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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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non-zero exit code error #385

Closed dkueltz closed 3 years ago

dkueltz commented 3 years ago

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


Cancelling 31 remaining tasks
08:43:59 ERROR: Error writing log to file
java.nio.channels.ClosedByInterruptException: null
    at java.nio.channels.spi.AbstractInterruptibleChannel.end(Unknown Source)
    at sun.nio.ch.FileChannelImpl.write(Unknown Source)
    at java.nio.channels.Channels.writeFullyImpl(Unknown Source)
    at java.nio.channels.Channels.writeFully(Unknown Source)
    at java.nio.channels.Channels.access$000(Unknown Source)
    at java.nio.channels.Channels$1.write(Unknown Source)
    at sun.nio.cs.StreamEncoder.writeBytes(Unknown Source)
    at sun.nio.cs.StreamEncoder.implWrite(Unknown Source)
    at sun.nio.cs.StreamEncoder.write(Unknown Source)
    at java.io.OutputStreamWriter.write(Unknown Source)
    at java.io.BufferedWriter.flushBuffer(Unknown Source)
    at java.io.BufferedWriter.write(Unknown Source)
    at java.io.Writer.write(Unknown Source)
    at com.dmtavt.fragpipe.tabs.TabRun.saveLogToFile(TabRun.java:354)
    at com.dmtavt.fragpipe.tabs.TabRun.on(TabRun.java:309)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:510)
    at org.greenrobot.eventbus.EventBus.postToSubscription(EventBus.java:447)
    at org.greenrobot.eventbus.EventBus.postSingleEventForEventType(EventBus.java:414)
    at org.greenrobot.eventbus.EventBus.postSingleEvent(EventBus.java:387)
    at org.greenrobot.eventbus.EventBus.post(EventBus.java:268)
    at com.dmtavt.fragpipe.api.Bus.post(Bus.java:51)
    at com.dmtavt.fragpipe.cmd.ProcessBuilderInfo.lambda$toRunnable$0(ProcessBuilderInfo.java:96)
    at java.util.concurrent.CompletableFuture$AsyncRun.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
    Suppressed: java.nio.channels.ClosedChannelException: null
        at sun.nio.ch.FileChannelImpl.ensureOpen(Unknown Source)
        at sun.nio.ch.FileChannelImpl.write(Unknown Source)
        at java.nio.channels.Channels.writeFullyImpl(Unknown Source)
        at java.nio.channels.Channels.writeFully(Unknown Source)
        at java.nio.channels.Channels.access$000(Unknown Source)
        at java.nio.channels.Channels$1.write(Unknown Source)
        at sun.nio.cs.StreamEncoder.writeBytes(Unknown Source)
        at sun.nio.cs.StreamEncoder.implClose(Unknown Source)
        at sun.nio.cs.StreamEncoder.close(Unknown Source)
        at java.io.OutputStreamWriter.close(Unknown Source)
        at java.io.BufferedWriter.close(Unknown Source)
        at com.dmtavt.fragpipe.tabs.TabRun.saveLogToFile(TabRun.java:355)
        ... 16 common frames omitted
fcyu commented 3 years ago

Can you send us the whole log file?

Best,

Fengchao

dkueltz commented 3 years ago

Hi Fengchao,

Where is the whole log file stored? It is not in the output directory. I copied all of the error message that was in the processing window.

Best, Dietmar

Dietmar Kültz, PhD Professor of Physiological Genomics Department of Animal Sciences University of California Davis One Shields Ave., Meyer Hall Davis, CA 95616, US Phone: 530-752-2991 · Fax: 530-752-0175 The Kültz Lab @ PanoramaWebhttps://panoramaweb.org/Kueltz%20Lab%20-%20UCDavis Stress-induced Evolution · Targeted DIA Proteomics

From: Fengchao @.> Sent: Wednesday, June 2, 2021 11:50 AM To: Nesvilab/FragPipe @.> Cc: Dietmar Kueltz @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] non-zero exit code error (#385)

Can you send us the whole log file?

