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Nesvilab / IonQuant

A label free quantification tool.
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Single Replicate Quant Issue #9

Closed enonimos closed 4 years ago

enonimos commented 4 years ago

Hello, I am trying to use FragPipe 13.0 (MSFragger 3.0 + Philosopher 3.2.9) for label-free quantification using IonQuant (see image of settings below). Initially, I was processing two files for comparison, treatment vs control. I noticed in my protein output that there are many proteins with > 5 - 10 peptides, but with zero intensity. I have tried to adjust several settings in the LFQ tab, but the result is the same. I dug into a few of the peptides belonging to the zero intensity proteins. The peptides are present in individual data folders (*_quant.csv and ion.tsv files) and are present in the combined_peptide.tsv, but they are absent from the mbr_ion.tsv. Also, these are not exclusively low intensity peptides, many are in 10^7 - 10^8 range.

I had acquired another technical replicate (with a different LC gradient) of these samples. For troubleshooting purposes, I setup another workflow that labeled each technical replicate as a biological replicate. With "N = 2" for each condition, the output witht the same settings resulted in several hundred less zero intensity proteins. So the addition of a second replicate seems to have allowed many more of the quantified peptides to be retained.

I am fairly confident that many of these peptides are strong hits, so I am not sure why they were discarded when a pair of treatment vs control samples was used?

I'm also getting the following warning during LFQ (with either set of two or four files).

[main] INFO smile.math.matrix.Factory - smile-netlib module is available. Jul 27, 2020 11:18:41 PM com.github.fommil.netlib.LAPACK WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK Jul 27, 2020 11:18:41 PM com.github.fommil.jni.JniLoader liberalLoad INFO: successfully loaded C:\Users\enoni\AppData\Local\Temp\jniloader5821154409928140893netlib-native_ref-win-x86_64.dll Jul 27, 2020 11:18:41 PM com.github.fommil.netlib.BLAS WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS Jul 27, 2020 11:18:41 PM com.github.fommil.jni.JniLoader load INFO: already loaded netlib-native_ref-win-x86_64.dll

Thanks for any insight you have.

Cheers, Todd

image

fcyu commented 4 years ago

Hi Todd,

Can you share the log files with us?

Those warnings can be ignored.

Best,

Fengchao

enonimos commented 4 years ago

Hi Fengchao, I've attached three log files, annotated with a suffix. The 2FILES was an analysis of the first condition I described in my post. The 4FILES_TECHREP, added the two additional raw files, but had FragPipe consider them as technical replicates. This had zero quant too, similar to the 2FILES case. The final 4FILES_BIOREP specified them as separated biological replicates. This was the best result, with much less zero quant.

Perhaps a related question, I was wondering what would be a typical or good correlation MBR correlation value? I am surprised that the values I see in the log file are not higher. I've tried analyzing another dataset and the correlation values are often not higher than 0.5 even for biological replicates. Yet the similarity at the ID level is often > 90% by qualitative comparison. So perhaps I don't understand what is being correlated during the MBR evaluation.

Thanks for your help!

On Tue, Jul 28, 2020 at 7:55 AM Fengchao notifications@github.com wrote:

Hi Todd,

Can you share the log files with us?

Those warnings can be ignored.

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/IonQuant/issues/9#issuecomment-665022519, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKFULXNEWRUBFZVPF6YHELDR53DFZANCNFSM4PKCVZ7Q .

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 13.0 MSFragger version 3.0 Philosopher version 3.2.9 (build 1593192429)

LCMS files: Experiment/Group: Mock

19 commands to execute: WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\Mock] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\Mock] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\OC43] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\OC43] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck PhilosopherDbAnnotate [Work dir: D:\Data\CoV-OC43\Mock] D:\Data\MSFragger\philosopher.exe database --annotate D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BKCoV-OC43.fasta --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe database --annotate D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BKCoV-OC43.fasta --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\CoV-OC43\OC43] D:\Data\MSFragger\philosopher.exe database --annotate D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BKCoV-OC43.fasta --prefix rev PhilosopherFilter [Work dir: D:\Data\CoV-OC43\OC43] D:\Data\MSFragger\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\CoV-OC43\OC43 --protxml D:\Data\CoV-OC43\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\CoV-OC43\Mock] D:\Data\MSFragger\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\CoV-OC43\Mock --protxml D:\Data\CoV-OC43\combined.prot.xml PhilosopherReport [Work dir: D:\Data\CoV-OC43\Mock] D:\Data\MSFragger\philosopher.exe report PhilosopherReport [Work dir: D:\Data\CoV-OC43\OC43] D:\Data\MSFragger\philosopher.exe report iProphet [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe iprophet --decoy rev_ --nonsp --output combined --threads 14 D:\Data\CoV-OC43\Mock\interact-202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pep.xml D:\Data\CoV-OC43\OC43\interact-202007_CoV-PRM_OC43-48hpi-1_DDA60min.pep.xml PhilosopherAbacus [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe abacus --razor --reprint --tag rev --protein --peptide OC43 Mock IonQuant [Work dir: D:\Data\CoV-OC43] java -Xmx16G -Dlibs.bruker.dir="D:\Data\MSFragger\ext\bruker" -Dlibs.thermo.dir="D:\Data\MSFragger\ext\thermo" -cp "D:\Data\MSFragger\fragpipe\tools\ionquant-1.3.6.jar;D:\Data\MSFragger\fragpipe\tools\batmass-io-1.17.4.jar" ionquant.IonQuant --threads 14 --ionmobility 0 --mbr 1 --proteinquant 2 --requantify 0 --mztol 5 --imtol 0.05 --rttol 0.4 --mbrmincorr 0.4 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 1 --ionfdr 0.01 --proteinfdr 0.01 --peptidefdr 0.01 --normalization 1 --minisotopes 2 --tp 3 --minfreq 0.5 --minions 2 --psm D:\Data\CoV-OC43\OC43\psm.tsv --psm D:\Data\CoV-OC43\Mock\psm.tsv --multidir D:\Data\CoV-OC43 D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.raw Mock\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pepXML D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.raw OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pepXML WorkspaceClean [Work dir: D:\Data\CoV-OC43\Mock] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\CoV-OC43\OC43] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [D:\Data\CoV-OC43]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\CoV-OC43\Mock]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\CoV-OC43]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\CoV-OC43\OC43]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Data\CoV-OC43]
    Cmd: [PhilosopherFilter], Work dir: [D:\Data\CoV-OC43]
    Cmd: [PhilosopherReport], Work dir: [D:\Data\CoV-OC43]
    Cmd: [iProphet], Work dir: [D:\Data\CoV-OC43]
    Cmd: [PhilosopherAbacus], Work dir: [D:\Data\CoV-OC43]
    Cmd: [IonQuant], Work dir: [D:\Data\CoV-OC43]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\CoV-OC43\Mock]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\CoV-OC43]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\CoV-OC43\OC43]

