search

Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
Other
184 stars 37 forks source link

Errors of EasyPOP #370

Closed FanLab2019 closed 3 years ago

FanLab2019 commented 3 years ago

AssertionError Process 'SpecLibGen' finished, exit code: 1 Process returned non-zero exit code, stoppingEasyPQP convert error END


Cancelling 1 remaining tasks

Here is the error we got. I could find the protein and peptide results, but it seems the library could not be generated at the end.
sarah-haynes commented 3 years ago

Hi, can you share the whole log file? --Sarah

FanLab2019 commented 3 years ago

Dear,

Thank you for your quick response.

Here is the whole log. When we started to use Fragpipe recently, we could get the whole process completed successfully, but keep getting this errors these two days. I tried to use the mzml files, which I already processed them on Fragpipe and got speblib successfully last week. But I still got the same error at the end.

Thanks, Jia

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

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

LCMS files: Experiment/Group:

39 commands to execute: WorkspaceCleanInit [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck MSFragger [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx48G D:\software\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\JiaF_SpecLib\Fat_EXO_Lib\fragger.params Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.mzML MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F1_20210415224028.pepXML MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F2_20210416010437.pepXML MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F3_20210416032849.pepXML MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F4.pepXML MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F5.pepXML MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F6.pepXML PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F2_20210416010437.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F6.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F3_20210416032849.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F5.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F1_20210415224028.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F4.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F220210416010437.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F2_20210416010437.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExoF6.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F6.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F320210416032849.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F3_20210416032849.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExoF5.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F5.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F120210415224028.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F1_20210415224028.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExoF4.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F4.pepXML PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F2_20210416010437.pepXML-temp PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F6.pepXML-temp PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F3_20210416032849.pepXML-temp PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F5.pepXML-temp PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F1_20210415224028.pepXML-temp PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F4.pepXML-temp Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.mzML Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.mzML Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.mzML Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.mzML Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.mzML Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.mzML ProteinProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml PhilosopherDbAnnotate [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe database --annotate D:\fasta\2021-03-18-decoys-contam-humanreviewed.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\JiaF_SpecLib\Fat_EXOLib] D:\software\fragpipe\tools\philosopher.exe filter --razor --picked --prot 0.01 --tag rev --pepxml D:\JiaF_SpecLib\Fat_EXO_Lib --protxml D:\JiaF_SpecLib\Fat_EXO_Lib\combined.prot.xml PhilosopherReport [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe report WorkspaceClean [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe workspace --clean --nocheck SpecLibGen [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] C:\Anaconda\python.exe -u D:\software\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas D:\JiaF_SpecLib\Fat_EXO_Lib unused D:\JiaF_SpecLib\Fat_EXO_Lib True unused use_easypqp ciRT 39 "--max_delta_unimod 0.020000 --max_delta_ppm 15.000000" "--rt_lowess_fraction 0.010000" Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.mzML


Execution order:

    Cmd: [START], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [MSFragger], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [PeptideProphet], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [ProteinProphet], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [PhilosopherFilter], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [PhilosopherReport], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [WorkspaceClean], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [SpecLibGen], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]

# FragPipe v15.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
crystalc.run-crystalc=false
database.db-path=D\:\\fasta\\2021-03-18-decoys-contam-human_reviewed.fasta.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=D\:\\software\\fragpipe\\tools\\MSFragger-3.2\\MSFragger-3.2.jar
fragpipe-config.bin-philosopher=D\:\\software\\fragpipe\\tools\\philosopher.exe
fragpipe-config.bin-python=C\:\\Anaconda\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=1
ionquant.minisotopes=1
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=120
msfragger.digest_min_length=6
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=0.02
msfragger.fragment_mass_units=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.00
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=350
msfragger.misc.fragger.enzyme-dropdown=stricttrypsin
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021464,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,true,1; -18.010600,nE,true,1; -131.040000,[^,true,1; -89.030000,[^,true,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=--razor --picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.print-decoys=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.9
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.diag_ions=
ptmshepherd.glyco_mode=false
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=false
run-diaumpire=false
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=true
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.groupby=0
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\JiaF_SpecLib\\Fat_EXO_Lib
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=39

WorkspaceCleanInit [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe workspace --clean --nocheck INFO[16:33:52] Executing Workspace v3.4.13 INFO[16:33:52] Removing workspace WARN[16:33:52] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:33:52] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck INFO[16:33:53] Executing Workspace v3.4.13 INFO[16:33:53] Creating workspace INFO[16:33:53] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx48G D:\software\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\JiaF_SpecLib\Fat_EXO_Lib\fragger.params Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.mzML MSFragger version MSFragger-3.2 Batmass-IO version 1.22.1 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 48 GB memory Checking database... Checking spectral files... Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.mzML: Scans = 41109 Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.mzML: Scans = 37918 Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.mzML: Scans = 40437 Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.mzML: Scans = 42587 Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.mzML: Scans = 40367 Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.mzML: Scans = 41217 ***FIRST SEARCH**** Parameters: num_threads = 39 database_name = D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 1 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_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 6 digest_max_length = 120 digest_mass_range_low = 350.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.10 Da. 322093030 fragments to be searched in 1 slices (4.80 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.88 s

  1. HumanFatExo_F1_20210415224028.mzML 37.3 s | deisotoping 0.8 s [progress: 38994/38994 (100%) - 15413 spectra/s] 2.5s | postprocessing 0.4 s
  2. HumanFatExo_F2_20210416010437.mzML 36.8 s | deisotoping 0.6 s [progress: 36782/36782 (100%) - 110789 spectra/s] 0.3s | postprocessing 0.5 s
  3. HumanFatExo_F3_20210416032849.mzML 38.8 s | deisotoping 0.2 s [progress: 40353/40353 (100%) - 124163 spectra/s] 0.3s | postprocessing 0.4 s
  4. HumanFatExo_F4.mzML 41.8 s | deisotoping 0.0 s [progress: 41880/41880 (100%) - 93482 spectra/s] 0.4s | postprocessing 0.4 s
  5. HumanFatExo_F5.mzML 38.8 s | deisotoping 0.0 s [progress: 39613/39613 (100%) - 117896 spectra/s] 0.3s | postprocessing 0.4 s
  6. HumanFatExo_F6.mzML 35.8 s | deisotoping 0.0 s [progress: 40386/40386 (100%) - 120555 spectra/s] 0.3s | postprocessing 0.4 s ***FIRST SEARCH DONE IN 6.321 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 0.21 1.34 -0.08 1.39 -0.20 4.08 -0.03 4.01
002 0.63 1.32 -0.04 1.33 -0.54 4.16 -0.28 4.18
003 0.59 1.40 -0.02 1.40 -0.61 3.99 -0.10 4.00
004 0.50 1.23 -0.10 1.35 -0.81 4.18 -0.26 4.16
005 0.38 1.07 -0.07 1.14 -0.78 4.11 -0.23 4.11
006 0.19 1.18 0.17 1.28 -0.89 4.34 -0.23 4.28
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 4701 5689 5985 5697 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- ------- -------
Peaks 500_0 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- ------- -------
Count 5985 5985 5984 skip rest
------- ------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 6040
------- -------
------- -------
Rm P. 1
------- -------
Count 5836
------- -------

