD003790-fragpipe_test\analysis_6\combined.prot.xml PhilosopherReport [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe report IonQuant [Work dir: D:\PXD003790-fragpipe_test\analysis_6] java -Xmx21G -Dlibs.bruker.dir="X:\assafk\Pipeline_30\external_software\MSFragger-3.1.1\ext\bruker" -Dlibs.thermo.dir="X:\assafk\Pipeline_30\external_software\MSFragger-3.1.1\ext\thermo" -cp "D:\FragPipe-14.1-build2\fragpipe\tools\ionquant-1.4.5.jar;D:\FragPipe-14.1-build2\fragpipe\tools\batmass-io-1.19.5.jar" ionquant.IonQuant --threads 6 --ionmobility 0 --mbr 1 --proteinquant 2 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 1 --writeindex 0 --tp 3 --minfreq 0.5 --minions 1 --minexps 1 --psm U-87\psm.tsv --multidir . --specdir D:\PXD003790-fragpipe_test U-87\Seq44763_QE2.pepXML U-87\Seq44762_QE2.pepXML WorkspaceClean [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\PXD003790-fragpipe_test\analysis_6] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [D:\PXD003790-fragpipe_test\analysis_6]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\PXD003790-fragpipe_test\analysis_6\U-87]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\PXD003790-fragpipe_test\analysis_6]
    Cmd: [MsFragger], Work dir: [D:\PXD003790-fragpipe_test\analysis_6]
    Cmd: [PeptideProphet], Work dir: [D:\PXD003790-fragpipe_test\analysis_6]
    Cmd: [ProteinProphet], Work dir: [D:\PXD003790-fragpipe_test\analysis_6]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\PXD003790-fragpipe_test\analysis_6]
    Cmd: [PhilosopherFilter], Work dir: [D:\PXD003790-fragpipe_test\analysis_6]
    Cmd: [PhilosopherReport], Work dir: [D:\PXD003790-fragpipe_test\analysis_6]
    Cmd: [IonQuant], Work dir: [D:\PXD003790-fragpipe_test\analysis_6]
    Cmd: [WorkspaceClean], Work dir: [D:\PXD003790-fragpipe_test\analysis_6\U-87]
    Cmd: [WorkspaceClean], Work dir: [D:\PXD003790-fragpipe_test\analysis_6]

# FragPipe v14.1-build2ui state cache

crystalc.run-crystalc=false
database.db-path=X\:\\assafk\\database\\2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=X\:\\assafk\\Pipeline_30\\external_software\\MSFragger-3.1.1\\MSFragger-3.1.1.jar
fragpipe-config.bin-philosopher=D\:\\FragPipe-14.0\\philosopher_v3.3.11_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=1
ionquant.minisotopes=1
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=15
msfragger.digest_min_length=8
msfragger.fragment_ion_series=a,b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=1
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1
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=4
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=5
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.00
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=200
msfragger.misc.fragger.enzyme-dropdown=nonspecific
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=4
msfragger.num_enzyme_termini=0
msfragger.output_format=pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=5
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=15
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=
msfragger.search_enzyme_cutafter=-
msfragger.search_enzyme_name=nonspecific
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),false,-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,2; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQ,false,1; -18.010600,nE,false,1; 119.004100,C,false,1; 0.984020,N,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=300
msfragger.write_calibrated_mgf=true
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 1
phi-report.pep-level-summary=false
phi-report.print-decoys=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.diag_ions=
ptmshepherd.glyco_mode=false
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_background=4
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
speclibgen.easypqp.extras.rt_lowess_fraction=0.05
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tmtintegrator.add_Ref=-1
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=0
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\PXD003790-fragpipe_test\\analysis_6
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=6