# FragPipe v13.0ui state cache

crystalc.correct_isotope_error=false
crystalc.isotope_number=3
crystalc.max-charge=6
crystalc.precursor_isolation_window=0.7
crystalc.precursor_mass=20
crystalc.run-crystalc=false
database.db-path=D\:\\Data\\_FASTA\\2020-07-17-decoys-2020_03_UniProtS_Human_BK_CoV-OC43.fasta
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=D\:\\Data\\MSFragger\\MSFragger-3.0.jar
fragpipe-config.bin-philosopher=D\:\\Data\\MSFragger\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\enoni\\miniconda3\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.label=
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0.4
ionquant.mbrrttol=1
ionquant.mbrtoprun=1
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.mztol=5
ionquant.normalization=1
ionquant.peptidefdr=0.01
ionquant.proteinfdr=0.01
ionquant.proteinquant=2
ionquant.requantify=0
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
msfragger.Y_type_masses=0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=1
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deltamass_allowed_residues=ST
msfragger.diagnostic_fragments=204.086646 186.076086 168.065526 366.139466 144.0656 138.055 126.055 163.060096 512.197375 292.1026925 274.0921325 657.2349 243.026426 405.079246 485.045576 308.09761
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown=trypsin
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-25
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=25
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.run-msfragger=false
msfragger.search_enzyme_butnotafter=P
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=trypsin
msfragger.table.fix-mods=0.00000,C-Term Peptide,true,-1; 0.00000,N-Term Peptide,true,-1; 0.00000,C-Term Protein,true,-1; 0.00000,N-Term Protein,true,-1; 0.00000,G (glycine),true,-1; 0.00000,A (alanine),true,-1; 0.00000,S (serine),true,-1; 0.00000,P (proline),true,-1; 0.00000,V (valine),true,-1; 0.00000,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.00000,L (leucine),true,-1; 0.00000,I (isoleucine),true,-1; 0.00000,N (asparagine),true,-1; 0.00000,D (aspartic acid),true,-1; 0.00000,Q (glutamine),true,-1; 0.00000,K (lysine),true,-1; 0.00000,E (glutamic acid),true,-1; 0.00000,M (methionine),true,-1; 0.00000,H (histidine),true,-1; 0.00000,F (phenylalanine),true,-1; 0.00000,R (arginine),true,-1; 0.00000,Y (tyrosine),true,-1; 0.00000,W (tryptophan),true,-1; 0.00000,B ,true,-1; 0.00000,J,true,-1; 0.00000,O,true,-1; 0.00000,U,true,-1; 0.00000,X,true,-1; 0.00000,Z,true,-1
msfragger.table.var-mods=15.99490,M,true,3; 42.01060,[^,true,1; 79.96633,STY,false,3; -17.02650,nQnC,true,1; -18.01060,nE,false,1; 0.98402,N,false,2; 0.00000,site_07,false,1; 0.00000,site_08,false,1; 0.00000,site_09,false,1; 0.00000,site_10,false,1; 0.00000,site_11,false,1; 0.00000,site_12,false,1; 0.00000,site_13,false,1; 0.00000,site_14,false,1; 0.00000,site_15,false,1; 0.00000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0.00
msfragger.zero_bin_mult_expect=1.00
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01
phi-report.pep-level-summary=true
phi-report.print-decoys=false
phi-report.run-report=true
phi-report.write-mzid=false
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=false
ptmshepherd.annotation_tol=0.01
ptmshepherd.histo_smoothbins=2
ptmshepherd.localization_background=4
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.run-shepherd=false
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
speclibgen.easypqp.extras.rt_lowess_fraction=0.04
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tmtintegrator.add_Ref=-1
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=0
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\Data\\CoV-OC43
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=14

WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\Mock] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck INFO[22:20:45] Executing Workspace v3.2.9
INFO[22:20:45] Removing workspace
INFO[22:20:45] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\Mock] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck INFO[22:20:45] Executing Workspace v3.2.9
INFO[22:20:45] Creating workspace
INFO[22:20:45] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck INFO[22:20:45] Executing Workspace v3.2.9
INFO[22:20:45] Removing workspace
INFO[22:20:45] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck INFO[22:20:45] Executing Workspace v3.2.9
INFO[22:20:45] Creating workspace
INFO[22:20:45] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\OC43] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck INFO[22:20:46] Executing Workspace v3.2.9
INFO[22:20:46] Removing workspace
INFO[22:20:46] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\OC43] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[22:20:46] Executing Workspace v3.2.9
INFO[22:20:46] Creating workspace
INFO[22:20:46] Done
PhilosopherDbAnnotate [Work dir: D:\Data\CoV-OC43\Mock] D:\Data\MSFragger\philosopher.exe database --annotate D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BKCoV-OC43.fasta --prefix rev INFO[22:20:46] Executing Database v3.2.9
INFO[22:20:46] Processing database
Process 'PhilosopherDbAnnotate' finished, exit code: 0 INFO[22:20:48] Done
PhilosopherDbAnnotate [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe database --annotate D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BKCoV-OC43.fasta --prefix rev INFO[22:20:48] Executing Database v3.2.9
INFO[22:20:48] Processing database
INFO[22:20:51] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\Data\CoV-OC43\OC43] D:\Data\MSFragger\philosopher.exe database --annotate D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BKCoV-OC43.fasta --prefix rev INFO[22:20:51] Executing Database v3.2.9
INFO[22:20:51] Processing database
INFO[22:20:53] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: D:\Data\CoV-OC43\OC43] D:\Data\MSFragger\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\CoV-OC43\OC43 --protxml D:\Data\CoV-OC43\combined.prot.xml INFO[22:20:53] Executing Filter v3.2.9
INFO[22:20:53] Processing peptide identification files
INFO[22:20:56] 1+ Charge profile decoy=0 target=0 INFO[22:20:56] 2+ Charge profile decoy=88 target=13273 INFO[22:20:56] 3+ Charge profile decoy=83 target=10740 INFO[22:20:56] 4+ Charge profile decoy=0 target=0 INFO[22:20:56] 5+ Charge profile decoy=0 target=0 INFO[22:20:56] 6+ Charge profile decoy=0 target=0 INFO[22:20:56] Database search results ions=21755 peptides=19243 psms=24184 INFO[22:20:56] Converged to 0.71 % FDR with 24013 PSMs decoy=171 threshold=0.0502 total=24184 INFO[22:20:56] Converged to 0.88 % FDR with 19075 Peptides decoy=168 threshold=0.0502 total=19243 INFO[22:20:56] Converged to 0.77 % FDR with 21587 Ions decoy=168 threshold=0.0502 total=21755 INFO[22:20:58] Protein inference results decoy=505 target=4810 INFO[22:20:58] Converged to 1.01 % FDR with 3776 Proteins decoy=38 threshold=0.9808 total=3814 INFO[22:20:59] Applying sequential FDR estimation ions=21416 peptides=18904 psms=23840 INFO[22:21:00] Converged to 0.10 % FDR with 23816 PSMs decoy=24 threshold=0.0506 total=23840 INFO[22:21:00] Converged to 0.12 % FDR with 18880 Peptides decoy=24 threshold=0.0507 total=18904 INFO[22:21:00] Converged to 0.11 % FDR with 21392 Ions decoy=24 threshold=0.0507 total=21416 INFO[22:21:00] Post processing identifications
INFO[22:21:02] Mapping modifications
INFO[22:21:06] Processing protein inference
INFO[22:21:13] Assigning protein identifications to layers
INFO[22:21:13] Updating razor PSM assignment to proteins
INFO[22:21:14] Calculating spectral counts
INFO[22:21:14] Saving
INFO[22:21:16] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\Data\CoV-OC43\Mock] D:\Data\MSFragger\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\CoV-OC43\Mock --protxml D:\Data\CoV-OC43\combined.prot.xml INFO[22:21:16] Executing Filter v3.2.9
INFO[22:21:16] Processing peptide identification files
INFO[22:21:19] 1+ Charge profile decoy=0 target=0 INFO[22:21:19] 2+ Charge profile decoy=138 target=18054 INFO[22:21:19] 3+ Charge profile decoy=104 target=11959 INFO[22:21:19] 4+ Charge profile decoy=0 target=0 INFO[22:21:19] 5+ Charge profile decoy=0 target=0 INFO[22:21:19] 6+ Charge profile decoy=0 target=0 INFO[22:21:19] Database search results ions=26871 peptides=23157 psms=30255 INFO[22:21:19] Converged to 0.80 % FDR with 30013 PSMs decoy=242 threshold=0.0501 total=30255 INFO[22:21:19] Converged to 1.00 % FDR with 22923 Peptides decoy=231 threshold=0.0519 total=23154 INFO[22:21:20] Converged to 0.89 % FDR with 26634 Ions decoy=237 threshold=0.0501 total=26871 INFO[22:21:22] Protein inference results decoy=505 target=4810 INFO[22:21:22] Converged to 1.01 % FDR with 3776 Proteins decoy=38 threshold=0.9808 total=3814 INFO[22:21:23] Applying sequential FDR estimation ions=26349 peptides=22639 psms=29721 INFO[22:21:23] Converged to 0.08 % FDR with 29696 PSMs decoy=25 threshold=0.0501 total=29721 INFO[22:21:23] Converged to 0.10 % FDR with 22615 Peptides decoy=24 threshold=0.0501 total=22639 INFO[22:21:24] Converged to 0.09 % FDR with 26324 Ions decoy=25 threshold=0.0501 total=26349 INFO[22:21:24] Post processing identifications
INFO[22:21:26] Mapping modifications
INFO[22:21:31] Processing protein inference
INFO[22:21:38] Assigning protein identifications to layers
INFO[22:21:38] Updating razor PSM assignment to proteins
INFO[22:21:39] Calculating spectral counts
INFO[22:21:39] Saving
INFO[22:21:42] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: D:\Data\CoV-OC43\Mock] D:\Data\MSFragger\philosopher.exe report INFO[22:21:42] Executing Report v3.2.9
INFO[22:21:46] Creating reports
INFO[22:21:47] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\Data\CoV-OC43\OC43] D:\Data\MSFragger\philosopher.exe report INFO[22:21:47] Executing Report v3.2.9
INFO[22:21:51] Creating reports
INFO[22:21:52] Done
Process 'PhilosopherReport' finished, exit code: 0 iProphet [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe iprophet --decoy rev_ --nonsp --output combined --threads 14 D:\Data\CoV-OC43\Mock\interact-202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pep.xml D:\Data\CoV-OC43\OC43\interact-202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pep.xml INFO[22:21:52] Executing InterProphet v3.2.9
Running FPKM NSS NRS NSE NSI NSM Model EM: Computing NSS values ...

Creating 14 threads Wait for threads to finish ... ........................................................ done Computing NRS values ...

Creating 14 threads Wait for threads to finish ... 0--------------------------------------------------50------------------------------------------------100% ..................................................................................................... done Computing NSE values ...

Creating 14 threads Wait for threads to finish ... 0--------------------------------------------------50------------------------------------------------100% ..................................................................................................... done Computing NSI values ...