New fragment_mass_tolerance = 10 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 0 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 7.286 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 39 database_name = D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 10.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 1 isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 6 digest_max_length = 120 digest_mass_range_low = 350.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_04 = -17.026500 nQnC 1 variable_mod_05 = -18.010600 nE 1 variable_mod_06 = -131.040000 [^ 1 variable_mod_07 = -89.030000 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.05 Da. 382840840 fragments to be searched in 1 slices (5.70 GB total) Operating on slice 1 of 1: Fragment index slice generated in 3.12 s

  1. HumanFatExo_F1_20210415224028.mzBIN_calibrated 2.2 s [progress: 38499/38499 (100%) - 43112 spectra/s] 0.9s | postprocessing 39.9 s
  2. HumanFatExo_F2_20210416010437.mzBIN_calibrated 2.1 s [progress: 36427/36427 (100%) - 98718 spectra/s] 0.4s | postprocessing 41.9 s
  3. HumanFatExo_F3_20210416032849.mzBIN_calibrated 2.7 s [progress: 40038/40038 (100%) - 85734 spectra/s] 0.5s | postprocessing 43.2 s
  4. HumanFatExo_F4.mzBIN_calibrated 2.6 s [progress: 41625/41625 (100%) - 85648 spectra/s] 0.5s | postprocessing 45.0 s
  5. HumanFatExo_F5.mzBIN_calibrated 2.4 s [progress: 39287/39287 (100%) - 107636 spectra/s] 0.4s | postprocessing 42.7 s
  6. HumanFatExo_F6.mzBIN_calibrated 2.1 s [progress: 39984/39984 (100%) - 113591 spectra/s] 0.4s | postprocessing 38.2 s MAIN SEARCH DONE IN 4.561 MIN

***TOTAL TIME 18.167 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F1_20210415224028.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F2_20210416010437.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F3_20210416032849.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F5.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F6.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F2_20210416010437.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck INFO[16:52:27] Executing Workspace v3.4.13 INFO[16:52:27] Creating workspace INFO[16:52:27] Done Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F6.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck INFO[16:52:28] Executing Workspace v3.4.13 INFO[16:52:28] Creating workspace INFO[16:52:28] Done Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F3_20210416032849.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck INFO[16:52:28] Executing Workspace v3.4.13 INFO[16:52:28] Creating workspace INFO[16:52:28] Done Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F5.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck INFO[16:52:28] Executing Workspace v3.4.13 INFO[16:52:28] Creating workspace INFO[16:52:28] Done Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F1_20210415224028.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck INFO[16:52:29] Executing Workspace v3.4.13 INFO[16:52:29] Creating workspace INFO[16:52:29] Done Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F4.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck Process 'PeptideProphet: Workspace init' finished, exit code: 0 INFO[16:52:29] Executing Workspace v3.4.13 INFO[16:52:29] Creating workspace INFO[16:52:29] Done PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F220210416010437.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F2_20210416010437.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExoF6.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F6.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F320210416032849.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F3_20210416032849.pepXML PeptideProphetPeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F5.pepXML-temp] [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExoF4.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExoF4.pepXML D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F5.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F120210415224028.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F1_20210415224028.pepXML INFO[16:52:29] Executing PeptideProphet v3.4.13 INFO[16:52:29] Executing PeptideProphet v3.4.13 INFO[16:52:29] Executing PeptideProphet v3.4.13 INFO[16:52:29] Executing PeptideProphet v3.4.13 INFO[16:52:29] Executing PeptideProphet v3.4.13 INFO[16:52:29] Executing PeptideProphet v3.4.13 file 1: D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F1_20210415224028.pepXML file 1: D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F6.pepXML file 1: D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F2_20210416010437.pepXML file 1: D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F5.pepXML file 1: D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F4.pepXML file 1: D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F3_20210416032849.pepXML processed altogether 16852 results processed altogether 19192 results processed altogether 19546 results processed altogether 24069 results processed altogether 26483 results INFO: Results written to file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. 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 stricttrypsin

PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 14632 2+, 639 3+, 76 4+, 0 5+, 3 6+, and 2 7+ spectra. Found 4774 Decoys, and 10578 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using searchoffsets in ACCMASS mixture distr: 0 init with X! Tandem stricttrypsin using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev". Decoy Probabilities will be reported. 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 stricttrypsin PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 10196 2+, 6326 3+, 405 4+, 3 5+, 55 6+, and 2 7+ spectra. Found 4708 Decoys, and 12279 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ...

PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 16844 2+, 741 3+, 11 4+, 0 5+, 4 6+, and 0 7+ spectra. Found 5103 Decoys, and 12497 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. 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 stricttrypsin

.Iterations: . PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 14299 2+, 6148 3+, 302 4+, 1 5+, 10 6+, and 1 7+ spectra. Found 6349 Decoys, and 14412 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. 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 stricttrypsin

..using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. 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 stricttrypsin .. PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 21346 2+, 2038 3+, 13 4+, 3 5+, 4 6+, and 0 7+ spectra. Found 7123 Decoys, and 16281 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... .. PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 20756 2+, 5467 3+, 124 4+, 0 5+, 12 6+, and 0 7+ spectra. Found 8242 Decoys, and 18117 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... .Iterations: ......Iterations: ......Iterations: ..........10.........10...10.................10...........20.....10...........20...10.20.......WARNING: Mixture model quality test failed for charge (1+).

.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 27 iterations ........INFO[16:53:08] Done Process 'PeptideProphet' finished, exit code: 0 .......20.WARNING: Mixture model quality test failed for charge (1+).

.WARNING: Mixture model quality test failed for charge (1+).

WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations ..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 27 iterations ...INFO[16:53:13] Done Process 'PeptideProphet' finished, exit code: 0 .INFO[16:53:14] Done Process 'PeptideProphet' finished, exit code: 0 ....20....WARNING: Mixture model quality test failed for charge (1+).

..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 27 iterations 20..INFO[16:53:21] Done Process 'PeptideProphet' finished, exit code: 0 ....WARNING: Mixture model quality test failed for charge (1+).

.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 27 iterations ..INFO[16:53:28] Done Process 'PeptideProphet' finished, exit code: 0 WARNING: Mixture model quality test failed for charge (1+).