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/385#issuecomment-853300005, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUFCPXT6253Y7BYML2OT4QDTQZ4PJANCNFSM457I2O5Q.

fcyu commented 3 years ago

Hi Dietmar,

You can export it by clicking "export log": image

Best,

Fengchao

dkueltz commented 3 years ago

okay, I'll rerun and then do the export log and email you the file. thanks for looking into this, dietmar

From: Fengchao @.> Sent: Wednesday, June 2, 2021 12:10 PM To: Nesvilab/FragPipe @.> Cc: Dietmar Kueltz @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] non-zero exit code error (#385)

Hi Dietmar,

You can export it by clicking "export log": [image]https://user-images.githubusercontent.com/6926299/120538547-a71a9980-c3b4-11eb-8a65-e7b07e485a09.png

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/385#issuecomment-853315187, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUFCPXSM2O7LZ65RA3SKNWLTQZ63JANCNFSM457I2O5Q.

dkueltz commented 3 years ago

Hi Fengchao,

The log file is attached FYI. I actually know the reason for the error now - it was insufficient memory, which makes sense since the error does not occur if I reduce the number of variable modifications.

Thanks for your help, Dietmar

From: Fengchao @.> Sent: Wednesday, June 2, 2021 12:10 PM To: Nesvilab/FragPipe @.> Cc: Dietmar Kueltz @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] non-zero exit code error (#385)

Hi Dietmar,

You can export it by clicking "export log": [image]https://user-images.githubusercontent.com/6926299/120538547-a71a9980-c3b4-11eb-8a65-e7b07e485a09.png

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/385#issuecomment-853315187, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUFCPXSM2O7LZ65RA3SKNWLTQZ63JANCNFSM457I2O5Q.

System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_291, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

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

LCMS files: Experiment/Group:

