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Nesvilab / FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
http://fragpipe.nesvilab.org
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20:56:17 ERROR: Error delivering events through the bus #206

Closed smalaker13 closed 4 years ago

smalaker13 commented 4 years ago

Trying to analyze glycoproteomic data and received this error:

20:56:17 ERROR: Error delivering events through the bus java.util.NoSuchElementException: Sticky note not on the bus: com.dmtavt.fragpipe.messages.NoteConfigPhilosopher at com.dmtavt.fragpipe.Fragpipe.getStickyStrict(Fragpipe.java:681) at com.dmtavt.fragpipe.FragpipeRun.configureTaskGraph(FragpipeRun.java:603) at com.dmtavt.fragpipe.FragpipeRun.run(FragpipeRun.java:204) at com.dmtavt.fragpipe.tabs.TabRun.on(TabRun.java:153) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:510) at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:504) at org.greenrobot.eventbus.AsyncPoster.run(AsyncPoster.java:46) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

Am I doing something wrong? I loaded the default n-glyco-open-HCD settings.

dpolasky commented 4 years ago

Hi, Can you please attach the full log file generated by FragPipe for this run? It should be in the output folder, called log_[date_time].txt.

smalaker13 commented 4 years ago

Hi Daniel,

First of all, great talk at ASMS this year! I am really excited about your program and look forward to using it.

Secondly, attached is the log. Please let me know if you need anything else.

Best, Stacy

On Wed, Jul 15, 2020 at 7:10 AM Daniel Polasky notifications@github.com wrote:

Hi, Can you please attach the full log file generated by FragPipe for this run? It should be in the output folder, called log_[date_time].txt.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/206#issuecomment-658791071, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQJGNJZOH4IOOAWBTDCEGHDR3W2EFANCNFSM4O2QPZTA .

-- Stacy A. Malaker, PhD NIH Postdoctoral Fellow Bertozzi Laboratory Stanford University Department of Chemistry (650)-721-4783

20:55:25 ERROR: Error delivering events through the bus

java.util.NoSuchElementException: Sticky note not on the bus: com.dmtavt.fragpipe.messages.NoteConfigPhilosopher

at com.dmtavt.fragpipe.Fragpipe.getStickyStrict(Fragpipe.java:681)

at com.dmtavt.fragpipe.FragpipeRun.configureTaskGraph(FragpipeRun.java:603)

at com.dmtavt.fragpipe.FragpipeRun.run(FragpipeRun.java:204)

at com.dmtavt.fragpipe.tabs.TabRun.on(TabRun.java:153)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:510)

at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:504)

at org.greenrobot.eventbus.AsyncPoster.run(AsyncPoster.java:46)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)
dpolasky commented 4 years ago

Hi Stacy, Thanks so much - I hope it can be helpful! I don't see anything attached to your previous message - could you double check that it was uploaded? If it's not working, you can also email it to me directly (dpolasky [at] umich.edu). Thanks!

anesvi commented 4 years ago

I think github removes attachments. Need to email directly

From: Daniel Polasky notifications@github.com Sent: Wednesday, July 15, 2020 3:41 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [Nesvilab/FragPipe] 20:56:17 ERROR: Error delivering events through the bus (#206)

External Email - Use Caution

Hi Stacy, Thanks so much - I hope it can be helpful! I don't see anything attached to your previous message - could you double check that it was uploaded? If it's not working, you can also email it to me directly (dpolasky [at] umich.edu). Thanks!

— 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/206#issuecomment-658968140, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM6Y23XQOHZRLE6SZLTDR3YA4PANCNFSM4O2QPZTA.

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chhh commented 4 years ago

Looks like philosopher wasn't configured. Could you please try re-downloading it and pointing to the binary on config tab?

smalaker13 commented 4 years ago

Sorry, redownloading what, exactly? MSFragger? Or FragPipe?

Best, Stacy

On Wed, Jul 15, 2020 at 2:25 PM Dmitry Avtonomov notifications@github.com wrote:

Looks like philosopher wasn't configured. Could you please try re-downloading it and pointing to the binary on config tab?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/206#issuecomment-659020672, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQJGNJ44JLIOVWLW3Q56E6DR3YNDHANCNFSM4O2QPZTA .