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[16:53:31] Done Process 'PeptideProphet' finished, exit code: 0 PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F2_20210416010437.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F6.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F3_20210416032849.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F5.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F1_20210415224028.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F4.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.mzML Fixing pepxml: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml Writing output to: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml7161536834552794579.temp-rewrite Deleting file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml Moving rewritten file to original location: [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml7161536834552794579.temp-rewrite] -> [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.mzML Fixing pepxml: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml Writing output to: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml16923240097360124703.temp-rewrite Deleting file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml Moving rewritten file to original location: [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml16923240097360124703.temp-rewrite] -> [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.mzML Fixing pepxml: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml Writing output to: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml5628861298069372572.temp-rewrite Deleting file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml Moving rewritten file to original location: [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml5628861298069372572.temp-rewrite] -> [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.mzML Fixing pepxml: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml Writing output to: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml385790691505989512.temp-rewrite Deleting file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml Moving rewritten file to original location: [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml385790691505989512.temp-rewrite] -> [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.mzML Fixing pepxml: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml Writing output to: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml9958446354983034528.temp-rewrite Deleting file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml Moving rewritten file to original location: [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml9958446354983034528.temp-rewrite] -> [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.mzML Fixing pepxml: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml Writing output to: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml17179956856879425557.temp-rewrite Deleting file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml Moving rewritten file to original location: [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml17179956856879425557.temp-rewrite] -> [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml INFO[16:54:02] Executing ProteinProphet v3.4.13 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) (no FPKM) (using degen pep info) Reading in D:/JiaF_SpecLib/Fat_EXO_Lib/interact-HumanFatExo_F6.pep.xml... ...read in 0 1+, 3630 2+, 1703 3+, 67 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Reading in D:/JiaF_SpecLib/Fat_EXO_Lib/interact-HumanFatExo_F2_20210416010437.pep.xml... ...read in 0 1+, 5273 2+, 132 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Reading in D:/JiaF_SpecLib/Fat_EXO_Lib/interact-HumanFatExo_F3_20210416032849.pep.xml... ...read in 0 1+, 6397 2+, 361 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Reading in D:/JiaF_SpecLib/Fat_EXO_Lib/interact-HumanFatExo_F5.pep.xml... ...read in 0 1+, 4431 2+, 1357 3+, 38 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Reading in D:/JiaF_SpecLib/Fat_EXO_Lib/interact-HumanFatExo_F4.pep.xml... ...read in 0 1+, 6378 2+, 1097 3+, 16 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Reading in D:/JiaF_SpecLib/Fat_EXO_Lib/interact-HumanFatExo_F1_20210415224028.pep.xml... ...read in 0 1+, 4058 2+, 103 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Initializing 10110 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database d:/fasta/2021-03-18-decoys-contam-human_reviewed.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|P07203|GPX1_HUMAN : U MCAARLAAAAAAAQSVYAFSARPLAGGEPVSLGSLRGKVLLIENVASLUGTTVRDYTQMNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGVPLRRYSRRFQTIDIEPDIEALLSQGPSCA ..24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|P22352|GPX3_HUMAN : U MARLLQASCLLSLLLAGFVSQSRGQEKSKMDCHGGISGTIYEYGALTIDGEEYIPFKQYAGKYVLFVNVASYUGLTGQYIELNALQEELAPFGLVILGFPCNQFGKQEPGENSEILPTLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTSELLGTSDRLFWEPMKVHDIRWNFEKFLVGPDGIPIMRWHHRTTVSNVKMDILSYMRRQAALGVKRK ..:.........:.........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|P36969|GPX4_HUMAN : U MSLGRLCRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF ...26000 .........:.........:.........:.........:.........WARNING: Found the following zero-mass residues in protein entry sp|P49908|SEPP1_HUMAN : UUUUUUUUUU MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSNGSVTVVALLQASUYLCILQASKLEDLRVKLKKEGYSNISYIVVNHQGISSRLKYTHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDRCGRLVYHLGLPFSFLTFPYVEEAIKIAYCEKKCGNCSLTTLKDEDFCKRVSLATVDKTVETPSPHYHHEHHHNHGHQHLGSSELSENQQPGAPNAPTHPAPPGLHHHHKHKGQHRQGHPENRDMPASEDLQDLQKKLCRKRCINQLLCKLPTDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPPAAUQISQQLIPTEASASURUKNQAKKUEUPSN :.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:......WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG ...:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|Q9BVL4|SELO_HUMAN : U MAVYRAALGASLAAARLLPLGRCSPSPAPRSTLSGAAMEPAPRWLAGLRFDNRALRAL

fcyu commented 3 years ago

Hi Jia,

Your log is truncated by GitHub. Can you send it in a zip file?

Best,

Fengchao

FanLab2019 commented 3 years ago

Dear Fengchao,

Attached is the text file of the whole log.

Thank you, Jia

From: Fengchao @.> Sent: Thursday, May 13, 2021 6:29 PM To: Nesvilab/FragPipe @.> Cc: Fan, Jia @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Errors of EasyPOP (#370)

External Sender. Be aware of links, attachments and requests.

Hi Jia,

Your log is truncated by GitHub. Can you send it in a zip file?

Best,

Fengchao

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNesvilab%2FFragPipe%2Fissues%2F370%23issuecomment-840892527&data=04%7C01%7Cjfan5%40tulane.edu%7Cb78d59a5fa4847d775fd08d91666ec98%7C9de9818325d94b139fc34de5489c1f3b%7C1%7C0%7C637565453591283042%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=RekrQbjUVcyiaaWJFs0llgPjE9jbPNpasZqQtx88JKc%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQQMQVJ5AVM3JQHD22WVUELTNROEXANCNFSM443MKY6Q&data=04%7C01%7Cjfan5%40tulane.edu%7Cb78d59a5fa4847d775fd08d91666ec98%7C9de9818325d94b139fc34de5489c1f3b%7C1%7C0%7C637565453591283042%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=fCuxM%2BfDMDNEk9SuXXoaT2U2w3nz1mUWBz5WcjMjfkg%3D&reserved=0.