Creating 14 threads Wait for threads to finish ... 0--------------------------------------------------50------------------------------------------------100% ..................................................................................................... done Computing NSM values ...

Creating 14 threads Wait for threads to finish ... 0--------------------------------------------------50------------------------------------------------100% ..................................................................................................... done FPKM values are unavailable ... Iterations: .........10.......done INFO[22:22:45] Done
Process 'iProphet' finished, exit code: 0 PhilosopherAbacus [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe abacus --razor --reprint --tag rev_ --protein --peptide OC43 Mock INFO[22:22:45] Executing Abacus v3.2.9
INFO[22:22:45] Processing combined file
INFO[22:22:51] Converged to 0.97 % FDR with 53914 PSMs decoy=525 threshold=0.0328578 total=54439 INFO[22:22:51] Converged to 1.00 % FDR with 27359 Peptides decoy=276 threshold=0.252497 total=27635 INFO[22:22:51] Restoring peptide results
INFO[22:22:53] Collecting data from individual experiments
INFO[22:22:53] Processing spectral counts
INFO[22:22:53] Processing intensities
INFO[22:22:53] Processing combined file
INFO[22:22:55] Converged to 1.01 % FDR with 3776 Proteins decoy=38 threshold=0.9808 total=3814 INFO[22:23:00] Restoring protein results
INFO[22:23:09] Processing spectral counts
INFO[22:23:15] Processing intensities
INFO[22:23:16] Creating Reprint reports
INFO[22:23:16] Done
Process 'PhilosopherAbacus' finished, exit code: 0 IonQuant [Work dir: D:\Data\CoV-OC43] java -Xmx16G -Dlibs.bruker.dir="D:\Data\MSFragger\ext\bruker" -Dlibs.thermo.dir="D:\Data\MSFragger\ext\thermo" -cp "D:\Data\MSFragger\fragpipe\tools\ionquant-1.3.6.jar;D:\Data\MSFragger\fragpipe\tools\batmass-io-1.17.4.jar" ionquant.IonQuant --threads 14 --ionmobility 0 --mbr 1 --proteinquant 2 --requantify 0 --mztol 5 --imtol 0.05 --rttol 0.4 --mbrmincorr 0.4 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 1 --ionfdr 0.01 --proteinfdr 0.01 --peptidefdr 0.01 --normalization 1 --minisotopes 2 --tp 3 --minfreq 0.5 --minions 2 --psm D:\Data\CoV-OC43\OC43\psm.tsv --psm D:\Data\CoV-OC43\Mock\psm.tsv --multidir D:\Data\CoV-OC43 D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.raw Mock\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pepXML D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.raw OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pepXML IonQuant version IonQuant-1.3.6 Batmass-IO version 1.17.4 timsdata library version timsdata-2-4-4 (c) University of Michigan System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 16 GB memory 2020-07-27 22:23:16 [INFO] - Parameters: 2020-07-27 22:23:16 [INFO] - threads = 14 2020-07-27 22:23:16 [INFO] - mztol = 5.0 2020-07-27 22:23:16 [INFO] - rttol = 0.4 2020-07-27 22:23:16 [INFO] - imtol = 0.05 2020-07-27 22:23:16 [INFO] - seedmz = 0 2020-07-27 22:23:16 [INFO] - minisotopes = 2 2020-07-27 22:23:16 [INFO] - psm = D:\Data\CoV-OC43\Mock\psm.tsv 2020-07-27 22:23:16 [INFO] - psm = D:\Data\CoV-OC43\OC43\psm.tsv 2020-07-27 22:23:16 [INFO] - multidir = D:\Data\CoV-OC43\ 2020-07-27 22:23:16 [INFO] - minions = 2 2020-07-27 22:23:16 [INFO] - proteinquant = 2 2020-07-27 22:23:16 [INFO] - normalization = 1 2020-07-27 22:23:16 [INFO] - minfreq = 0.5 2020-07-27 22:23:16 [INFO] - tp = 3 2020-07-27 22:23:16 [INFO] - mbr = 1 2020-07-27 22:23:16 [INFO] - mbrrttol = 1.0 2020-07-27 22:23:16 [INFO] - mbrimtol = 0.05 2020-07-27 22:23:16 [INFO] - mbrtoprun = 1 2020-07-27 22:23:16 [INFO] - mbrmincorr = 0.4 2020-07-27 22:23:16 [INFO] - ionmobility = 0 2020-07-27 22:23:16 [INFO] - ionfdr = 0.01 2020-07-27 22:23:16 [INFO] - peptidefdr = 0.01 2020-07-27 22:23:16 [INFO] - proteinfdr = 0.01 2020-07-27 22:23:16 [INFO] - requantify = 0 2020-07-27 22:23:16 [INFO] - D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.raw 2020-07-27 22:23:16 [INFO] - D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.raw 2020-07-27 22:23:16 [INFO] - D:\Data\CoV-OC43\Mock\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pepXML 2020-07-27 22:23:16 [INFO] - D:\Data\CoV-OC43\OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pepXML 2020-07-27 22:23:16 [INFO] - Checking D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.raw... 2020-07-27 22:23:18 [INFO] - Checking D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.raw... 2020-07-27 22:23:19 [INFO] - There is an existing index D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.quantindex for run D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.raw. Will use that index in the analysis. 2020-07-27 22:23:19 [INFO] - There is an existing index D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.quantindex for run D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.raw. Will use that index in the analysis. 