-- Stacy A. Malaker, PhD NIH Postdoctoral Fellow Bertozzi Laboratory Stanford University Department of Chemistry (650)-721-4783

sarah-haynes commented 4 years ago

Sorry I accidentally closed the issue! Can you try re-downloading Philosopher? This tutorial might also help. --Sarah

smalaker13 commented 4 years ago

Thank you, that seemed to work!

Best, Stacy

On Wed, Jul 15, 2020 at 3:25 PM Sarah Haynes notifications@github.com wrote:

Sorry I accidentally closed the issue! Can you try re-downloading Philosopher https://github.com/nesvilab/philosopher/releases/tag/v3.2.9? This tutorial https://msfragger.nesvilab.org/tutorial_setup_fragpipe.html might also help. --Sarah

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/206#issuecomment-659046303, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQJGNJ4CBVDFKY3NSIDUD5LR3YUG7ANCNFSM4O2QPZTA .

-- Stacy A. Malaker, PhD NIH Postdoctoral Fellow Bertozzi Laboratory Stanford University Department of Chemistry (650)-721-4783

smalaker13 commented 4 years ago

Except now I have an issue with the output, it seems? There is no excel file in the output directory. I have attached the log for this search.

Best, Stacy

On Wed, Jul 15, 2020 at 3:42 PM Stacy Malaker smalaker@stanford.edu wrote:

Thank you, that seemed to work!

Best, Stacy

On Wed, Jul 15, 2020 at 3:25 PM Sarah Haynes notifications@github.com wrote:

Sorry I accidentally closed the issue! Can you try re-downloading Philosopher https://github.com/nesvilab/philosopher/releases/tag/v3.2.9? This tutorial https://msfragger.nesvilab.org/tutorial_setup_fragpipe.html might also help. --Sarah

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/206#issuecomment-659046303, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQJGNJ4CBVDFKY3NSIDUD5LR3YUG7ANCNFSM4O2QPZTA .

-- Stacy A. Malaker, PhD NIH Postdoctoral Fellow Bertozzi Laboratory Stanford University Department of Chemistry (650)-721-4783

-- Stacy A. Malaker, PhD NIH Postdoctoral Fellow Bertozzi Laboratory Stanford University Department of Chemistry (650)-721-4783

System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, AdoptOpenJDK

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

LCMS files: Experiment/Group:

13 commands to execute: WorkspaceCleanInit [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windows_amd64\philosopher.exe workspace --init --nocheck MsFragger [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx5G C:\Users\stacy\Desktop\MSFragger-3.0\MSFragger-3.0.jar C:\Users\stacy\Documents\MSFragger_Results\fragger.params D:\071019_SAM_E447D_AscElute2_Slice4.mzML MsFragger C:\Users\stacy\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\stacy\Desktop\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\071019_SAM_E447D_AscElute2_Slice4.pepXML C:\Users\stacy\Documents\MSFragger_Results\071019_SAM_E447D_AscElute2_Slice4.pepXML MsFragger C:\Users\stacy\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\stacy\Desktop\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\071019_SAM_E447D_AscElute2_Slice4.tsv C:\Users\stacy\Documents\MSFragger_Results\071019_SAM_E447D_AscElute2_Slice4.tsv Crystal-C [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\stacy\Desktop\MSFragger-3.0\ext\thermo" -Xmx5G -cp "C:\Users\stacy\Desktop\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\stacy\Desktop\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\stacy\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run C:\Users\stacy\Documents\MSFragger_Results\crystalc-0-071019_SAM_E447D_AscElute2_Slice4.pepXML.params C:\Users\stacy\Documents\MSFragger_Results\071019_SAM_E447D_AscElute2_Slice4.pepXML PeptideProphet [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windowsamd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 4000.0 --clevel -2 --decoy rev --database C:\Users\stacy\Documents\Bertozzi Lab\Experiments\2020-07-15-decoys-reviewed-contam-UP000005640.fas --combine 071019_SAM_E447D_AscElute2_Slice4_c.pepXML ProteinProphet [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\stacy\Documents\MSFragger_Results\interact.pep.xml PhilosopherDbAnnotate [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windowsamd64\philosopher.exe database --annotate C:\Users\stacy\Documents\Bertozzi Lab\Experiments\2020-07-15-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherFilter [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev --pepxml C:\Users\stacy\Documents\MSFragger_Results --protxml C:\Users\stacy\Documents\MSFragger_Results\combined.prot.xml PhilosopherReport [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windows_amd64\philosopher.exe report WorkspaceClean [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windows_amd64\philosopher.exe workspace --clean --nocheck PTMShepherd [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\stacy\Desktop\MSFragger-3.0\ext\thermo" -cp "C:\Users\stacy\Desktop\fragpipe\tools\ptmshepherd-0.3.4.jar;C:\Users\stacy\Desktop\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\stacy\Desktop\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "C:\Users\stacy\Documents\MSFragger_Results\shepherd.config"