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

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

LCMS files: Experiment/Group:

39 commands to execute: WorkspaceCleanInit [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck MSFragger [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx48G D:\software\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\JiaF_SpecLib\Fat_EXO_Lib\fragger.params Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.mzML MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F1_20210415224028.pepXML MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F2_20210416010437.pepXML MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F3_20210416032849.pepXML MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F4.pepXML MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F5.pepXML MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F6.pepXML PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F2_20210416010437.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F6.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F3_20210416032849.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F5.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F1_20210415224028.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F4.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F220210416010437.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F2_20210416010437.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExoF6.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F6.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F320210416032849.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F3_20210416032849.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExoF5.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F5.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F120210415224028.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F1_20210415224028.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExoF4.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F4.pepXML PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F2_20210416010437.pepXML-temp PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F6.pepXML-temp PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F3_20210416032849.pepXML-temp PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F5.pepXML-temp PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F1_20210415224028.pepXML-temp PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F4.pepXML-temp Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.mzML Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.mzML Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.mzML Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.mzML Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.mzML Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.mzML ProteinProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml PhilosopherDbAnnotate [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe database --annotate D:\fasta\2021-03-18-decoys-contam-humanreviewed.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\JiaF_SpecLib\Fat_EXOLib] D:\software\fragpipe\tools\philosopher.exe filter --razor --picked --prot 0.01 --tag rev --pepxml D:\JiaF_SpecLib\Fat_EXO_Lib --protxml D:\JiaF_SpecLib\Fat_EXO_Lib\combined.prot.xml PhilosopherReport [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe report WorkspaceClean [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe workspace --clean --nocheck SpecLibGen [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] C:\Anaconda\python.exe -u D:\software\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas D:\JiaF_SpecLib\Fat_EXO_Lib unused D:\JiaF_SpecLib\Fat_EXO_Lib True unused use_easypqp ciRT 39 "--max_delta_unimod 0.020000 --max_delta_ppm 15.000000" "--rt_lowess_fraction 0.010000" Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.mzML


Execution order:

    Cmd: [START], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [MSFragger], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [PeptideProphet], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [ProteinProphet], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [PhilosopherFilter], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [PhilosopherReport], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [WorkspaceClean], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]
    Cmd: [SpecLibGen], Work dir: [D:\JiaF_SpecLib\Fat_EXO_Lib]

# FragPipe v15.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
crystalc.run-crystalc=false
database.db-path=D\:\\fasta\\2021-03-18-decoys-contam-human_reviewed.fasta.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=D\:\\software\\fragpipe\\tools\\MSFragger-3.2\\MSFragger-3.2.jar
fragpipe-config.bin-philosopher=D\:\\software\\fragpipe\\tools\\philosopher.exe
fragpipe-config.bin-python=C\:\\Anaconda\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=1
ionquant.minisotopes=1
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=120
msfragger.digest_min_length=6
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=0.02
msfragger.fragment_mass_units=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.00
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=350
msfragger.misc.fragger.enzyme-dropdown=stricttrypsin
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021464,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,true,1; -18.010600,nE,true,1; -131.040000,[^,true,1; -89.030000,[^,true,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=--razor --picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.print-decoys=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.9
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.diag_ions=
ptmshepherd.glyco_mode=false
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=false
run-diaumpire=false
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=true
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.groupby=0
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\JiaF_SpecLib\\Fat_EXO_Lib
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=39

WorkspaceCleanInit [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe workspace --clean --nocheck INFO[16:33:52] Executing Workspace v3.4.13
INFO[16:33:52] Removing workspace
WARN[16:33:52] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[16:33:52] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck INFO[16:33:53] Executing Workspace v3.4.13
INFO[16:33:53] Creating workspace
INFO[16:33:53] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx48G D:\software\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar D:\JiaF_SpecLib\Fat_EXO_Lib\fragger.params Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.mzML Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.mzML MSFragger version MSFragger-3.2 Batmass-IO version 1.22.1 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 48 GB memory Checking database... Checking spectral files... Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.mzML: Scans = 41109 Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.mzML: Scans = 37918 Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.mzML: Scans = 40437 Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.mzML: Scans = 42587 Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.mzML: Scans = 40367 Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.mzML: Scans = 41217 ***FIRST SEARCH**** Parameters: num_threads = 39 database_name = D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 1 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_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 6 digest_max_length = 120 digest_mass_range_low = 350.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.10 Da. 322093030 fragments to be searched in 1 slices (4.80 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.88 s

  1. HumanFatExo_F1_20210415224028.mzML 37.3 s | deisotoping 0.8 s [progress: 38994/38994 (100%) - 15413 spectra/s] 2.5s | postprocessing 0.4 s
  2. HumanFatExo_F2_20210416010437.mzML 36.8 s | deisotoping 0.6 s [progress: 36782/36782 (100%) - 110789 spectra/s] 0.3s | postprocessing 0.5 s
  3. HumanFatExo_F3_20210416032849.mzML 38.8 s | deisotoping 0.2 s [progress: 40353/40353 (100%) - 124163 spectra/s] 0.3s | postprocessing 0.4 s
  4. HumanFatExo_F4.mzML 41.8 s | deisotoping 0.0 s [progress: 41880/41880 (100%) - 93482 spectra/s] 0.4s | postprocessing 0.4 s
  5. HumanFatExo_F5.mzML 38.8 s | deisotoping 0.0 s [progress: 39613/39613 (100%) - 117896 spectra/s] 0.3s | postprocessing 0.4 s
  6. HumanFatExo_F6.mzML 35.8 s | deisotoping 0.0 s [progress: 40386/40386 (100%) - 120555 spectra/s] 0.3s | postprocessing 0.4 s ***FIRST SEARCH DONE IN 6.321 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 0.21 1.34 -0.08 1.39 -0.20 4.08 -0.03 4.01
002 0.63 1.32 -0.04 1.33 -0.54 4.16 -0.28 4.18
003 0.59 1.40 -0.02 1.40 -0.61 3.99 -0.10 4.00
004 0.50 1.23 -0.10 1.35 -0.81 4.18 -0.26 4.16
005 0.38 1.07 -0.07 1.14 -0.78 4.11 -0.23 4.11
006 0.19 1.18 0.17 1.28 -0.89 4.34 -0.23 4.28
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 4701 5689 5985 5697 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- ------- -------
Peaks 500_0 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- ------- -------
Count 5985 5985 5984 skip rest
------- ------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 6040
------- -------
------- -------
Rm P. 1
------- -------
Count 5836
------- -------

New fragment_mass_tolerance = 10 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 0 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 7.286 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 39 database_name = D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 10.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 1 isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 6 digest_max_length = 120 digest_mass_range_low = 350.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_04 = -17.026500 nQnC 1 variable_mod_05 = -18.010600 nE 1 variable_mod_06 = -131.040000 [^ 1 variable_mod_07 = -89.030000 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.05 Da. 382840840 fragments to be searched in 1 slices (5.70 GB total) Operating on slice 1 of 1: Fragment index slice generated in 3.12 s