WorkspaceCleanInit [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[18:11:49] Executing Workspace v3.3.11
INFO[18:11:49] Removing workspace
WARN[18:11:49] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[18:11:49] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[18:12:05] Executing Workspace v3.3.11
INFO[18:12:05] Creating workspace
INFO[18:12:05] Done
WorkspaceCleanInit [Work dir: D:\PXD003790-fragpipe_test\analysis_6] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[18:12:20] Executing Workspace v3.3.11
INFO[18:12:20] Removing workspace
WARN[18:12:20] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[18:12:20] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\PXD003790-fragpipe_test\analysis_6] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --init --nocheck INFO[18:12:35] Executing Workspace v3.3.11
INFO[18:12:35] Creating workspace
INFO[18:12:35] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MsFragger [Work dir: D:\PXD003790-fragpipe_test\analysis_6] C:\ProgramData\Anaconda3\python.exe D:\FragPipe-14.1-build2\fragpipe\tools\msfragger_pep_split.py 4 "java -jar -Dfile.encoding=UTF-8 -Xmx21G" X:\assafk\Pipeline_30\external_software\MSFragger-3.1.1\MSFragger-3.1.1.jar D:\PXD003790-fragpipe_test\analysis_6\fragger.params D:\PXD003790-fragpipe_test\Seq44762_QE2.mzML D:\PXD003790-fragpipe_test\Seq44763_QE2.mzML ['java', '-jar', '-Dfile.encoding=UTF-8', '-Xmx21G', WindowsPath('//data.wexac.weizmann.ac.il/yifatlab/assafk/Pipeline_30/external_software/MSFragger-3.1.1/MSFragger-3.1.1.jar'), WindowsPath('D:/PXD003790-fragpipe_test/analysis_6/split_peptide_index_tempdir/fragger.params'), '--split1', WindowsPath('D:/PXD003790-fragpipe_test/Seq44762_QE2.mzML'), WindowsPath('D:/PXD003790-fragpipe_test/Seq44763_QE2.mzML')] MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 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: Windows 10, Architecture: AMD64 Java Info: 1.8.0_144, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 18 GB memory Checking database... Checking D:\PXD003790-fragpipe_test\Seq44762_QE2.mzML... Checking D:\PXD003790-fragpipe_test\Seq44763_QE2.mzML... ***FIRST SEARCH**** Parameters: num_threads = 6 database_name = 2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas decoyprefix = rev precursor_mass_lower = -15.0 precursor_mass_upper = 15.0 precursor_mass_units = 1 precursor_true_tolerance = 15.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = true isotope_error = 0 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 = a,b,y ion_series_definitions = search_enzyme_name = nonspecific search_enzyme_cutafter = - search_enzyme_butnotafter = num_enzyme_termini = 0 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 8 digest_max_length = 15 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 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 = 5 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Number of unique peptides of length 8: 20540712 of length 9: 20784756 of length 10: 20911738 of length 11: 20998525 of length 12: 21060874 of length 13: 21106562 of length 14: 21139448 of length 15: 21162123 In total 167704738 peptides. Generated 168175624 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 5307704355 fragments to be searched in 7 slices (79.09 GB total) Operating on slice 1 of 7: Fragment index slice generated in 7.03 s

  1. Seq44762_QE2.mzML 2.4 s | deisotoping 0.6 s [progress: 61098/61098 (100%) - 10326 spectra/s] 5.9s
  2. Seq44763_QE2.mzML 2.0 s | deisotoping 0.1 s [progress: 58478/58478 (100%) - 14532 spectra/s] 4.0s Operating on slice 2 of 7: Fragment index slice generated in 6.05 s
  3. Seq44762_QE2.mzML 2.3 s | deisotoping 0.2 s [progress: 61098/61098 (100%) - 9602 spectra/s] 6.4s
  4. Seq44763_QE2.mzML 1.8 s | deisotoping 0.0 s [progress: 58478/58478 (100%) - 13565 spectra/s] 4.3s Operating on slice 3 of 7: Fragment index slice generated in 5.87 s
  5. Seq44762_QE2.mzML 2.1 s | deisotoping 0.2 s [progress: 61098/61098 (100%) - 16036 spectra/s] 3.8s
  6. Seq44763_QE2.mzML 1.8 s | deisotoping 0.0 s [progress: 58478/58478 (100%) - 25337 spectra/s] 2.3s Operating on slice 4 of 7: Fragment index slice generated in 5.92 s
  7. Seq44762_QE2.mzML 2.1 s | deisotoping 0.2 s [progress: 61098/61098 (100%) - 23364 spectra/s] 2.6s
  8. Seq44763_QE2.mzML 1.8 s | deisotoping 0.0 s [progress: 58478/58478 (100%) - 40163 spectra/s] 1.5s Operating on slice 5 of 7: Fragment index slice generated in 6.16 s
  9. Seq44762_QE2.mzML 2.2 s | deisotoping 0.2 s [progress: 61098/61098 (100%) - 28510 spectra/s] 2.1s
  10. Seq44763_QE2.mzML 1.8 s | deisotoping 0.1 s [progress: 58478/58478 (100%) - 47894 spectra/s] 1.2s Operating on slice 6 of 7: Fragment index slice generated in 6.05 s
  11. Seq44762_QE2.mzML 1.8 s | deisotoping 0.2 s [progress: 61098/61098 (100%) - 25092 spectra/s] 2.4s
  12. Seq44763_QE2.mzML 1.9 s | deisotoping 0.1 s [progress: 58478/58478 (100%) - 48489 spectra/s] 1.2s Operating on slice 7 of 7: Fragment index slice generated in 5.96 s
  13. Seq44762_QE2.mzML 2.0 s | deisotoping 0.2 s [progress: 61098/61098 (100%) - 28234 spectra/s] 2.2s | postprocessing 0.4 s
  14. Seq44763_QE2.mzML 1.8 s | deisotoping 0.1 s [progress: 58478/58478 (100%) - 48529 spectra/s] 1.2s | postprocessing 0.2 s ***FIRST SEARCH DONE IN 4.517 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 5.00 2.40 -0.01 2.00 1.77 2.85 -0.08 3.25
002 4.55 1.67 0.11 1.39 1.67 3.30 -0.07 3.61
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- MS2 7 10 15 20 25 30
Count 2245 947 skip rest
------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- -------
Peaks 300_0 200_0 150_1 100_1
------- ------- ------- ------- -------
Count 2245 2929 2677 skip rest
------- ------- ------- ------- -------
------- -------
Int. 0
------- -------
Count 2736
------- -------
------- -------
Rm P. 0
------- -------
Count 2946
------- -------