15 commands to execute: WorkspaceCleanInit [Work dir: E:\LT0001_Cotja\MSfragger\MSF6] E:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\LT0001_Cotja\MSfragger\MSF6] E:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: E:\LT0001_Cotja\MSfragger\MSF6] java -jar -Dfile.encoding=UTF-8 -Xmx44G E:\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar E:\LT0001_Cotja\MSfragger\MSF6\fragger.params E:\LT0001_Cotja\DDA\LT0001_TN-6796_100ng_2-B_1_01_3763.mzML MSFragger move pepxml java -cp E:\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/E:/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove E:\LT0001_Cotja\DDA\LT0001_TN-6796_100ng_2-B_1_01_3763.pepXML E:\LT0001_Cotja\MSfragger\MSF6\LT0001_TN-6796_100ng_2-B_1_01_3763.pepXML MSFragger move tsv java -cp E:\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/E:/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err E:\LT0001_Cotja\DDA\LT0001_TN-6796_100ng_2-B_1_01_3763.tsv E:\LT0001_Cotja\MSfragger\MSF6\LT0001_TN-6796_100ng_2-B_1_01_3763.tsv PeptideProphet: Workspace init [Work dir: E:\LT0001_Cotja\MSfragger\MSF6\fragpipe-LT0001_TN-6796_100ng_2-B_1_01_3763.pepXML-temp] E:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: E:\LT0001_Cotja\MSfragger\MSF6\fragpipe-LT0001_TN-6796_100ng_2-B_1_013763.pepXML-temp] E:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\Databases\Cotja\2021-05-31-decoys-contam-Cotja_NCBI-Refseq-40894_29May21.fasta.fas ..\LT0001_TN-6796_100ng_2-B_1_01_3763.pepXML PeptideProphet: Delete temp java -cp E:\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete E:\LT0001_Cotja\MSfragger\MSF6\fragpipe-LT0001_TN-6796_100ng_2-B_1_01_3763.pepXML-temp Rewrite pepxml [Work dir: E:\LT0001_Cotja\MSfragger\MSF6] java -cp E:\FragPipe-15.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml E:\LT0001_Cotja\MSfragger\MSF6\interact-LT0001_TN-6796_100ng_2-B_1_01_3763.pep.xml E:\LT0001_Cotja\DDA\LT0001_TN-6796_100ng_2-B_1_01_3763.mzML ProteinProphet [Work dir: E:\LT0001_Cotja\MSfragger\MSF6] E:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\LT0001_Cotja\MSfragger\MSF6\interact-LT0001_TN-6796_100ng_2-B_1_01_3763.pep.xml PhilosopherDbAnnotate [Work dir: E:\LT0001_Cotja\MSfragger\MSF6] E:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe database --annotate D:\Databases\Cotja\2021-05-31-decoys-contam-Cotja_NCBI-Refseq-4089429May21.fasta.fas --prefix rev PhilosopherFilter [Work dir: E:\LT0001Cotja\MSfragger\MSF6] E:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml E:\LT0001_Cotja\MSfragger\MSF6 --protxml E:\LT0001_Cotja\MSfragger\MSF6\combined.prot.xml PhilosopherReport [Work dir: E:\LT0001_Cotja\MSfragger\MSF6] E:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe report IonQuant [Work dir: E:\LT0001_Cotja\MSfragger\MSF6] java -Xmx44G -Dlibs.bruker.dir="E:\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\ext\bruker" -Dlibs.thermo.dir="E:\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\ext\thermo" -cp "E:\FragPipe-15.0\fragpipe\tools\ionquant-1.5.5.jar;E:\FragPipe-15.0\fragpipe\tools\batmass-io-1.22.1.jar" ionquant.IonQuant --threads 15 --ionmobility 0 --mbr 0 --proteinquant 2 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 3 --minfreq 0.5 --minions 2 --minexps 1 --psm psm.tsv --specdir E:\LT0001_Cotja\DDA LT0001_TN-6796_100ng_2-B_1_01_3763.pepXML WorkspaceClean [Work dir: E:\LT0001_Cotja\MSfragger\MSF6] E:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [E:\LT0001_Cotja\MSfragger\MSF6]
    Cmd: [WorkspaceCleanInit], Work dir: [E:\LT0001_Cotja\MSfragger\MSF6]
    Cmd: [MSFragger], Work dir: [E:\LT0001_Cotja\MSfragger\MSF6]
    Cmd: [PeptideProphet], Work dir: [E:\LT0001_Cotja\MSfragger\MSF6]
    Cmd: [ProteinProphet], Work dir: [E:\LT0001_Cotja\MSfragger\MSF6]
    Cmd: [PhilosopherDbAnnotate], Work dir: [E:\LT0001_Cotja\MSfragger\MSF6]
    Cmd: [PhilosopherFilter], Work dir: [E:\LT0001_Cotja\MSfragger\MSF6]
    Cmd: [PhilosopherReport], Work dir: [E:\LT0001_Cotja\MSfragger\MSF6]
    Cmd: [IonQuant], Work dir: [E:\LT0001_Cotja\MSfragger\MSF6]
    Cmd: [WorkspaceClean], Work dir: [E:\LT0001_Cotja\MSfragger\MSF6]