  1. HumanFatExo_F1_20210415224028.mzBIN_calibrated 2.2 s [progress: 38499/38499 (100%) - 43112 spectra/s] 0.9s | postprocessing 39.9 s
  2. HumanFatExo_F2_20210416010437.mzBIN_calibrated 2.1 s [progress: 36427/36427 (100%) - 98718 spectra/s] 0.4s | postprocessing 41.9 s
  3. HumanFatExo_F3_20210416032849.mzBIN_calibrated 2.7 s [progress: 40038/40038 (100%) - 85734 spectra/s] 0.5s | postprocessing 43.2 s
  4. HumanFatExo_F4.mzBIN_calibrated 2.6 s [progress: 41625/41625 (100%) - 85648 spectra/s] 0.5s | postprocessing 45.0 s
  5. HumanFatExo_F5.mzBIN_calibrated 2.4 s [progress: 39287/39287 (100%) - 107636 spectra/s] 0.4s | postprocessing 42.7 s
  6. HumanFatExo_F6.mzBIN_calibrated 2.1 s [progress: 39984/39984 (100%) - 113591 spectra/s] 0.4s | postprocessing 38.2 s MAIN SEARCH DONE IN 4.561 MIN

***TOTAL TIME 18.167 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F1_20210415224028.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F2_20210416010437.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F3_20210416032849.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F5.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar;/D:/software/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.pepXML D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F6.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F2_20210416010437.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck INFO[16:52:27] Executing Workspace v3.4.13
INFO[16:52:27] Creating workspace
INFO[16:52:27] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F6.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck INFO[16:52:28] Executing Workspace v3.4.13
INFO[16:52:28] Creating workspace
INFO[16:52:28] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F3_20210416032849.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck INFO[16:52:28] Executing Workspace v3.4.13
INFO[16:52:28] Creating workspace
INFO[16:52:28] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F5.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck INFO[16:52:28] Executing Workspace v3.4.13
INFO[16:52:28] Creating workspace
INFO[16:52:28] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F1_20210415224028.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck INFO[16:52:29] Executing Workspace v3.4.13
INFO[16:52:29] Creating workspace
INFO[16:52:29] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F4.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe workspace --init --nocheck Process 'PeptideProphet: Workspace init' finished, exit code: 0 INFO[16:52:29] Executing Workspace v3.4.13
INFO[16:52:29] Creating workspace
INFO[16:52:29] Done
PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F220210416010437.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F2_20210416010437.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExoF6.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F6.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F320210416032849.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F3_20210416032849.pepXML PeptideProphetPeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F5.pepXML-temp] [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExoF4.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExoF4.pepXML D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F5.pepXML PeptideProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F120210415224028.pepXML-temp] D:\software\fragpipe\tools\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\fasta\2021-03-18-decoys-contam-human_reviewed.fasta.fas ..\HumanFatExo_F1_20210415224028.pepXML INFO[16:52:29] Executing PeptideProphet v3.4.13
INFO[16:52:29] Executing PeptideProphet v3.4.13
INFO[16:52:29] Executing PeptideProphet v3.4.13
INFO[16:52:29] Executing PeptideProphet v3.4.13
INFO[16:52:29] Executing PeptideProphet v3.4.13
INFO[16:52:29] Executing PeptideProphet v3.4.13
file 1: D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F1_20210415224028.pepXML file 1: D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F6.pepXML file 1: D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F2_20210416010437.pepXML file 1: D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F5.pepXML file 1: D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F4.pepXML file 1: D:\JiaF_SpecLib\Fat_EXO_Lib\HumanFatExo_F3_20210416032849.pepXML processed altogether 16852 results processed altogether 19192 results processed altogether 19546 results processed altogether 24069 results processed altogether 26483 results INFO: Results written to file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. 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 stricttrypsin

INFO: Processing standard MixtureModel ... Initialising statistical models ... using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using searchoffsets in ACCMASS mixture distr: 0 init with X! Tandem stricttrypsin using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev". Decoy Probabilities will be reported. 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 stricttrypsin PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 10196 2+, 6326 3+, 405 4+, 3 5+, 55 6+, and 2 7+ spectra. Found 4708 Decoys, and 12279 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ...

INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. 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 stricttrypsin

.Iterations: . PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 14299 2+, 6148 3+, 302 4+, 1 5+, 10 6+, and 1 7+ spectra. Found 6349 Decoys, and 14412 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. 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 stricttrypsin

..using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. 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 stricttrypsin .. PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 21346 2+, 2038 3+, 13 4+, 3 5+, 4 6+, and 0 7+ spectra. Found 7123 Decoys, and 16281 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... .. PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 20756 2+, 5467 3+, 124 4+, 0 5+, 12 6+, and 0 7+ spectra. Found 8242 Decoys, and 18117 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... .Iterations: ......Iterations: ......Iterations: ..........10.........10...10.................10...........20.....10...........20...10.20.......WARNING: Mixture model quality test failed for charge (1+).

.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 27 iterations ........INFO[16:53:08] Done
Process 'PeptideProphet' finished, exit code: 0 .......20.WARNING: Mixture model quality test failed for charge (1+).

.WARNING: Mixture model quality test failed for charge (1+).

WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterations ..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 27 iterations ...INFO[16:53:13] Done
Process 'PeptideProphet' finished, exit code: 0 .INFO[16:53:14] Done
Process 'PeptideProphet' finished, exit code: 0 ....20....WARNING: Mixture model quality test failed for charge (1+).

..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 27 iterations 20..INFO[16:53:21] Done
Process 'PeptideProphet' finished, exit code: 0 ....WARNING: Mixture model quality test failed for charge (1+).

.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 27 iterations ..INFO[16:53:28] Done
Process 'PeptideProphet' finished, exit code: 0 WARNING: Mixture model quality test failed for charge (1+).