New fragment_mass_tolerance = 7 PPM New use_topN_peaks = 200 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 0 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 9.483 MIN* ***TOTAL TIME 14.000 MIN**** STARTED: slice 1 of 4 ['java', '-jar', '-Dfile.encoding=UTF-8', '-Xmx21G', WindowsPath('//data.wexac.weizmann.ac.il/yifatlab/assafk/Pipeline_30/external_software/MSFragger-3.1.1/MSFragger-3.1.1.jar'), 'fragger.params', WindowsPath('D:/PXD003790-fragpipe_test/analysis_6/split_peptide_index_tempdir/Seq44762_QE2.mzBIN_calibrated'), WindowsPath('D:/PXD003790-fragpipe_test/analysis_6/split_peptide_index_tempdir/Seq44763_QE2.mzBIN_calibrated'), '--partial', '0'] MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 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: Windows 10, Architecture: AMD64 Java Info: 1.8.0_144, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 18 GB memory Checking database... Checking D:\PXD003790-fragpipe_test\analysis_6\split_peptide_index_tempdir\Seq44762_QE2.mzBIN_calibrated... Checking D:\PXD003790-fragpipe_test\analysis_6\split_peptide_index_tempdir\Seq44763_QE2.mzBIN_calibrated...

****MAIN SEARCH**** Checking database... Parameters: num_threads = 6 database_name = 2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 15.0 precursor_true_units = 1 fragment_mass_tolerance = 7.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = true 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 = a,b,y ion_series_definitions = search_enzyme_name = nonspecific search_enzyme_cutafter = - search_enzyme_butnotafter = num_enzyme_termini = 0 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 4 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 5 output_max_expect = 50.0 report_alternative_proteins = true override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 8 digest_max_length = 15 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 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 = 5 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 2 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Number of unique peptides of length 8: 4956311 of length 9: 4995965 of length 10: 5020522 of length 11: 5038078 of length 12: 5050878 of length 13: 5060212 of length 14: 5066862 of length 15: 5071370 In total 40260198 peptides. Generated 50817552 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.03 Da. 1619015913 fragments to be searched in 2 slices (24.13 GB total) Operating on slice 1 of 2: Fragment index slice generated in 9.61 s

  1. Seq44762_QE2.mzBIN_calibrated 1.0 s [progress: 60592/60592 (100%) - 7058 spectra/s] 8.6s
  2. Seq44763_QE2.mzBIN_calibrated 0.7 s [progress: 57910/57910 (100%) - 11451 spectra/s] 5.1s Operating on slice 2 of 2: Fragment index slice generated in 8.61 s
  3. Seq44762_QE2.mzBIN_calibrated 0.7 s [progress: 60592/60592 (100%) - 23513 spectra/s] 2.6s | postprocessing 7.2 s
  4. Seq44763_QE2.mzBIN_calibrated 0.7 s [progress: 57910/57910 (100%) - 52455 spectra/s] 1.1s | postprocessing 5.6 s MAIN SEARCH DONE IN 1.574 MIN

***TOTAL TIME 1.578 MIN**** DONE: slice 1 of 4 STARTED: slice 2 of 4 ['java', '-jar', '-Dfile.encoding=UTF-8', '-Xmx21G', WindowsPath('//data.wexac.weizmann.ac.il/yifatlab/assafk/Pipeline_30/external_software/MSFragger-3.1.1/MSFragger-3.1.1.jar'), 'fragger.params', WindowsPath('D:/PXD003790-fragpipe_test/analysis_6/split_peptide_index_tempdir/Seq44762_QE2.mzBIN_calibrated'), WindowsPath('D:/PXD003790-fragpipe_test/analysis_6/split_peptide_index_tempdir/Seq44763_QE2.mzBIN_calibrated'), '--partial', '1'] MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 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: Windows 10, Architecture: AMD64 Java Info: 1.8.0_144, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 18 GB memory Checking database... Checking D:\PXD003790-fragpipe_test\analysis_6\split_peptide_index_tempdir\Seq44762_QE2.mzBIN_calibrated... Checking D:\PXD003790-fragpipe_test\analysis_6\split_peptide_index_tempdir\Seq44763_QE2.mzBIN_calibrated...