2020-07-27 22:23:19 [INFO] - Loading D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.quantindex... 2020-07-27 22:23:19 [INFO] - Loading D:\Data\CoV-OC43\Mock\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pepXML... 2020-07-27 22:23:21 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2020-07-27 22:23:21 [INFO] - Quantifying... 2020-07-27 22:23:22 [INFO] - Loading D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.quantindex... 2020-07-27 22:23:22 [INFO] - Loading D:\Data\CoV-OC43\OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pepXML... 2020-07-27 22:23:23 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2020-07-27 22:23:23 [INFO] - Quantifying... 2020-07-27 22:23:23 [INFO] - Updating Philosopher's tables... 2020-07-27 22:23:26 [INFO] - Matching-between-runs: 202007_CoV-PRM_Mock-48hpi-1_DDA_60min... 2020-07-27 22:23:26 [INFO] - Calculating correlations between all other runs... 2020-07-27 22:23:26 [INFO] - Correlation with 202007_CoV-PRM_OC43-48hpi-1_DDA_60min: 0.46005568 2020-07-27 22:23:26 [INFO] - Reading index from D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.quantindex 2020-07-27 22:23:27 [INFO] - Mapping ions from 202007_CoV-PRM_OC43-48hpi-1_DDA_60min to 202007_CoV-PRM_Mock-48hpi-1_DDA_60min... [main] INFO smile.math.matrix.Factory - smile-netlib module is available. 2020-07-27 22:23:27 [INFO] - Training LDA models for all matched features. Jul 27, 2020 10:23:28 PM com.github.fommil.netlib.LAPACK WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK Jul 27, 2020 10:23:28 PM com.github.fommil.jni.JniLoader liberalLoad INFO: successfully loaded C:\Users\enoni\AppData\Local\Temp\jniloader8963428966453624780netlib-native_ref-win-x86_64.dll Jul 27, 2020 10:23:28 PM com.github.fommil.netlib.BLAS WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS Jul 27, 2020 10:23:28 PM com.github.fommil.jni.JniLoader load INFO: already loaded netlib-native_ref-win-x86_64.dll 2020-07-27 22:23:28 [INFO] - Standardized coefficients: 2020-07-27 22:23:28 [INFO] - log10(intensity): 0.11712324273380982 2020-07-27 22:23:28 [INFO] - log10(KL): -0.17729299080844574 2020-07-27 22:23:28 [INFO] - log10(KL_negative_1): 0.12514602489480633 2020-07-27 22:23:28 [INFO] - log10(KL_negative_2): 0.09393291492432893 2020-07-27 22:23:28 [INFO] - abs(ppm): -0.5843479243558867 2020-07-27 22:23:28 [INFO] - RT diff: -0.12245229293553139 2020-07-27 22:23:28 [INFO] - log10(intensity) diff: -0.7575359376813993 2020-07-27 22:23:28 [INFO] - correlation between runs: -0.006731412314652197 2020-07-27 22:23:28 [INFO] - matched run percentage: 0.0011626838657226145 2020-07-27 22:23:28 [INFO] - Fitting a mixture model... 2020-07-27 22:23:30 [INFO] - Matching-between-runs: 202007_CoV-PRM_OC43-48hpi-1_DDA_60min... 2020-07-27 22:23:30 [INFO] - Calculating correlations between all other runs... 2020-07-27 22:23:30 [INFO] - Correlation with 202007_CoV-PRM_Mock-48hpi-1_DDA_60min: 0.46005568 2020-07-27 22:23:30 [INFO] - Reading index from D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.quantindex 2020-07-27 22:23:31 [INFO] - Mapping ions from 202007_CoV-PRM_Mock-48hpi-1_DDA_60min to 202007_CoV-PRM_OC43-48hpi-1_DDA_60min... 2020-07-27 22:23:32 [INFO] - Training LDA models for all matched features. 2020-07-27 22:23:32 [INFO] - Standardized coefficients: 2020-07-27 22:23:32 [INFO] - log10(intensity): 0.09045735809811224 2020-07-27 22:23:32 [INFO] - log10(KL): -0.14856047635298286 2020-07-27 22:23:32 [INFO] - log10(KL_negative_1): 0.10960170139270961 2020-07-27 22:23:32 [INFO] - log10(KL_negative_2): 0.07444602265495577 2020-07-27 22:23:32 [INFO] - abs(ppm): -0.5364735596752676 2020-07-27 22:23:32 [INFO] - RT diff: -0.11287509317008243 2020-07-27 22:23:32 [INFO] - log10(intensity) diff: -0.8072436415266602 2020-07-27 22:23:32 [INFO] - correlation between runs: -0.00232214846266086 2020-07-27 22:23:32 [INFO] - matched run percentage: -3.8980360798251067E-4 2020-07-27 22:23:32 [INFO] - Fitting a mixture model... 2020-07-27 22:23:32 [INFO] - Estimating match-between-runs FDR... 2020-07-27 22:23:33 [INFO] - Updating Philosopher's tables... 2020-07-27 22:23:35 [INFO] - Combining experiments and estimating protein intensity... 2020-07-27 22:23:36 [INFO] - Done! Process 'IonQuant' finished, exit code: 0 WorkspaceClean [Work dir: D:\Data\CoV-OC43\Mock] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck INFO[22:23:37] Executing Workspace v3.2.9
INFO[22:23:37] Removing workspace
INFO[22:23:37] Done
Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck INFO[22:23:37] Executing Workspace v3.2.9
INFO[22:23:37] Removing workspace
INFO[22:23:37] Done
Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: D:\Data\CoV-OC43\OC43] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck INFO[22:23:37] Executing Workspace v3.2.9
INFO[22:23:37] Removing workspace
INFO[22:23:37] Done