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[16:53:31] Done
Process 'PeptideProphet' finished, exit code: 0 PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F2_20210416010437.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F6.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F3_20210416032849.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F5.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F1_20210415224028.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete D:\JiaF_SpecLib\Fat_EXO_Lib\fragpipe-HumanFatExo_F4.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F6.mzML Fixing pepxml: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml Writing output to: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml7161536834552794579.temp-rewrite Deleting file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml Moving rewritten file to original location: [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml7161536834552794579.temp-rewrite] -> [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F3_20210416032849.mzML Fixing pepxml: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml Writing output to: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml16923240097360124703.temp-rewrite Deleting file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml Moving rewritten file to original location: [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml16923240097360124703.temp-rewrite] -> [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F2_20210416010437.mzML Fixing pepxml: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml Writing output to: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml5628861298069372572.temp-rewrite Deleting file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml Moving rewritten file to original location: [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml5628861298069372572.temp-rewrite] -> [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F4.mzML Fixing pepxml: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml Writing output to: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml385790691505989512.temp-rewrite Deleting file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml Moving rewritten file to original location: [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml385790691505989512.temp-rewrite] -> [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F5.mzML Fixing pepxml: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml Writing output to: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml9958446354983034528.temp-rewrite Deleting file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml Moving rewritten file to original location: [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml9958446354983034528.temp-rewrite] -> [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\jre\bin\java.exe -cp D:\software\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml Y:\Jia Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\HumanFatExo_F1_20210415224028.mzML Fixing pepxml: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml Writing output to: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml17179956856879425557.temp-rewrite Deleting file: D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml Moving rewritten file to original location: [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml17179956856879425557.temp-rewrite] -> [D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: D:\JiaF_SpecLib\Fat_EXO_Lib] D:\software\fragpipe\tools\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F6.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F2_20210416010437.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F3_20210416032849.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F5.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F4.pep.xml D:\JiaF_SpecLib\Fat_EXO_Lib\interact-HumanFatExo_F1_20210415224028.pep.xml INFO[16:54:02] Executing ProteinProphet v3.4.13
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) (no FPKM) (using degen pep info) Reading in D:/JiaF_SpecLib/Fat_EXO_Lib/interact-HumanFatExo_F6.pep.xml... ...read in 0 1+, 3630 2+, 1703 3+, 67 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Reading in D:/JiaF_SpecLib/Fat_EXO_Lib/interact-HumanFatExo_F2_20210416010437.pep.xml... ...read in 0 1+, 5273 2+, 132 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Reading in D:/JiaF_SpecLib/Fat_EXO_Lib/interact-HumanFatExo_F3_20210416032849.pep.xml... ...read in 0 1+, 6397 2+, 361 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Reading in D:/JiaF_SpecLib/Fat_EXO_Lib/interact-HumanFatExo_F5.pep.xml... ...read in 0 1+, 4431 2+, 1357 3+, 38 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Reading in D:/JiaF_SpecLib/Fat_EXO_Lib/interact-HumanFatExo_F4.pep.xml... ...read in 0 1+, 6378 2+, 1097 3+, 16 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Reading in D:/JiaF_SpecLib/Fat_EXO_Lib/interact-HumanFatExo_F1_20210415224028.pep.xml... ...read in 0 1+, 4058 2+, 103 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Initializing 10110 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database d:/fasta/2021-03-18-decoys-contam-human_reviewed.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|P07203|GPX1_HUMAN : U MCAARLAAAAAAAQSVYAFSARPLAGGEPVSLGSLRGKVLLIENVASLUGTTVRDYTQMNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGVPLRRYSRRFQTIDIEPDIEALLSQGPSCA ..24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|P22352|GPX3_HUMAN : U MARLLQASCLLSLLLAGFVSQSRGQEKSKMDCHGGISGTIYEYGALTIDGEEYIPFKQYAGKYVLFVNVASYUGLTGQYIELNALQEELAPFGLVILGFPCNQFGKQEPGENSEILPTLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTSELLGTSDRLFWEPMKVHDIRWNFEKFLVGPDGIPIMRWHHRTTVSNVKMDILSYMRRQAALGVKRK ..:.........:.........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|P36969|GPX4_HUMAN : U MSLGRLCRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF ...26000 .........:.........:.........:.........:.........WARNING: Found the following zero-mass residues in protein entry sp|P49908|SEPP1_HUMAN : UUUUUUUUUU MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSNGSVTVVALLQASUYLCILQASKLEDLRVKLKKEGYSNISYIVVNHQGISSRLKYTHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDRCGRLVYHLGLPFSFLTFPYVEEAIKIAYCEKKCGNCSLTTLKDEDFCKRVSLATVDKTVETPSPHYHHEHHHNHGHQHLGSSELSENQQPGAPNAPTHPAPPGLHHHHKHKGQHRQGHPENRDMPASEDLQDLQKKLCRKRCINQLLCKLPTDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPPAAUQISQQLIPTEASASURUKNQAKKUEUPSN :.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:......WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPG

fcyu commented 3 years ago

Hi Jia,

Your text file is truncated by GitHub. Can you send it in a zip file?

Best,

Fengchao

FanLab2019 commented 3 years ago

Hi Fengchao,

Here is the zip file. Hope this one works.

Thank you, Jia

From: Fengchao @.> Reply-To: Nesvilab/FragPipe @.> Date: Friday, May 14, 2021 at 10:07 AM To: Nesvilab/FragPipe @.> Cc: "Fan, Jia" @.>, Author @.***> Subject: Re: [Nesvilab/FragPipe] Errors of EasyPOP (#370)

External Sender. Be aware of links, attachments and requests.

Hi Jia,

Your text file is truncated by GitHub. Can you send it in a zip file?

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNesvilab%2FFragPipe%2Fissues%2F370%23issuecomment-841301902&data=04%7C01%7Cjfan5%40tulane.edu%7Ca0468348f1c2430e35a308d916e9f18b%7C9de9818325d94b139fc34de5489c1f3b%7C1%7C0%7C637566016306355504%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Kynvi7b79rZ8rhg7hHYjPevcZbi9jgstrLsJwmXWA0g%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQQMQVOIYVRLTYUIRE3V6GDTNU4BZANCNFSM443MKY6Q&data=04%7C01%7Cjfan5%40tulane.edu%7Ca0468348f1c2430e35a308d916e9f18b%7C9de9818325d94b139fc34de5489c1f3b%7C1%7C0%7C637566016306365459%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=uO%2FrMWrkuu0VKBP7RNkY3%2BczA3AwI3h%2F57X5h%2F2go9Y%3D&reserved=0.

fcyu commented 3 years ago

No, I cannot find it. Can you send it to yufe@umich.edu?

Thanks,

Fengchao

fcyu commented 3 years ago

Thanks @FanLab2019 , I received your log.

Hi @guoci Attached is the log. The error was from speclib part. Can you take a look when you have time?

Best,

Fengchao

log_2021-05-14_09-17-43.txt.zip

guoci commented 3 years ago

Can you try reinstalling EasyPQP with the following in Anaconda Prompt and try again?

pip uninstall -y easypqp
pip install git+https://github.com/grosenberger/easypqp.git@master
FanLab2019 commented 3 years ago

Dear,

We still have issue on specLib, and keep getting error on SpecLib build up. We have tried to re-install everything, it doesn’t work.

Thanks,

Jia

From: Fengchao @.> Reply-To: Nesvilab/FragPipe @.> Date: Friday, May 14, 2021 at 10:20 AM To: Nesvilab/FragPipe @.> Cc: "Fan, Jia" @.>, Mention @.***> Subject: Re: [Nesvilab/FragPipe] Errors of EasyPOP (#370)

External Sender. Be aware of links, attachments and requests.

Thanks @FanLab2019https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FFanLab2019&data=04%7C01%7Cjfan5%40tulane.edu%7Ce0c73651fa1447b8b28708d916ebc400%7C9de9818325d94b139fc34de5489c1f3b%7C1%7C0%7C637566024134534264%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=yCad8uYbZYtGoyAvdRyVvyv8jYZjpOQ%2BIH8VqmR2nio%3D&reserved=0 , I received your log.