****MAIN SEARCH**** Checking database... Parameters: num_threads = 6 database_name = 2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 15.0 precursor_true_units = 1 fragment_mass_tolerance = 7.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = true 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 = a,b,y ion_series_definitions = search_enzyme_name = nonspecific search_enzyme_cutafter = - search_enzyme_butnotafter = num_enzyme_termini = 0 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 4 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 5 output_max_expect = 50.0 report_alternative_proteins = true override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 8 digest_max_length = 15 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 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 = 5 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 2 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Number of unique peptides of length 8: 5533272 of length 9: 5566388 of length 10: 5584753 of length 11: 5596481 of length 12: 5603724 of length 13: 5607921 of length 14: 5609685 of length 15: 5609541 In total 44711765 peptides. Generated 56303416 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.03 Da. 1792479570 fragments to be searched in 2 slices (26.71 GB total) Operating on slice 1 of 2: Fragment index slice generated in 10.50 s

  1. Seq44762_QE2.mzBIN_calibrated 0.9 s [progress: 60592/60592 (100%) - 7024 spectra/s] 8.6s
  2. Seq44763_QE2.mzBIN_calibrated 0.7 s [progress: 57910/57910 (100%) - 10308 spectra/s] 5.6s Operating on slice 2 of 2: Fragment index slice generated in 8.73 s
  3. Seq44762_QE2.mzBIN_calibrated 0.9 s [progress: 60592/60592 (100%) - 24792 spectra/s] 2.4s | postprocessing 5.8 s
  4. Seq44763_QE2.mzBIN_calibrated 0.7 s [progress: 57910/57910 (100%) - 52455 spectra/s] 1.1s | postprocessing 5.4 s MAIN SEARCH DONE IN 1.596 MIN

***TOTAL TIME 1.599 MIN**** DONE: slice 2 of 4 STARTED: slice 3 of 4 ['java', '-jar', '-Dfile.encoding=UTF-8', '-Xmx21G', WindowsPath('//data.wexac.weizmann.ac.il/yifatlab/assafk/Pipeline_30/external_software/MSFragger-3.1.1/MSFragger-3.1.1.jar'), 'fragger.params', WindowsPath('D:/PXD003790-fragpipe_test/analysis_6/split_peptide_index_tempdir/Seq44762_QE2.mzBIN_calibrated'), WindowsPath('D:/PXD003790-fragpipe_test/analysis_6/split_peptide_index_tempdir/Seq44763_QE2.mzBIN_calibrated'), '--partial', '2'] MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 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: Windows 10, Architecture: AMD64 Java Info: 1.8.0_144, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 18 GB memory Checking database... Checking D:\PXD003790-fragpipe_test\analysis_6\split_peptide_index_tempdir\Seq44762_QE2.mzBIN_calibrated... Checking D:\PXD003790-fragpipe_test\analysis_6\split_peptide_index_tempdir\Seq44763_QE2.mzBIN_calibrated...

****MAIN SEARCH**** Checking database... Parameters: num_threads = 6 database_name = 2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 15.0 precursor_true_units = 1 fragment_mass_tolerance = 7.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = true 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 = a,b,y ion_series_definitions = search_enzyme_name = nonspecific search_enzyme_cutafter = - search_enzyme_butnotafter = num_enzyme_termini = 0 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 4 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 5 output_max_expect = 50.0 report_alternative_proteins = true override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 8 digest_max_length = 15 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 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 = 5 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 2 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Number of unique peptides of length 8: 4965446 of length 9: 5005127 of length 10: 5029708 of length 11: 5047286 of length 12: 5060101 of length 13: 5069440 of length 14: 5076107 of length 15: 5080625 In total 40333840 peptides. Generated 50995764 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.03 Da. 1624678839 fragments to be searched in 2 slices (24.21 GB total) Operating on slice 1 of 2: Fragment index slice generated in 9.66 s

  1. Seq44762_QE2.mzBIN_calibrated 0.9 s [progress: 60592/60592 (100%) - 7549 spectra/s] 8.0s
  2. Seq44763_QE2.mzBIN_calibrated 0.8 s [progress: 57910/57910 (100%) - 11313 spectra/s] 5.1s Operating on slice 2 of 2: Fragment index slice generated in 7.39 s
  3. Seq44762_QE2.mzBIN_calibrated 1.2 s [progress: 60592/60592 (100%) - 26185 spectra/s] 2.3s | postprocessing 6.1 s
  4. Seq44763_QE2.mzBIN_calibrated 0.7 s [progress: 57910/57910 (100%) - 57794 spectra/s] 1.0s | postprocessing 5.8 s MAIN SEARCH DONE IN 1.508 MIN

***TOTAL TIME 1.511 MIN**** DONE: slice 3 of 4 STARTED: slice 4 of 4 ['java', '-jar', '-Dfile.encoding=UTF-8', '-Xmx21G', WindowsPath('//data.wexac.weizmann.ac.il/yifatlab/assafk/Pipeline_30/external_software/MSFragger-3.1.1/MSFragger-3.1.1.jar'), 'fragger.params', WindowsPath('D:/PXD003790-fragpipe_test/analysis_6/split_peptide_index_tempdir/Seq44762_QE2.mzBIN_calibrated'), WindowsPath('D:/PXD003790-fragpipe_test/analysis_6/split_peptide_index_tempdir/Seq44763_QE2.mzBIN_calibrated'), '--partial', '3'] MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 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: Windows 10, Architecture: AMD64 Java Info: 1.8.0_144, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 18 GB memory Checking database... Checking D:\PXD003790-fragpipe_test\analysis_6\split_peptide_index_tempdir\Seq44762_QE2.mzBIN_calibrated... Checking D:\PXD003790-fragpipe_test\analysis_6\split_peptide_index_tempdir\Seq44763_QE2.mzBIN_calibrated...