# FragPipe v15.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
Table.editor=57.02146
crystalc.run-crystalc=false
database.db-path=D\:\\Databases\\Cotja\\2021-05-31-decoys-contam-Cotja_NCBI-Refseq-40894_29May21.fasta.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=E\:\\FragPipe-15.0\\fragpipe\\tools\\MSFragger-3.2\\MSFragger-3.2.jar
fragpipe-config.bin-philosopher=E\:\\FragPipe-15.0\\fragpipe\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=0.05
msfragger.fragment_mass_units=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=2
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=tsv_pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-50
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=50
msfragger.precursor_true_tolerance=10
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=P
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=trypsin
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021464,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,1; 42.010600,[^,true,1; 79.966330,STY,true,1; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 15.994900,P,true,1; 31.989800,P,true,1; 8.014199,K,false,3; 10.008269,R,false,2; 0.000000,C,true,1; 42.010600,K,true,1; -18.010600,STY,true,1; 14.015600,KR,true,1; 42.047000,KR,true,1; 28.031300,KR,true,1; 114.042900,KST,true,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=true
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01
phi-report.pep-level-summary=false
phi-report.print-decoys=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.annotation-common=true
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=false
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.diag_ions=
ptmshepherd.glyco_mode=false
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_allowed_res=all
ptmshepherd.localization_background=4
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=1
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=3
ptmshepherd.precursor_mass_units=1
ptmshepherd.precursor_tol=3
ptmshepherd.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
run-diaumpire=false
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.groupby=0
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=E\:\\LT0001_Cotja\\MSfragger\\MSF6
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=15

WorkspaceCleanInit [Work dir: E:\LT0001_Cotja\MSfragger\MSF6] E:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[08:50:31] Executing Workspace v3.4.13
INFO[08:50:31] Removing workspace
INFO[08:50:31] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\LT0001_Cotja\MSfragger\MSF6] E:\FragPipe-15.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[08:50:32] Executing Workspace v3.4.13
INFO[08:50:32] Creating workspace
INFO[08:50:32] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: E:\LT0001_Cotja\MSfragger\MSF6] java -jar -Dfile.encoding=UTF-8 -Xmx44G E:\FragPipe-15.0\fragpipe\tools\MSFragger-3.2\MSFragger-3.2.jar E:\LT0001_Cotja\MSfragger\MSF6\fragger.params E:\LT0001_Cotja\DDA\LT0001_TN-6796_100ng_2-B_1_01_3763.mzML MSFragger version MSFragger-3.2 Batmass-IO version 1.22.1 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_291, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 39 GB memory Checking database... Checking spectral files... E:\LT0001_Cotja\DDA\LT0001_TN-6796_100ng_2-B_1_01_3763.mzML: Scans = 40814 ***FIRST SEARCH**** Parameters: num_threads = 15 database_name = D:\Databases\Cotja\2021-05-31-decoys-contam-Cotja_NCBI-Refseq-40894_29May21.fasta.fas decoyprefix = rev precursor_mass_lower = -10.0 precursor_mass_upper = 10.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 10.0 precursor_true_units = 1 fragment_mass_tolerance = 50.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 1 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = trypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = P num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = tsv_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 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 1 variable_mod_02 = 42.010600 [^ 1 variable_mod_03 = 79.966330 STY 1 variable_mod_11 = 42.010600 K 1 variable_mod_14 = 42.047000 KR 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.25 Da. 8491378854 fragments to be searched in 5 slices (126.53 GB total) Operating on slice 1 of 5: Fragment index slice generated in 29.00 s

  1. LT0001_TN-6796_100ng_2-B_1_01_3763.mzML 7.4 s | deisotoping 6.6 s [progress: 40814/40814 (100%) - 2741 spectra/s] 14.9s Operating on slice 2 of 5: Fragment index slice generated in 20.66 s
  2. LT0001_TN-6796_100ng_2-B_1_01_3763.mzML 6.9 s | deisotoping 6.4 s [progress: 40814/40814 (100%) - 9967 spectra/s] 4.1s Operating on slice 3 of 5: Fragment index slice generated in 21.86 s
  3. LT0001_TN-6796_100ng_2-B_1_01_3763.mzML 7.7 s | deisotoping 6.5 s [progress: 40814/40814 (100%) - 15931 spectra/s] 2.6s Operating on slice 4 of 5: Fragment index slice generated in 21.30 s
  4. LT0001_TN-6796_100ng_2-B_1_01_3763.mzML 8.0 s | deisotoping 6.7 s [progress: 40814/40814 (100%) - 19688 spectra/s] 2.1s Operating on slice 5 of 5: Fragment index slice generated in 20.65 s
  5. LT0001_TN-6796_100ng_2-B_1_01_3763.mzML 6.9 s | deisotoping 6.7 s [progress: 40814/40814 (100%) - 20592 spectra/s] 2.0s | postprocessing 2.6 s ***FIRST SEARCH DONE IN 4.137 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 5.07 1.37 0.09 0.73 4.82 3.66 0.35 3.38
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- MS2 7 10 15 20 25 30
Count 17798 18006 17868 skip rest
------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- -------
Peaks 300_0 200_0 150_1 100_1
------- ------- ------- ------- -------
Count 18339 18173 skip rest
------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 18670
------- -------
------- -------
Rm P. 1
------- -------
Count 18723
------- -------