Hi @guocihttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fguoci&data=04%7C01%7Cjfan5%40tulane.edu%7Ce0c73651fa1447b8b28708d916ebc400%7C9de9818325d94b139fc34de5489c1f3b%7C1%7C0%7C637566024134544224%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Bp042Y5E0GNNjwi2rO6X8ZGEUavVfMX7zaGakKbax3U%3D&reserved=0 Attached is the log. The error was from speclib part. Can you take a look when you have time?

Best,

Fengchao

log_2021-05-14_09-17-43.txt.ziphttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNesvilab%2FFragPipe%2Ffiles%2F6479669%2Flog_2021-05-14_09-17-43.txt.zip&data=04%7C01%7Cjfan5%40tulane.edu%7Ce0c73651fa1447b8b28708d916ebc400%7C9de9818325d94b139fc34de5489c1f3b%7C1%7C0%7C637566024134544224%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=9b7%2FrZVO3DeyhvoMrPodx78VI2UxGWVEJbW3BLjUT6k%3D&reserved=0

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNesvilab%2FFragPipe%2Fissues%2F370%23issuecomment-841309987&data=04%7C01%7Cjfan5%40tulane.edu%7Ce0c73651fa1447b8b28708d916ebc400%7C9de9818325d94b139fc34de5489c1f3b%7C1%7C0%7C637566024134554177%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=enJnGxW05o4J74MFPqePmjk3CrnDPYfVX8rNh0fYG44%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQQMQVOOXUPBEPIW67SNYFLTNU5SVANCNFSM443MKY6Q&data=04%7C01%7Cjfan5%40tulane.edu%7Ce0c73651fa1447b8b28708d916ebc400%7C9de9818325d94b139fc34de5489c1f3b%7C1%7C0%7C637566024134554177%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=yrr4Ckp%2FBEEOs7o87yc8T6Ipt6C%2FxClMIojMYkzdX%2Bw%3D&reserved=0.

fcyu commented 3 years ago

I will reopen this issue.

@guoci Can you take a look when you have time?

Best,

Fengchao

FanLab2019 commented 3 years ago

Thank you, Jia

From: Fengchao @.> Reply-To: Nesvilab/FragPipe @.> Date: Friday, June 4, 2021 at 5:48 PM To: Nesvilab/FragPipe @.> Cc: "Fan, Jia" @.>, Mention @.***> Subject: Re: [Nesvilab/FragPipe] Errors of EasyPOP (#370)

External Sender. Be aware of links, attachments and requests.

I will reopen this issue.

@guocihttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fguoci&data=04%7C01%7Cjfan5%40tulane.edu%7C3b527452ba7e4694abcd08d927aae3df%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637584437183958378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=CQXsWau0kFmOPkl81U5oK1kx2Rw93cDBmnpkKjyhXe0%3D&reserved=0 Can you take a look when you have time?

Best,

Fengchao

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNesvilab%2FFragPipe%2Fissues%2F370%23issuecomment-855072010&data=04%7C01%7Cjfan5%40tulane.edu%7C3b527452ba7e4694abcd08d927aae3df%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637584437183968332%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jVCwqzc4A32Ec0PIlNYEl2ytb01WDHk4Tpg6tIozt%2F8%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQQMQVL2ZSB4HMNU5DHF64TTRFJ4HANCNFSM443MKY6Q&data=04%7C01%7Cjfan5%40tulane.edu%7C3b527452ba7e4694abcd08d927aae3df%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637584437183968332%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=22DIA%2Bw84X4%2BDm6mWszIO3ehkvsol7AariQmZRFfAMc%3D&reserved=0.

guoci commented 3 years ago

@FanLab2019 please post the log.

FanLab2019 commented 3 years ago

Attached please find the entire log.

Thanks, Jia

From: guoci @.> Reply-To: Nesvilab/FragPipe @.> Date: Saturday, June 5, 2021 at 2:19 PM To: Nesvilab/FragPipe @.> Cc: "Fan, Jia" @.>, Mention @.***> Subject: Re: [Nesvilab/FragPipe] Errors of EasyPOP (#370)

External Sender. Be aware of links, attachments and requests.

@FanLab2019https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FFanLab2019&data=04%7C01%7Cjfan5%40tulane.edu%7C2fa68e6000e24d54ebb108d92856da37%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637585175762924282%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ZmfbaRaOnpirq48S6oq5Jt837oCwF%2BZuezGfhmJbiNA%3D&reserved=0 please post the log.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNesvilab%2FFragPipe%2Fissues%2F370%23issuecomment-855284111&data=04%7C01%7Cjfan5%40tulane.edu%7C2fa68e6000e24d54ebb108d92856da37%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637585175762934248%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=NEMxA1w07NsZ49mlA9MWYJjVMvfEOKEWOpClB%2BZkf9U%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQQMQVITJH67NTFKEYX3BHLTRJ2ENANCNFSM443MKY6Q&data=04%7C01%7Cjfan5%40tulane.edu%7C2fa68e6000e24d54ebb108d92856da37%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637585175762934248%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6SV5AlV4VdbwO1bQAGXR3CUWx2AiZIcr7R326i28Q%2Fc%3D&reserved=0.

guoci commented 3 years ago

@FanLab2019 I did not receive your log

anesvi commented 3 years ago

I think GitHub removes attachments, please email us directly

From: guoci @.> Sent: Saturday, June 5, 2021 4:17 PM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: Re: [Nesvilab/FragPipe] Errors of EasyPOP (#370)

External Email - Use Caution

@FanLab2019https://github.com/FanLab2019 I did not receive your log

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/370#issuecomment-855290391, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM63QQFEPKZOE2VEUMP3TRKA3ZANCNFSM443MKY6Q.

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

FanLab2019 commented 3 years ago

Could I know the email address?

From: Alexey Nesvizhskii @.> Reply-To: Nesvilab/FragPipe @.> Date: Saturday, June 5, 2021 at 3:17 PM To: Nesvilab/FragPipe @.> Cc: "Fan, Jia" @.>, Mention @.***> Subject: Re: [Nesvilab/FragPipe] Errors of EasyPOP (#370)

External Sender. Be aware of links, attachments and requests. I think GitHub removes attachments, please email us directly

From: guoci @.> Sent: Saturday, June 5, 2021 4:17 PM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: Re: [Nesvilab/FragPipe] Errors of EasyPOP (#370)

External Email - Use Caution

@FanLab2019https://github.com/FanLab2019 I did not receive your log

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/370#issuecomment-855290391, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM63QQFEPKZOE2VEUMP3TRKA3ZANCNFSM443MKY6Q.