****MAIN SEARCH**** Checking database... Parameters: num_threads = 6 database_name = 2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 15.0 precursor_true_units = 1 fragment_mass_tolerance = 7.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = true 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 = a,b,y ion_series_definitions = search_enzyme_name = nonspecific search_enzyme_cutafter = - search_enzyme_butnotafter = num_enzyme_termini = 0 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 4 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 5 output_max_expect = 50.0 report_alternative_proteins = true override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 8 digest_max_length = 15 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 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 = 5 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 2 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Number of unique peptides of length 8: 5542887 of length 9: 5576016 of length 10: 5594396 of length 11: 5606134 of length 12: 5613388 of length 13: 5617593 of length 14: 5619370 of length 15: 5619233 In total 44789017 peptides. Generated 56485702 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.03 Da. 1798260237 fragments to be searched in 2 slices (26.80 GB total) Operating on slice 1 of 2: Fragment index slice generated in 12.23 s

  1. Seq44762_QE2.mzBIN_calibrated 0.9 s [progress: 60592/60592 (100%) - 6422 spectra/s] 9.4s
  2. Seq44763_QE2.mzBIN_calibrated 0.7 s [progress: 57910/57910 (100%) - 9687 spectra/s] 6.0s Operating on slice 2 of 2: Fragment index slice generated in 8.23 s
  3. Seq44762_QE2.mzBIN_calibrated 0.9 s [progress: 60592/60592 (100%) - 26140 spectra/s] 2.3s | postprocessing 6.3 s
  4. Seq44763_QE2.mzBIN_calibrated 0.7 s [progress: 57910/57910 (100%) - 52218 spectra/s] 1.1s | postprocessing 5.4 s MAIN SEARCH DONE IN 1.671 MIN