Execution order:

    Cmd: [START], Work dir: [C:\Users\stacy\Documents\MSFragger_Results]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\stacy\Documents\MSFragger_Results]
    Cmd: [MsFragger], Work dir: [C:\Users\stacy\Documents\MSFragger_Results]
    Cmd: [Crystal-C], Work dir: [C:\Users\stacy\Documents\MSFragger_Results]
    Cmd: [PeptideProphet], Work dir: [C:\Users\stacy\Documents\MSFragger_Results]
    Cmd: [ProteinProphet], Work dir: [C:\Users\stacy\Documents\MSFragger_Results]
    Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\stacy\Documents\MSFragger_Results]
    Cmd: [PhilosopherFilter], Work dir: [C:\Users\stacy\Documents\MSFragger_Results]
    Cmd: [PhilosopherReport], Work dir: [C:\Users\stacy\Documents\MSFragger_Results]
    Cmd: [WorkspaceClean], Work dir: [C:\Users\stacy\Documents\MSFragger_Results]
    Cmd: [PTMShepherd], Work dir: [C:\Users\stacy\Documents\MSFragger_Results]

# 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=true
database.db-path=C\:\\Users\\stacy\\Documents\\Bertozzi Lab\\Experiments\\2020-07-15-decoys-reviewed-contam-UP000005640.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\Users\\stacy\\Desktop\\MSFragger-3.0\\MSFragger-3.0.jar
fragpipe-config.bin-philosopher=C\:\\Users\\stacy\\Desktop\\philosopher_v3.2.9_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\stacy\\anaconda3\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=true
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.label=
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0.5
ionquant.mbrrttol=1
ionquant.mbrtoprun=3
ionquant.minfreq=0.5
ionquant.minions=1
ionquant.minisotopes=1
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=0.01
ionquant.proteinfdr=0.01
ionquant.proteinquant=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=false
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 138.055 512.197375 292.1026925 274.0921325 657.2349 243.026426 405.079246 485.045576 308.09761
msfragger.diagnostic_intensity_filter=0.1
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y,b~,y~,Y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0
msfragger.labile_search_mode=nglycan
msfragger.localize_delta_mass=true
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.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=400
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=-10
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=10
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=1
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,false,1; -18.01060,nE,false,1; 0.00000,site_06,false,3; 0.00000,site_07,false,3
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=300
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0.00
msfragger.zero_bin_mult_expect=1.00
peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 4000.0 --clevel -2
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01 --mapmods
phi-report.pep-level-summary=false
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=true
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=false
speclibgen.easypqp.extras.rt_lowess_fraction=0.05
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tmtintegrator.add_Ref=-1
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=0
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=C\:\\Users\\stacy\\Documents\\MSFragger_Results
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=3