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNesvilab%2FFragPipe%2Fissues%2F370%23issuecomment-855290471&data=04%7C01%7Cjfan5%40tulane.edu%7Cda987b4b81894165e88b08d9285efc59%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637585210686338653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=fhxbUt4JX6gh1rTBwi57wbiEdVwjnxUwis7%2BT69TiCU%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQQMQVJKS43BDLUZIHRC3DTTRKA6VANCNFSM443MKY6Q&data=04%7C01%7Cjfan5%40tulane.edu%7Cda987b4b81894165e88b08d9285efc59%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637585210686348609%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=FLPce%2BKTKlGiexHcTnhSlpEjbyJw0LWSKrBBda44ARA%3D&reserved=0.

guoci commented 3 years ago

@FanLab2019 teog@umich.edu

FanLab2019 commented 3 years ago

Thank you, Hope you can receive the attachment.

Jia

From: guoci @.> Reply-To: Nesvilab/FragPipe @.> Date: Saturday, June 5, 2021 at 3:21 PM To: Nesvilab/FragPipe @.> Cc: "Fan, Jia" @.>, Mention @.***> Subject: Re: [Nesvilab/FragPipe] Errors of EasyPOP (#370)

External Sender. Be aware of links, attachments and requests.

@FanLab2019https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FFanLab2019&data=04%7C01%7Cjfan5%40tulane.edu%7C3538e9a0fa1f4bb3956b08d9285f7eb4%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637585212877650408%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=JZd7CjrJY5heCRALyRGiZhVpYdBhfb6YAXRjgvFZJws%3D&reserved=0 @.**@.>

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNesvilab%2FFragPipe%2Fissues%2F370%23issuecomment-855290863&data=04%7C01%7Cjfan5%40tulane.edu%7C3538e9a0fa1f4bb3956b08d9285f7eb4%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637585212877650408%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=bC05ZnFKTzhbpKkf%2FzjMoFFB167f2lBZS32aBtt6wjc%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQQMQVLFS3W3GWEQL5KHKI3TRKBMNANCNFSM443MKY6Q&data=04%7C01%7Cjfan5%40tulane.edu%7C3538e9a0fa1f4bb3956b08d9285f7eb4%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637585212877650408%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=LoUfzZbFdN0pYI4h31jls5dLwG%2Fie3NlCQiouU2EOW0%3D&reserved=0.

guoci commented 3 years ago

@FanLab2019 I have received the log, the reinstall did resolve the earlier issue. The log shows a different error. Can you send the following 2 files for me to investigate the issue? D:\\JiaF_SpecLib\\BC_Exo_test\\interact-BC_Exo_F1_20210415003310.pep.xml \\\\imgmt.tulane.local\\CCMD_MassSpec\\Jia_Fan\\2021Q2\\20210413_FatExo_BCExo_DDALibrary\\BC_Exo_F1_20210415003310.mzML

FanLab2019 commented 3 years ago

Both are too large to share through email. How could I share the files with you?

Thank you, Jia

From: guoci @.> Reply-To: Nesvilab/FragPipe @.> Date: Saturday, June 5, 2021 at 9:51 PM To: Nesvilab/FragPipe @.> Cc: "Fan, Jia" @.>, Mention @.***> Subject: Re: [Nesvilab/FragPipe] Errors of EasyPOP (#370)

External Sender. Be aware of links, attachments and requests.

@FanLab2019https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FFanLab2019&data=04%7C01%7Cjfan5%40tulane.edu%7Cfcb733da675b4c6a167508d92895f89a%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637585446857654636%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ZiNHDXPC%2Fl4PvqJLtA9S40L67EQHvjEEFYWisdtKPrU%3D&reserved=0 I have received the log, the reinstall did resolve the earlier issue. The log shows a different error. Can you send the following 2 files for me to investigate the issue? D:\JiaF_SpecLib\BC_Exo_test\interact-BC_Exo_F1_20210415003310.pep.xml \\imgmt.tulane.local\CCMD_MassSpec\Jia_Fan\2021Q2\20210413_FatExo_BCExo_DDALibrary\BC_Exo_F1_20210415003310.mzML

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNesvilab%2FFragPipe%2Fissues%2F370%23issuecomment-855328118&data=04%7C01%7Cjfan5%40tulane.edu%7Cfcb733da675b4c6a167508d92895f89a%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637585446857664584%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=fbYtJu2UXkQlSi6035T8PyWtzcX%2Bf3hDwWxDOadcFXk%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQQMQVJZSD6I36YRLYW7HX3TRLPCXANCNFSM443MKY6Q&data=04%7C01%7Cjfan5%40tulane.edu%7Cfcb733da675b4c6a167508d92895f89a%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637585446857664584%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=UUI9SH3PZa68oefsHFYrXUdOsZQmpxuWX7sTe4ysj9o%3D&reserved=0.

guoci commented 3 years ago

@FanLab2019 I have sent you a link to upload the files

FanLab2019 commented 3 years ago

Sorry. It seems I didn't get the link either on GitHub or my email. Could you please send the link to my email, jfan5@tulane.edu?

Thank you, Jia

guoci commented 3 years ago

@FanLab2019 The following mods you use are not in UniMod and triggered a bug in EasyPQP, I have made a fix.

variable_mod_06 = -131.040000 [^ 1
variable_mod_07 = -89.030000 [^ 1

Can you try installing my modified version of EasyPQP with the following in Anaconda Prompt and try again?

pip uninstall -y easypqp
pip install git+https://github.com/guoci/easypqp.git@fix_fc3c4a59c2bf36dfb295851de109bb12b0c88293
guoci commented 3 years ago

@FanLab2019 Please let me know if the fix worked.

FanLab2019 commented 3 years ago

Thank you it works now.

Sent from my iPhone

On Jun 12, 2021, at 3:11 PM, guoci @.***> wrote:

 External Sender. Be aware of links, attachments and requests.

@FanLab2019https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FFanLab2019&data=04%7C01%7Cjfan5%40tulane.edu%7Cb5b419b410284090268208d92dde4543%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637591254937366511%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=U6lXS9DvMBxtOOz8ZWPeo2qLrSrta1bNZsYTcdjiyfI%3D&reserved=0 Please let me know if the fix worked.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNesvilab%2FFragPipe%2Fissues%2F370%23issuecomment-860103157&data=04%7C01%7Cjfan5%40tulane.edu%7Cb5b419b410284090268208d92dde4543%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637591254937366511%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=iDh1sWpZpSkCQiy6ufSZefb0VfkjHA9Zhvq775ew%2Fh8%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQQMQVLV5YDCE77ZL2VV2KTTSO5PHANCNFSM443MKY6Q&data=04%7C01%7Cjfan5%40tulane.edu%7Cb5b419b410284090268208d92dde4543%7C9de9818325d94b139fc34de5489c1f3b%7C0%7C0%7C637591254937376465%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=SXG5xeFSrq%2BO77uTjPP69JmQL68AfXJJ2OAFfwT0STE%3D&reserved=0.