***TOTAL TIME 1.674 MIN**** DONE: slice 4 of 4 ['java', '-jar', '-Dfile.encoding=UTF-8', '-Xmx21G', WindowsPath('//data.wexac.weizmann.ac.il/yifatlab/assafk/Pipeline_30/external_software/MSFragger-3.1.1/MSFragger-3.1.1.jar'), '--generate_expect_functions', 'Seq44762_QE2_scores_histogram.tsv', 'Seq44763_QE2_scores_histogram.tsv'] MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 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: Windows 10, Architecture: AMD64 Java Info: 1.8.0_144, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation Writing: Seq44762_QE2 spectrum: 0 Writing: Seq44762_QE2 spectrum: 1024 Writing: Seq44762_QE2 spectrum: 2048 Writing: Seq44762_QE2 spectrum: 3072 Writing: Seq44762_QE2 spectrum: 4096 Writing: Seq44762_QE2 spectrum: 5120 Writing: Seq44762_QE2 spectrum: 6144 Writing: Seq44762_QE2 spectrum: 7168 Writing: Seq44762_QE2 spectrum: 8192 Writing: Seq44762_QE2 spectrum: 9216 Writing: Seq44762_QE2 spectrum: 10240 Writing: Seq44763_QE2 spectrum: 0 Writing: Seq44763_QE2 spectrum: 1024 Writing: Seq44763_QE2 spectrum: 2048 Writing: Seq44763_QE2 spectrum: 3072 Writing: Seq44763_QE2 spectrum: 4096 Writing: Seq44763_QE2 spectrum: 5120 Writing: Seq44763_QE2 spectrum: 6144 Writing: Seq44762_QE2 spectrum: 11264 Writing: Seq44762_QE2 spectrum: 12288 Writing: Seq44763_QE2 spectrum: 7168 Writing: Seq44762_QE2 spectrum: 13312 Writing: Seq44763_QE2 spectrum: 8192 Writing: Seq44762_QE2 spectrum: 14336 Writing: Seq44763_QE2 spectrum: 9216 Writing: Seq44763_QE2 spectrum: 10240 Writing: Seq44762_QE2 spectrum: 15360 Writing: Seq44763_QE2 spectrum: 11264 Writing: Seq44762_QE2 spectrum: 16384 Writing: Seq44762_QE2 spectrum: 17408 Writing: Seq44763_QE2 spectrum: 12288 Writing: Seq44762_QE2 spectrum: 18432 Writing: Seq44763_QE2 spectrum: 13312 Writing: Seq44762_QE2 spectrum: 19456 Writing: Seq44763_QE2 spectrum: 14336 Writing: Seq44762_QE2 spectrum: 20480 Writing: Seq44763_QE2 spectrum: 15360 Writing: Seq44762_QE2 spectrum: 21504 Writing: Seq44763_QE2 spectrum: 16384 Writing: Seq44762_QE2 spectrum: 22528 Writing: Seq44763_QE2 spectrum: 17408 Writing: Seq44762_QE2 spectrum: 23552 Writing: Seq44763_QE2 spectrum: 18432 Writing: Seq44762_QE2 spectrum: 24576 Writing: Seq44762_QE2 spectrum: 25600 Writing: Seq44763_QE2 spectrum: 19456 Writing: Seq44763_QE2 spectrum: 20480 Writing: Seq44762_QE2 spectrum: 26624 Writing: Seq44762_QE2 spectrum: 27648 Writing: Seq44763_QE2 spectrum: 21504 Writing: Seq44762_QE2 spectrum: 28672 Writing: Seq44763_QE2 spectrum: 22528 Writing: Seq44762_QE2 spectrum: 29696 Writing: Seq44763_QE2 spectrum: 23552 Writing: Seq44762_QE2 spectrum: 30720 Writing: Seq44763_QE2 spectrum: 24576 Writing: Seq44762_QE2 spectrum: 31744 Writing: Seq44763_QE2 spectrum: 25600 Writing: Seq44762_QE2 spectrum: 32768 Writing: Seq44763_QE2 spectrum: 26624 Writing: Seq44762_QE2 spectrum: 33792 Writing: Seq44763_QE2 spectrum: 27648 Writing: Seq44762_QE2 spectrum: 34816 Writing: Seq44763_QE2 spectrum: 28672 Writing: Seq44762_QE2 spectrum: 35840 Writing: Seq44763_QE2 spectrum: 29696 Writing: Seq44762_QE2 spectrum: 36864 Writing: Seq44763_QE2 spectrum: 30720 Writing: Seq44762_QE2 spectrum: 37888 Writing: Seq44763_QE2 spectrum: 31744 Writing: Seq44762_QE2 spectrum: 38912 Writing: Seq44763_QE2 spectrum: 32768 Writing: Seq44762_QE2 spectrum: 39936 Writing: Seq44763_QE2 spectrum: 33792 Writing: Seq44762_QE2 spectrum: 40960 Writing: Seq44763_QE2 spectrum: 34816 Writing: Seq44762_QE2 spectrum: 41984 Writing: Seq44763_QE2 spectrum: 35840 Writing: Seq44762_QE2 spectrum: 43008 Writing: Seq44763_QE2 spectrum: 36864 Writing: Seq44762_QE2 spectrum: 44032 Writing: Seq44763_QE2 spectrum: 37888 Writing: Seq44762_QE2 spectrum: 45056 Writing: Seq44763_QE2 spectrum: 38912 Writing: Seq44762_QE2 spectrum: 46080 Writing: Seq44763_QE2 spectrum: 39936 Writing: Seq44762_QE2 spectrum: 47104 Writing: Seq44763_QE2 spectrum: 40960 Writing: Seq44763_QE2 spectrum: 41984 Writing: Seq44762_QE2 