WorkspaceCleanInit [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[15:40:46] Executing Workspace v3.2.9
INFO[15:40:46] Removing workspace
WARN[15:40:46] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[15:40:46] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windows_amd64\philosopher.exe workspace --init --nocheck INFO[15:40:46] Executing Workspace v3.2.9
INFO[15:40:46] Creating workspace
INFO[15:40:46] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MsFragger [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx5G C:\Users\stacy\Desktop\MSFragger-3.0\MSFragger-3.0.jar C:\Users\stacy\Documents\MSFragger_Results\fragger.params D:\071019_SAM_E447D_AscElute2_Slice4.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: 1.8.0_242, OpenJDK 64-Bit Server VM, JVM started with 4 GB memory Checking database... Checking D:\071019_SAM_E447D_AscElute2_Slice4.mzML... ***FIRST SEARCH**** Parameters: num_threads = 3 database_name = C:\Users\stacy\Documents\Bertozzi Lab\Experiments\2020-07-15-decoys-reviewed-contam-UP000005640.fas 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 = NGLYCAN precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y,b~,y~, diagnostic_intensity_filter = 0.1 Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279 diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.0656/138.055/512.197375/292.1026925/274.0921325/657.2349/243.026426/405.079246/485.045576/308.09761 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 = 400.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 remove_precursor_peak = 1 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 Number of unique peptides of length 7: 217647 of length 8: 201898 of length 9: 193753 of length 10: 177265 of length 11: 163088 of length 12: 150989 of length 13: 142741 of length 14: 128086 of length 15: 119903 of length 16: 109389 of length 17: 100143 of length 18: 93276 of length 19: 87564 of length 20: 79523 of length 21: 74377 of length 22: 68133 of length 23: 63263 of length 24: 59287 of length 25: 54929 of length 26: 50360 of length 27: 47785 of length 28: 44549 of length 29: 40951 of length 30: 38130 of length 31: 35162 of length 32: 32895 of length 33: 30230 of length 34: 27904 of length 35: 25408 of length 36: 24279 of length 37: 21518 of length 38: 20131 of length 39: 17929 of length 40: 17084 of length 41: 16072 of length 42: 14286 of length 43: 12514 of length 44: 10071 of length 45: 7889 of length 46: 5323 of length 47: 3473 of length 48: 2132 of length 49: 1116 of length 50: 702 In total 2833147 peptides. Generated 4301635 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment tolerance 0.10 Da. 319576384 fragments to be searched in 2 slices (4.76 GB total) Operating on slice 1 of 2: Fragment index slice generated in 5.67 s

  1. 071019_SAM_E447D_AscElute2_Slice4.mzML 8.0 s | deisotoping 2.1 s [progress: 60315/60315 (100%) - 7409 spectra/s] 8.1s Operating on slice 2 of 2: Fragment index slice generated in 4.21 s
  2. 071019_SAM_E447D_AscElute2_Slice4.mzML 4.8 s | deisotoping 1.0 s [progress: 60315/60315 (100%) - 13368 spectra/s] 4.5s | postprocessing 0.4 s ***FIRST SEARCH DONE IN 0.876 MIN**
*****MASS CALIBRATION** ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 5.69 1.51 0.01 0.77 3.86 1.82 0.06 1.54
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 8530 8657 8512 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- -------
Peaks 500_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- -------
Count 8660 8703 8694 skip rest
------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 8715
------- -------
------- -------
Rm P. 0
------- -------
Count 8707
------- -------

New fragment_mass_tolerance = 7 PPM New use_topN_peaks = 200 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 **MASS CALIBRATION DONE IN 3.358 MIN***

****MAIN SEARCH**** Checking database... WARNING: It is a closed search while localize delta mass is on. Turning it off. Done. Parameters: num_threads = 3 database_name = C:\Users\stacy\Documents\Bertozzi Lab\Experiments\2020-07-15-decoys-reviewed-contam-UP000005640.fas decoyprefix = rev precursor_mass_lower = -10.0 precursor_mass_upper = 10.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 7.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false isotope_error = 0 mass_offsets = 0 labile_search_mode = NGLYCAN precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y,b~,y~, diagnostic_intensity_filter = 0.1 Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279 diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.0656/138.055/512.197375/292.1026925/274.0921325/657.2349/243.026426/405.079246/485.045576/308.09761 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 = 400.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 200 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 1 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 0.03 Da. 319576384 fragments to be searched in 2 slices (4.76 GB total) Operating on slice 1 of 2: Fragment index slice generated in 7.61 s

  1. 071019_SAM_E447D_AscElute2_Slice4.mzBIN_calibrated 1.3 s [progress: 60069/60069 (100%) - 13596 spectra/s] 4.4s Operating on slice 2 of 2: Fragment index slice generated in 5.95 s
  2. 071019_SAM_E447D_AscElute2_Slice4.mzBIN_calibrated 1.3 s [progress: 60069/60069 (100%) - 22719 spectra/s] 2.6s | postprocessing 3.6 s MAIN SEARCH DONE IN 0.469 MIN