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 13.0 MSFragger version 3.0 Philosopher version 3.2.9 (build 1593192429)

LCMS files: Experiment/Group: Mock_01

49 commands to execute: WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\OC43_02] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\OC43_02] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\OC43_01] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\OC43_01] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\Mock_02] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\Mock_02] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\Mock_01] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\Mock_01] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck MsFragger [Work dir: D:\Data\CoV-OC43] java -jar -Dfile.encoding=UTF-8 -Xmx17G D:\Data\MSFragger\MSFragger-3.0.jar D:\Data\CoV-OC43\fragger.params D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.raw D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_90min.mzML D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.raw D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_90min.mzML MsFragger java -cp D:\Data\MSFragger\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pepXML D:\Data\CoV-OC43\Mock_01\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pepXML MsFragger java -cp D:\Data\MSFragger\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_90min.pepXML D:\Data\CoV-OC43\Mock_02\202007_CoV-PRM_Mock-48hpi-1_DDA_90min.pepXML MsFragger java -cp D:\Data\MSFragger\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pepXML D:\Data\CoV-OC43\OC43_01\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pepXML MsFragger java -cp D:\Data\MSFragger\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_90min.pepXML D:\Data\CoV-OC43\OC43_02\202007_CoV-PRM_OC43-48hpi-1_DDA_90min.pepXML PeptideProphet: Workspace init [Work dir: D:\Data\CoV-OC43\Mock_02\fragpipe-202007_CoV-PRM_Mock-48hpi-1_DDA_90min.pepXML-temp] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Data\CoV-OC43\OC43_02\fragpipe-202007_CoV-PRM_OC43-48hpi-1_DDA_90min.pepXML-temp] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Data\CoV-OC43\OC43_01\fragpipe-202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pepXML-temp] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Data\CoV-OC43\Mock_01\fragpipe-202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pepXML-temp] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: D:\Data\CoV-OC43\Mock_02\fragpipe-202007_CoV-PRM_Mock-48hpi-1_DDA90min.pepXML-temp] D:\Data\MSFragger\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BK_CoV-OC43.fasta ..\202007_CoV-PRM_Mock-48hpi-1_DDA_90min.pepXML PeptideProphet [Work dir: D:\Data\CoV-OC43\OC43_02\fragpipe-202007_CoV-PRM_OC43-48hpi-1_DDA90min.pepXML-temp] D:\Data\MSFragger\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BK_CoV-OC43.fasta ..\202007_CoV-PRM_OC43-48hpi-1_DDA_90min.pepXML PeptideProphet [Work dir: D:\Data\CoV-OC43\OC43_01\fragpipe-202007_CoV-PRM_OC43-48hpi-1_DDA60min.pepXML-temp] D:\Data\MSFragger\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BK_CoV-OC43.fasta ..\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pepXML PeptideProphet [Work dir: D:\Data\CoV-OC43\Mock_01\fragpipe-202007_CoV-PRM_Mock-48hpi-1_DDA60min.pepXML-temp] D:\Data\MSFragger\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BK_CoV-OC43.fasta ..\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pepXML PeptideProphet: Delete temp java -cp D:\Data\MSFragger\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\Data\CoV-OC43\Mock_02\fragpipe-202007_CoV-PRM_Mock-48hpi-1_DDA_90min.pepXML-temp PeptideProphet: Delete temp java -cp D:\Data\MSFragger\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\Data\CoV-OC43\OC43_02\fragpipe-202007_CoV-PRM_OC43-48hpi-1_DDA_90min.pepXML-temp PeptideProphet: Delete temp java -cp D:\Data\MSFragger\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\Data\CoV-OC43\OC43_01\fragpipe-202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pepXML-temp PeptideProphet: Delete temp java -cp D:\Data\MSFragger\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileDelete D:\Data\CoV-OC43\Mock_01\fragpipe-202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pepXML-temp ProteinProphet [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\Data\CoV-OC43\Mock_02\interact-202007_CoV-PRM_Mock-48hpi-1_DDA_90min.pep.xml D:\Data\CoV-OC43\OC43_02\interact-202007_CoV-PRM_OC43-48hpi-1_DDA_90min.pep.xml D:\Data\CoV-OC43\OC43_01\interact-202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pep.xml D:\Data\CoV-OC43\Mock_01\interact-202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pep.xml PhilosopherDbAnnotate [Work dir: D:\Data\CoV-OC43\OC43_02] D:\Data\MSFragger\philosopher.exe database --annotate D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BKCoV-OC43.fasta --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\CoV-OC43\OC43_01] D:\Data\MSFragger\philosopher.exe database --annotate D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BKCoV-OC43.fasta --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe database --annotate D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BKCoV-OC43.fasta --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\CoV-OC43\Mock_02] D:\Data\MSFragger\philosopher.exe database --annotate D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BKCoV-OC43.fasta --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\CoV-OC43\Mock_01] D:\Data\MSFragger\philosopher.exe database --annotate D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BKCoV-OC43.fasta --prefix rev PhilosopherFilter [Work dir: D:\Data\CoV-OC43\OC4302] D:\Data\MSFragger\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\CoV-OC43\OC43_02 --protxml D:\Data\CoV-OC43\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\CoV-OC43\Mock01] D:\Data\MSFragger\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\CoV-OC43\Mock_01 --protxml D:\Data\CoV-OC43\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\CoV-OC43\Mock02] D:\Data\MSFragger\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\CoV-OC43\Mock_02 --protxml D:\Data\CoV-OC43\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\CoV-OC43\OC4301] D:\Data\MSFragger\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\CoV-OC43\OC43_01 --protxml D:\Data\CoV-OC43\combined.prot.xml PhilosopherReport [Work dir: D:\Data\CoV-OC43\OC43_02] D:\Data\MSFragger\philosopher.exe report PhilosopherReport [Work dir: D:\Data\CoV-OC43\OC43_01] D:\Data\MSFragger\philosopher.exe report PhilosopherReport [Work dir: D:\Data\CoV-OC43\Mock_02] D:\Data\MSFragger\philosopher.exe report PhilosopherReport [Work dir: D:\Data\CoV-OC43\Mock01] D:\Data\MSFragger\philosopher.exe report iProphet [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe iprophet --decoy rev --nonsp --output combined --threads 14 D:\Data\CoV-OC43\Mock_02\interact-202007_CoV-PRM_Mock-48hpi-1_DDA_90min.pep.xml D:\Data\CoV-OC43\OC43_02\interact-202007_CoV-PRM_OC43-48hpi-1_DDA_90min.pep.xml D:\Data\CoV-OC43\OC43_01\interact-202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pep.xml D:\Data\CoV-OC43\Mock_01\interact-202007_CoV-PRM_Mock-48hpi-1_DDA60min.pep.xml PhilosopherAbacus [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe abacus --razor --reprint --tag rev --protein --peptide OC43_02 Mock_01 Mock_02 OC43_01 IonQuant [Work dir: D:\Data\CoV-OC43] java -Xmx17G -Dlibs.bruker.dir="D:\Data\MSFragger\ext\bruker" -Dlibs.thermo.dir="D:\Data\MSFragger\ext\thermo" -cp "D:\Data\MSFragger\fragpipe\tools\ionquant-1.3.6.jar;D:\Data\MSFragger\fragpipe\tools\batmass-io-1.17.4.jar" ionquant.IonQuant --threads 14 --ionmobility 0 --mbr 1 --proteinquant 2 --requantify 0 --mztol 5 --imtol 0.05 --rttol 0.4 --mbrmincorr 0.4 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 3 --ionfdr 0.01 --proteinfdr 0.01 --peptidefdr 0.01 --normalization 1 --minisotopes 2 --tp 3 --minfreq 0.5 --minions 2 --psm D:\Data\CoV-OC43\OC43_02\psm.tsv --psm D:\Data\CoV-OC43\Mock_01\psm.tsv --psm D:\Data\CoV-OC43\Mock_02\psm.tsv --psm D:\Data\CoV-OC43\OC43_01\psm.tsv --multidir D:\Data\CoV-OC43 D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_90min.mzML Mock_02\202007_CoV-PRM_Mock-48hpi-1_DDA_90min.pepXML D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_90min.mzML OC43_02\202007_CoV-PRM_OC43-48hpi-1_DDA_90min.pepXML D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.raw OC43_01\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.pepXML D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.raw Mock_01\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.pepXML WorkspaceClean [Work dir: D:\Data\CoV-OC43\OC43_02] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\CoV-OC43\OC43_01] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\CoV-OC43\Mock_02] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\CoV-OC43\Mock_01] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [D:\Data\CoV-OC43]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\CoV-OC43\OC43_02]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\CoV-OC43\OC43_01]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\CoV-OC43]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\CoV-OC43\Mock_02]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\CoV-OC43\Mock_01]
    Cmd: [MsFragger], Work dir: [D:\Data\CoV-OC43]
    Cmd: [PeptideProphet], Work dir: [D:\Data\CoV-OC43]
    Cmd: [ProteinProphet], Work dir: [D:\Data\CoV-OC43]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Data\CoV-OC43]
    Cmd: [PhilosopherFilter], Work dir: [D:\Data\CoV-OC43]
    Cmd: [PhilosopherReport], Work dir: [D:\Data\CoV-OC43]
    Cmd: [iProphet], Work dir: [D:\Data\CoV-OC43]
    Cmd: [PhilosopherAbacus], Work dir: [D:\Data\CoV-OC43]
    Cmd: [IonQuant], Work dir: [D:\Data\CoV-OC43]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\CoV-OC43\OC43_02]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\CoV-OC43\OC43_01]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\CoV-OC43]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\CoV-OC43\Mock_02]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\CoV-OC43\Mock_01]