spectrum: 48128 Writing: Seq44763_QE2 spectrum: 43008 Writing: Seq44762_QE2 spectrum: 49152 Writing: Seq44763_QE2 spectrum: 44032 Writing: Seq44762_QE2 spectrum: 50176 Writing: Seq44763_QE2 spectrum: 45056 Writing: Seq44762_QE2 spectrum: 51200 Writing: Seq44763_QE2 spectrum: 46080 Writing: Seq44763_QE2 spectrum: 47104 Writing: Seq44762_QE2 spectrum: 52224 Writing: Seq44763_QE2 spectrum: 48128 Writing: Seq44763_QE2 spectrum: 49152 Writing: Seq44762_QE2 spectrum: 53248 Writing: Seq44762_QE2 spectrum: 54272 Writing: Seq44762_QE2 spectrum: 55296 Writing: Seq44762_QE2 spectrum: 56320 Writing: Seq44762_QE2 spectrum: 57344 Writing: Seq44762_QE2 spectrum: 58368 Writing: Seq44762_QE2 spectrum: 59392 Writing: Seq44762_QE2 spectrum: 60416 Writing: Seq44763_QE2 spectrum: 50176 Writing: Seq44763_QE2 spectrum: 51200 Writing: Seq44763_QE2 spectrum: 52224 Writing: Seq44763_QE2 spectrum: 53248 Writing: Seq44763_QE2 spectrum: 54272 Writing: Seq44763_QE2 spectrum: 55296 Writing: Seq44763_QE2 spectrum: 56320 Writing: Seq44763_QE2 spectrum: 57344 Process 'MsFragger' finished, exit code: 0 MsFragger move pepxml java -cp D:\FragPipe-14.1-build2\fragpipe\lib\fragpipe-14.1-build2.jar com.github.chhh.utils.FileMove D:\PXD003790-fragpipe_test\Seq44762_QE2.pepXML D:\PXD003790-fragpipe_test\analysis_6\U-87\Seq44762_QE2.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp D:\FragPipe-14.1-build2\fragpipe\lib\fragpipe-14.1-build2.jar com.github.chhh.utils.FileMove D:\PXD003790-fragpipe_test\Seq44763_QE2.pepXML D:\PXD003790-fragpipe_test\analysis_6\U-87\Seq44763_QE2.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87\fragpipe-Seq44763_QE2.pepXML-temp] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --init --nocheck INFO[18:38:32] Executing Workspace v3.3.11
INFO[18:38:32] Creating workspace
INFO[18:38:32] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87\fragpipe-Seq44762_QE2.pepXML-temp] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe workspace --init --nocheck Process 'PeptideProphet: Workspace init' finished, exit code: 0 INFO[18:38:47] Executing Workspace v3.3.11
INFO[18:38:47] Creating workspace
INFO[18:38:47] Done
PeptideProphetPeptideProphet [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87\fragpipe-Seq44763_QE2.pepXML-temp] [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87\fragpipe-Seq44762_QE2.pepXML-temp] D:\FragPipe-14.0\philosopher_v3.3.11_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --decoy rev --database X:\assafk\database\2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas ..\Seq44763_QE2.pepXML D:\FragPipe-14.0\philosopher_v3.3.11_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --decoy rev --database X:\assafk\database\2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas ..\Seq44762_QE2.pepXML INFO[18:39:01] Executing PeptideProphet v3.3.11
Unknown file type. No file loaded.D:\PXD003790-fragpipe_test\analysis_6\U-87/Seq44763_QE2.mzBIN_calibrated WARNING: cannot open data file D:\PXD003790-fragpipe_test\analysis_6\U-87/Seq44763_QE2.mzBIN_calibrated in msms_run_summary tag... unrecognized extension .mzBIN_calibrated, trying .mzML ... WARNING: CANNOT correct data file D:\PXD003790-fragpipe_test\analysis_6\U-87/Seq44763_QE2.mzML in msms_run_summary tag... Unknown file type. No file loaded.D:\PXD003790-fragpipe_test\analysis_6\U-87/Seq44763_QE2.mzBIN_calibrated WARNING: cannot open data file D:\PXD003790-fragpipe_test\analysis_6\U-87/Seq44763_QE2.mzBIN_calibrated in msms_run_summary tag... unrecognized extension .mzBIN_calibrated, trying .mzML ... WARNING: CANNOT correct data file D:\PXD003790-fragpipe_test\analysis_6\U-87/Seq44763_QE2.mzML in msms_run_summary tag... file 1: D:\PXD003790-fragpipe_test\analysis_6\U-87\Seq44763_QE2.pepXML processed altogether 25776 results INFO[18:39:10] Executing PeptideProphet v3.3.11
INFO: Results written to file: D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44763_QE2.pep.xml