***TOTAL TIME 4.703 MIN**** Process 'MsFragger' finished, exit code: 0 MsFragger C:\Users\stacy\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\stacy\Desktop\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\071019_SAM_E447D_AscElute2_Slice4.pepXML C:\Users\stacy\Documents\MSFragger_Results\071019_SAM_E447D_AscElute2_Slice4.pepXML Process 'MsFragger' finished, exit code: 0 MsFragger C:\Users\stacy\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\stacy\Desktop\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\071019_SAM_E447D_AscElute2_Slice4.tsv C:\Users\stacy\Documents\MSFragger_Results\071019_SAM_E447D_AscElute2_Slice4.tsv Process 'MsFragger' finished, exit code: 0 Crystal-C [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\stacy\Desktop\MSFragger-3.0\ext\thermo" -Xmx5G -cp "C:\Users\stacy\Desktop\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\stacy\Desktop\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\stacy\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run C:\Users\stacy\Documents\MSFragger_Results\crystalc-0-071019_SAM_E447D_AscElute2_Slice4.pepXML.params C:\Users\stacy\Documents\MSFragger_Results\071019_SAM_E447D_AscElute2_Slice4.pepXML 071019_SAM_E447D_AscElute2_Slice4.pepXML Done! The execution time is 0.15397 min. Process 'Crystal-C' finished, exit code: 0 PeptideProphet [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windowsamd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 4000.0 --clevel -2 --decoy rev --database C:\Users\stacy\Documents\Bertozzi Lab\Experiments\2020-07-15-decoys-reviewed-contam-UP000005640.fas --combine 071019_SAM_E447D_AscElute2_Slice4_c.pepXML INFO[15:45:45] Executing PeptideProphet v3.2.9
WARNING: cannot open data file C:\Users\stacy\Documents\MSFragger_Results/071019_SAM_E447D_AscElute2_Slice4.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file C:\Users\stacy\Documents\MSFragger_Results/071019_SAM_E447D_AscElute2_Slice4.mzXML in msms_run_summary tag... WARNING: cannot open data file C:\Users\stacy\Documents\MSFragger_Results/071019_SAM_E447D_AscElute2_Slice4.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file C:\Users\stacy\Documents\MSFragger_Results/071019_SAM_E447D_AscElute2_Slice4.mzXML in msms_run_summary tag... file 1: C:\Users\stacy\Documents\MSFragger_Results\071019_SAM_E447D_AscElute2_Slice4_c.pepXML processed altogether 2848 results INFO: Results written to file: C:\Users\stacy\Documents\MSFragger_Results\interact.pep.xml

Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) init with X! Tandem trypsin PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 1773 2+, 738 3+, 252 4+, 81 5+, 4 6+, and 0 7+ spectra. Found 801 Decoys, and 2047 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .........10.........20...WARNING: Mixture model quality test failed for charge (1+). .. WARNING: Mixture model quality test failed for charge (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[15:45:56] Done
Process 'PeptideProphet' finished, exit code: 0 ProteinProphet [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\stacy\Documents\MSFragger_Results\interact.pep.xml INFO[15:45:56] Executing ProteinProphet v3.2.9
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 C:/Users/stacy/Documents/MSFragger_Results/interact.pep.xml... ...read in 0 1+, 1456 2+, 588 3+, 252 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 1239 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database c:/Users/stacy/Documents/Bertozzi Lab/Experiments/2020-07-15-decoys-reviewed-contam-UP000005640.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........: Total: 40802 Computing degenerate peptides for 919 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 944 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 944 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 944 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 944 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 850 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... INFO: mu=1.49502e-05, db_size=45472679 Computing MU for 944 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%