# FragPipe v13.0ui state cache

crystalc.correct_isotope_error=false
crystalc.isotope_number=3
crystalc.max-charge=6
crystalc.precursor_isolation_window=0.7
crystalc.precursor_mass=20
crystalc.run-crystalc=false
database.db-path=D\:\\Data\\_FASTA\\2020-07-17-decoys-2020_03_UniProtS_Human_BK_CoV-OC43.fasta
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=D\:\\Data\\MSFragger\\MSFragger-3.0.jar
fragpipe-config.bin-philosopher=D\:\\Data\\MSFragger\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\enoni\\miniconda3\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.label=
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0.4
ionquant.mbrrttol=1
ionquant.mbrtoprun=3
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.mztol=5
ionquant.normalization=1
ionquant.peptidefdr=0.01
ionquant.proteinfdr=0.01
ionquant.proteinquant=2
ionquant.requantify=0
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
msfragger.Y_type_masses=0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=1
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deltamass_allowed_residues=ST
msfragger.diagnostic_fragments=204.086646 186.076086 168.065526 366.139466 144.0656 138.055 126.055 163.060096 512.197375 292.1026925 274.0921325 657.2349 243.026426 405.079246 485.045576 308.09761
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown=trypsin
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-25
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=25
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=P
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=trypsin
msfragger.table.fix-mods=0.00000,C-Term Peptide,true,-1; 0.00000,N-Term Peptide,true,-1; 0.00000,C-Term Protein,true,-1; 0.00000,N-Term Protein,true,-1; 0.00000,G (glycine),true,-1; 0.00000,A (alanine),true,-1; 0.00000,S (serine),true,-1; 0.00000,P (proline),true,-1; 0.00000,V (valine),true,-1; 0.00000,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.00000,L (leucine),true,-1; 0.00000,I (isoleucine),true,-1; 0.00000,N (asparagine),true,-1; 0.00000,D (aspartic acid),true,-1; 0.00000,Q (glutamine),true,-1; 0.00000,K (lysine),true,-1; 0.00000,E (glutamic acid),true,-1; 0.00000,M (methionine),true,-1; 0.00000,H (histidine),true,-1; 0.00000,F (phenylalanine),true,-1; 0.00000,R (arginine),true,-1; 0.00000,Y (tyrosine),true,-1; 0.00000,W (tryptophan),true,-1; 0.00000,B ,true,-1; 0.00000,J,true,-1; 0.00000,O,true,-1; 0.00000,U,true,-1; 0.00000,X,true,-1; 0.00000,Z,true,-1
msfragger.table.var-mods=15.99490,M,true,3; 42.01060,[^,true,1; 79.96633,STY,false,3; -17.02650,nQnC,true,1; -18.01060,nE,false,1; 0.98402,N,false,2; 0.00000,site_07,false,1; 0.00000,site_08,false,1; 0.00000,site_09,false,1; 0.00000,site_10,false,1; 0.00000,site_11,false,1; 0.00000,site_12,false,1; 0.00000,site_13,false,1; 0.00000,site_14,false,1; 0.00000,site_15,false,1; 0.00000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0.00
msfragger.zero_bin_mult_expect=1.00
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01
phi-report.pep-level-summary=true
phi-report.print-decoys=false
phi-report.run-report=true
phi-report.write-mzid=false
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmshepherd.annotation_tol=0.01
ptmshepherd.histo_smoothbins=2
ptmshepherd.localization_background=4
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.run-shepherd=false
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
speclibgen.easypqp.extras.rt_lowess_fraction=0.04
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tmtintegrator.add_Ref=-1
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=0
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\Data\\CoV-OC43
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=14

WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\OC43_02] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck INFO[23:04:35] Executing Workspace v3.2.9
INFO[23:04:35] Removing workspace
WARN[23:04:35] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[23:04:35] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\OC43_02] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[23:04:35] Executing Workspace v3.2.9
INFO[23:04:35] Creating workspace
INFO[23:04:35] Done
WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\OC43_01] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck INFO[23:04:35] Executing Workspace v3.2.9
INFO[23:04:35] Removing workspace
WARN[23:04:35] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[23:04:35] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\OC43_01] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck INFO[23:04:35] Executing Workspace v3.2.9
INFO[23:04:35] Creating workspace
INFO[23:04:35] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck INFO[23:04:36] Executing Workspace v3.2.9
INFO[23:04:36] Removing workspace
WARN[23:04:36] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[23:04:36] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck INFO[23:04:36] Executing Workspace v3.2.9
INFO[23:04:36] Creating workspace
INFO[23:04:36] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\Mock_02] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck INFO[23:04:36] Executing Workspace v3.2.9
INFO[23:04:36] Removing workspace
WARN[23:04:36] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[23:04:36] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\Mock_02] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck INFO[23:04:36] Executing Workspace v3.2.9
INFO[23:04:36] Creating workspace
INFO[23:04:36] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\Mock_01] D:\Data\MSFragger\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\CoV-OC43\Mock_01] D:\Data\MSFragger\philosopher.exe workspace --init --nocheck INFO[23:04:37] Executing Workspace v3.2.9
INFO[23:04:37] Removing workspace
WARN[23:04:37] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[23:04:37] Done
INFO[23:04:37] Executing Workspace v3.2.9
INFO[23:04:37] Creating workspace
INFO[23:04:37] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MsFragger [Work dir: D:\Data\CoV-OC43] java -jar -Dfile.encoding=UTF-8 -Xmx17G D:\Data\MSFragger\MSFragger-3.0.jar D:\Data\CoV-OC43\fragger.params D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.raw D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_90min.mzML D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.raw D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_90min.mzML MSFragger version MSFragger-3.0 Batmass-IO version 1.17.4 (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: 11.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 17 GB memory Checking database... Checking D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_60min.raw... Checking D:\Data\CoV-OC43\202007_CoV-PRM_Mock-48hpi-1_DDA_90min.mzML... Checking D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_60min.raw... Checking D:\Data\CoV-OC43\202007_CoV-PRM_OC43-48hpi-1_DDA_90min.mzML... ***FIRST SEARCH**** Parameters: num_threads = 14 database_name = D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BK_CoV-OC43.fasta decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y diagnostic_intensity_filter = 0.0 Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279 diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.0656/138.055/126.055/163.060096/512.197375/292.1026925/274.0921325/657.2349/243.026426/405.079246/485.045576/308.09761 search_enzyme_name = trypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = P num_enzyme_termini = 2 allowed_missed_cleavage = 1 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.50,1.50 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.99490 M 3 variable_mod_02 = 42.01060 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 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 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 tolerance 0.10 Da. 160316790 fragments to be searched in 1 slices (2.39 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.26 s

  1. 202007_CoV-PRM_Mock-48hpi-1_DDA_60min.raw 26.1 s | deisotoping 1.5 s [progress: 40158/40158 (100%) - 10339 spectra/s] 3.9s | postprocessing 0.3 s
  2. 202007_CoV-PRM_Mock-48hpi-1_DDA_90min.mzML 1.9 s | deisotoping 0.2 s [progress: 55609/55609 (100%) - 31453 spectra/s] 1.8s | postprocessing 0.2 s
  3. 202007_CoV-PRM_OC43-48hpi-1_DDA_60min.raw 21.9 s | deisotoping 0.0 s [progress: 35283/35283 (100%) - 45061 spectra/s] 0.8s | postprocessing 0.1 s
  4. 202007_CoV-PRM_OC43-48hpi-1_DDA_90min.mzML 1.1 s | deisotoping 0.0 s [progress: 44055/44055 (100%) - 57214 spectra/s] 0.8s | postprocessing 0.1 s ***FIRST SEARCH DONE IN 1.162 MIN**
*****MASS CALIBRATION** ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 3.78 1.41 -0.03 0.95 1.73 2.21 0.06 2.29
002 3.28 0.78 0.00 0.49 1.62 2.33 0.04 2.43
003 3.85 1.32 -0.02 0.88 1.65 2.45 0.03 2.50
004 3.78 0.73 0.04 0.51 1.88 2.58 0.04 2.61
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 104341 108520 110531 111215 110527 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- -------
Peaks 500_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- -------
Count 110852 110963 111137 111215 111161 skip rest
------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 112219
------- -------
------- -------
Rm P. 1
------- -------
Count 112251
------- -------

New fragment_mass_tolerance = 15 PPM New use_topN_peaks = 150 New minimum_ratio = 0.010000 New intensity_transform = 1 New remove_precursor_peak = 1 **MASS CALIBRATION DONE IN 2.809 MIN***

****MAIN SEARCH**** Checking database... Parameters: num_threads = 14 database_name = D:\Data_FASTA\2020-07-17-decoys-2020_03_UniProtS_Human_BK_CoV-OC43.fasta decoyprefix = rev precursor_mass_lower = -25.0 precursor_mass_upper = 25.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y diagnostic_intensity_filter = 0.0 Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279 diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.065

fcyu commented 4 years ago

Hi Todd,

I am sorry that GitHub cut the message from the middle so that I cannot find the whole log. Could you send them to yufe@umich.edu?

Regarding your MBR correlation question, we calculated Spearman correlation of retention time, intensity, and ion mobility (if applicable) weighted by the overlapping rate. So, it tends to be lower than the identification overlapping level.

Best,

Fengchao

fcyu commented 4 years ago

Issue solved.