INFO: Processing standard MixtureModel ... Initialising statistical models ... INFO: Results written to file: D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44762_QE2.pep.xml

.using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Not using ntt model Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using search_offsets in ACCMASS mixture distr: 0 init with X! Tandem nonspecific PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 4515 1+, 14307 2+, 5125 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Found 6645 Decoys, and 17302 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... .Iterations: .........10........10...........20......20.... WARNING: Mixture model quality test failed for charge (4+). 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 26 iterations ... INFO[18:39:57] Done
Process 'PeptideProphet' finished, exit code: 0 WARNING: Mixture model quality test failed for charge (4+). 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 26 iterations INFO[18:40:01] Done
Process 'PeptideProphet' finished, exit code: 0 PeptideProphet: Delete temp java -cp D:\FragPipe-14.1-build2\fragpipe\lib\fragpipe-14.1-build2.jar com.github.chhh.utils.FileDelete D:\PXD003790-fragpipe_test\analysis_6\U-87\fragpipe-Seq44763_QE2.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp java -cp D:\FragPipe-14.1-build2\fragpipe\lib\fragpipe-14.1-build2.jar com.github.chhh.utils.FileDelete D:\PXD003790-fragpipe_test\analysis_6\U-87\fragpipe-Seq44762_QE2.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 Rewrite pepxml [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87] java -cp D:\FragPipe-14.1-build2\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44762_QE2.pep.xml D:\PXD003790-fragpipe_test\Seq44762_QE2.mzML Fixing pepxml: D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44762_QE2.pep.xml Writing output to: D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44762_QE2.pep.xml2025640495506684363.temp-rewrite Deleting file: D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44762_QE2.pep.xml Moving rewritten file to original location: [D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44762_QE2.pep.xml2025640495506684363.temp-rewrite] -> [D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44762_QE2.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: D:\PXD003790-fragpipe_test\analysis_6\U-87] java -cp D:\FragPipe-14.1-build2\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44763_QE2.pep.xml D:\PXD003790-fragpipe_test\Seq44763_QE2.mzML Fixing pepxml: D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44763_QE2.pep.xml Writing output to: D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44763_QE2.pep.xml1870025368923106674.temp-rewrite Deleting file: D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44763_QE2.pep.xml Moving rewritten file to original location: [D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44763_QE2.pep.xml1870025368923106674.temp-rewrite] -> [D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44763_QE2.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: D:\PXD003790-fragpipe_test\analysis_6] D:\FragPipe-14.0\philosopher_v3.3.11_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44763_QE2.pep.xml D:\PXD003790-fragpipe_test\analysis_6\U-87\interact-Seq44762_QE2.pep.xml INFO[18:40:20] Executing ProteinProphet v3.3.11
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) (no FPKM) (using degen pep info) Reading in D:/PXD003790-fragpipe_test/analysis_6/U-87/interact-Seq44763_QE2.pep.xml... ...read in 1716 1+, 8700 2+, 2768 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/PXD003790-fragpipe_test/analysis_6/U-87/interact-Seq44762_QE2.pep.xml... ...read in 2088 1+, 6654 2+, 2533 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 14747 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database x:/assafk/database/2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry rev_sp|P59797|SELV_HUMAN : U RKKIEEDIVSVIKQLRSENVFGDGRKKSHVLRGNVFVEFEGTAQAARDEEFLLHNPFQQELSKKLLIYRLSYSULGCYTVRILVRKDLAFNESSSPFTETCNQLSIASPITGLIPSPVPSPIPPDALGIASPDARFTFDLTPGPSNAALPTRTPLPGPAPGAESSVSPILKLSPAPEPDEEPLLPLEPAPEPPPDLPLAPALYSDLVPLAARIGALLQAPAPAPVRVPPTLTRAPTPVPTPNRVPVPTPVPTPIWAPAPPPVLRPIRALAPTPVLTPIQAPAPTLVLPSTGAPSPTLVPTLTRIPTRTRVPTPTRLPTPTRTPTSARVSTSTRASSPAPTRAQNNM .......:.........:.........:.........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 .........:.........:.........:.........:.........:.........:.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|P07203|GPX1_HUMAN : U MCAARLAAAAAAAQSVYAFSARPLAGGEPVSLGSLRGKVLLIENVASLUGTTVRDYTQMNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGVPLRRYSRRFQTIDIEPDIEALLSQGPSCA ......24000 .........:...

fcyu commented 4 years ago

Hi Assaf,

There are some differences between two jobs:

database_name = 2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas vs database_name = 2020-10-07-decoys-contam-Human_SP_27042020.fasta-with-contaminate-with-decoy.fasta

min_matched_fragments = 5 vs min_matched_fragments = 4

isotope_error = 0/1 vs isotope_error = 0/1/2

max_variable_mods_per_peptide = 4 vs max_variable_mods_per_peptide = 3

max_variable_mods_combinations = 5000 vs max_variable_mods_combinations = 65000

Could you please unify the parameters (using the same fragger.params) and try again?

Best,

Fengchao

merbllab commented 4 years ago

HI Fengchao,

You are right – after aligning those parameters it gave the same results. My bad – I should have notice those differences.

Thanks

Assaf

From: Fengchao notifications@github.com Sent: Saturday, October 10, 2020 10:25 PM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: merbllab assafkacen@gmail.com; Author author@noreply.github.com Subject: Re: [Nesvilab/MSFragger] MSFragger 3.1.1 on Linux couldn't find optimal parameters after mass calibration (#103)

Hi Assaf,

There are some differences between two jobs:

database_name = 2020-10-07-decoys-contam-Human_SP_27042020.fasta.fas vs database_name = 2020-10-07-decoys-contam-Human_SP_27042020.fasta-with-contaminate-with-decoy.fasta

min_matched_fragments = 5 vs min_matched_fragments = 4

isotope_error = 0/1 vs isotope_error = 0/1/2

max_variable_mods_per_peptide = 4 vs max_variable_mods_per_peptide = 3

max_variable_mods_combinations = 5000 vs max_variable_mods_combinations = 65000

Could you please unify the parameters (using the same fragger.params) and try again?

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/103#issuecomment-706599308 , or unsubscribe https://github.com/notifications/unsubscribe-auth/APGKVN2B7TO57CSHPKJEDLLSKCYI5ANCNFSM4SLAPPDA . https://github.com/notifications/beacon/APGKVNZ3UQJ2PJGL3LPQYRTSKCYI5A5CNFSM4SLAPPDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOFIO5TDA.gif

fcyu commented 4 years ago

Hi Assaf,

No problem!

Please feel free to contact us if there is any further questions.

Best,

Fengchao