Finished. INFO[15:46:00] Done
Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windowsamd64\philosopher.exe database --annotate C:\Users\stacy\Documents\Bertozzi Lab\Experiments\2020-07-15-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[15:46:00] Executing Database v3.2.9
INFO[15:46:00] Processing database
INFO[15:46:04] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windowsamd64\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev --pepxml C:\Users\stacy\Documents\MSFragger_Results --protxml C:\Users\stacy\Documents\MSFragger_Results\combined.prot.xml INFO[15:46:05] Executing Filter v3.2.9
INFO[15:46:05] Processing peptide identification files
INFO[15:46:05] 1+ Charge profile decoy=0 target=0 INFO[15:46:05] 2+ Charge profile decoy=276 target=1180 INFO[15:46:05] 3+ Charge profile decoy=158 target=431 INFO[15:46:05] 4+ Charge profile decoy=114 target=138 INFO[15:46:05] 5+ Charge profile decoy=0 target=0 INFO[15:46:05] 6+ Charge profile decoy=0 target=0 INFO[15:46:05] Database search results ions=1234 peptides=1178 psms=2297 INFO[15:46:05] Converged to 1.00 % FDR with 1200 PSMs decoy=12 threshold=0.6608 total=1212 INFO[15:46:05] Converged to 0.82 % FDR with 366 Peptides decoy=3 threshold=0.9394 total=369 INFO[15:46:05] Converged to 0.95 % FDR with 419 Ions decoy=4 threshold=0.9067 total=423 INFO[15:46:05] Protein inference results decoy=380 target=470 INFO[15:46:05] Converged to 1.06 % FDR with 94 Proteins decoy=1 threshold=0.9701 total=95 INFO[15:46:06] Applying sequential FDR estimation ions=428 peptides=384 psms=1161 INFO[15:46:06] Converged to 0.08 % FDR with 1160 PSMs decoy=1 threshold=0.6632 total=1161 INFO[15:46:06] Converged to 0.26 % FDR with 383 Peptides decoy=1 threshold=0.6658 total=384 INFO[15:46:06] Converged to 0.23 % FDR with 427 Ions decoy=1 threshold=0.6658 total=428 INFO[15:46:06] Post processing identifications
INFO[15:46:06] Mapping modifications
INFO[15:46:06] Processing modifications
INFO[15:46:08] Processing protein inference
INFO[15:46:09] Assigning protein identifications to layers
INFO[15:46:09] Updating razor PSM assignment to proteins
INFO[15:46:09] Calculating spectral counts
INFO[15:46:09] Saving
INFO[15:46:09] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windows_amd64\philosopher.exe report INFO[15:46:09] Executing Report v3.2.9
INFO[15:46:10] Creating reports
INFO[15:46:10] Done
Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\philosopher_v3.2.9_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[15:46:10] Executing Workspace v3.2.9
INFO[15:46:10] Removing workspace
INFO[15:46:10] Done
Process 'WorkspaceClean' finished, exit code: 0 PTMShepherd [Work dir: C:\Users\stacy\Documents\MSFragger_Results] C:\Users\stacy\Desktop\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\stacy\Desktop\MSFragger-3.0\ext\thermo" -cp "C:\Users\stacy\Desktop\fragpipe\tools\ptmshepherd-0.3.4.jar;C:\Users\stacy\Desktop\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\stacy\Desktop\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "C:\Users\stacy\Documents\MSFragger_Results\shepherd.config" Exception in thread "main" java.lang.NullPointerException at edu.umich.andykong.ptmshepherd.PSMFile.getMappings(PSMFile.java:89) at edu.umich.andykong.ptmshepherd.PSMFile.getMappings(PSMFile.java:90) at edu.umich.andykong.ptmshepherd.PSMFile.getMappings(PSMFile.java:90) at edu.umich.andykong.ptmshepherd.PTMShepherd.main(PTMShepherd.java:216) PTM-Shepherd version 0.3.4(c) University of Michigan

Using Java 1.8.0_242 on 2702MB memory

Process 'PTMShepherd' finished, exit code: 1 Process returned non-zero exit code, stopping=========================

=== Done

=========================


Cancelling 0 remaining tasks
15:46:11 ERROR: Error writing log to file

java.nio.channels.ClosedByInterruptException: null

    at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202)

    at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:216)

    at java.nio.channels.Channels.writeFullyImpl(Channels.java:78)

    at java.nio.channels.Channels.writeFully(Channels.java:101)

    at java.nio.channels.Channels.access$000(Channels.java:61)

    at java.nio.channels.Channels$1.write(Channels.java:174)

    at java.nio.file.Files.write(Files.java:3297)

    at com.dmtavt.fragpipe.tabs.TabRun.saveLogToFile(TabRun.java:354)

    at com.dmtavt.fragpipe.tabs.TabRun.on(TabRun.java:308)

    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

    at java.lang.reflect.Method.invoke(Method.java:498)

    at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:510)

    at org.greenrobot.eventbus.EventBus.postToSubscription(EventBus.java:447)

    at org.greenrobot.eventbus.EventBus.postSingleEventForEventType(EventBus.java:414)

    at org.greenrobot.eventbus.EventBus.postSingleEvent(EventBus.java:387)

    at org.greenrobot.eventbus.EventBus.post(EventBus.java:268)

    at com.dmtavt.fragpipe.api.Bus.post(Bus.java:51)

    at com.dmtavt.fragpipe.FragpipeRun.lambda$run$6(FragpipeRun.java:316)

    at java.util.concurrent.CompletableFuture$AsyncRun.run(CompletableFuture.java:1640)

    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

    at java.lang.Thread.run(Thread.java:748)
fcyu commented 4 years ago

Hi @smalaker13 ,

According to your log, you should be able to find psm.tsv, ion.tsv, peptide.tsv, and protein.tsv from your result directory. However, PTM-Shepherd crashed. @danielgeiszler Can you take a look when you have time?

Thanks,

Fengchao

dpolasky commented 4 years ago

Hi Stacy, Glad it's running now! The output .tsv files Fengchao mentioned can be opened and viewed in Excel (they are just tab separated text files) to see the results. The psm.tsv file is the best place to start for now, as glycans are not propagated completely to peptide.tsv and protein.tsv files (that will be fixed in an upcoming release soon though!).

It looks like PTM-Shepherd (our tool for analyzing open search results) crashed because the search wasn't actually run as an open search according to the log. If you want to do an open search (any mass allowed rather than specific glycan masses), the MSFragger parameters should look like in the attached image (most importantly, the precursor mass units in Da, not ppm). I don't know if those were changed or got corrupted somehow, but what's in the screenshot are the default values for the glyco-N-open-HCD workflow. If you aren't trying to do an open search, you can turn off PTM-Shepherd (in the "PTMs" tab in FragPipe), or load the "glyco-N-HCD" workflow instead of the "glyco-N-open-HCD" one. Annotation

Hopefully that all makes sense - let us know if you still have questions/issues!

smalaker13 commented 4 years ago

Oh, thank you! I changed that to -10 to +10 because I thought that was the precursor mass tolerance. I'll try it again with those parameters.

Thanks again, Stacy

On Thu, Jul 16, 2020 at 6:27 AM Daniel Polasky notifications@github.com wrote:

Hi Stacy, Glad it's running now! The output .tsv files Fengchao mentioned can be opened and viewed in Excel (they are just tab separated text files) to see the results. The psm.tsv file is the best place to start for now, as glycans are not propagated completely to peptide.tsv and protein.tsv files (that will be fixed in an upcoming release soon though!).

It looks like PTM-Shepherd (our tool for analyzing open search results) crashed because the search wasn't actually run as an open search according to the log. If you want to do an open search (any mass allowed rather than specific glycan masses), the MSFragger parameters should look like in the attached image (most importantly, the precursor mass units in Da, not ppm). I don't know if those were changed or got corrupted somehow, but what's in the screenshot are the default values for the glyco-N-open-HCD workflow. If you aren't trying to do an open search, you can turn off PTM-Shepherd (in the "PTMs" tab in FragPipe), or load the "glyco-N-HCD" workflow instead of the "glyco-N-open-HCD" one. [image: Annotation] https://user-images.githubusercontent.com/15036076/87675887-f1b40880-c745-11ea-8f00-ac06902feb7a.png

Hopefully that all makes sense - let us know if you still have questions/issues!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/206#issuecomment-659410873, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQJGNJYTW2556BNT3I6UVETR3353LANCNFSM4O2QPZTA .

-- Stacy A. Malaker, PhD NIH Postdoctoral Fellow Bertozzi Laboratory Stanford University Department of Chemistry (650)-721-4783

YaraMS1 commented 2 years ago

I also tried to run my study and a similar error appeared! I loaded the iTRAQ4 workflow and modified it because my samples were enriched with phosphopeptides.

java.lang.UnsupportedOperationException: Renaming not yet implemented at com.dmtavt.fragpipe.FragpipeRun.checkInputLcmsFiles1(FragpipeRun.java:466) at com.dmtavt.fragpipe.FragpipeRun.run(FragpipeRun.java:165) at com.dmtavt.fragpipe.tabs.TabRun.on(TabRun.java:153) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.base/java.lang.reflect.Method.invoke(Unknown Source) at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:510) at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:504) at org.greenrobot.eventbus.AsyncPoster.run(AsyncPoster.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source)

fcyu commented 2 years ago

Your file path has space or some disallowed characters. Can you remove them and try again?

Thanks,

Fengchao

YaraMS1 commented 2 years ago

Hi, Fengchao I would like thank you, I didn't see this before.

Thanks!!