New fragment_mass_tolerance = 10 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 19.879 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 15 database_name = D:\Databases\Cotja\2021-05-31-decoys-contam-Cotja_NCBI-Refseq-40894_29May21.fasta.fas decoyprefix = rev precursor_mass_lower = -50.0 precursor_mass_upper = 50.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 10.0 precursor_true_units = 1 fragment_mass_tolerance = 10.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 1 isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = trypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = P num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 2 max_variable_mods_combinations = 5000 output_format = tsv_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 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 1 variable_mod_02 = 42.010600 [^ 1 variable_mod_03 = 79.966330 STY 1 variable_mod_06 = 15.994900 P 1 variable_mod_07 = 31.989800 P 1 variable_mod_10 = 0.000000 C 1 variable_mod_11 = 42.010600 K 1 variable_mod_12 = -18.010600 STY 1 variable_mod_13 = 14.015600 KR 1 variable_mod_14 = 42.047000 KR 1 variable_mod_15 = 28.031300 KR 1 variable_mod_16 = 114.042900 KST 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Number of unique peptides of length 7: 245451 of length 8: 236489 of length 9: 228670 of length 10: 219100 of length 11: 212239 of length 12: 200408 of length 13: 192556 of length 14: 183106 of length 15: 174240 of length 16: 164578 of length 17: 155489 of length 18: 149287 of length 19: 140805 of length 20: 134144 of length 21: 127541 of length 22: 118103 of length 23: 111009 of length 24: 107022 of length 25: 100224 of length 26: 95020 of length 27: 90051 of length 28: 84909 of length 29: 79144 of length 30: 74886 of length 31: 70523 of length 32: 66874 of length 33: 62950 of length 34: 58690 of length 35: 54577 of length 36: 52181 of length 37: 47816 of length 38: 45615 of length 39: 41702 of length 40: 39226 of length 41: 36881 of length 42: 33964 of length 43: 29269 of length 44: 23318 of length 45: 17385 of length 46: 11215 of length 47: 7001 of length 48: 3910 of length 49: 1990 of length 50: 1068 In total 4330626 peptides. Generated 963240736 modified peptides. Number of peptides with more than 5000 modification patterns: 47861 Not enough memory allocated to MSFragger. If running using FragPipe: in MSFragger tab, increase the amount of memory allocated using RAM (Gb) parameter. If your computer does not have enough memory, use “Split database” option (requires python; see Configuration page of FragPipe). Set “Split database” parameter to 2. If the program continues to crash, gradually increase the “Split database” value (e.g. to 4, then to 8, etc.) until the program runs successfully. Alternatively, or in combination with the “Split database” option, consider the following options: reduce the number of variable modifications specified; reduce the range of allowed peptide length (from 7-50 to e.g. 7-35). For users running the stand-alone version of MSFragger (i.e. not through FragPipe): try allocating more memory using the -Xmx option. Process 'MSFragger' finished, exit code: 1 Process returned non-zero exit code, stopping


Cancelling 13 remaining tasks
16:42:16 ERROR: Error writing log to file

java.nio.channels.ClosedByInterruptException: null

    at java.nio.channels.spi.AbstractInterruptibleChannel.end(Unknown Source)

    at sun.nio.ch.FileChannelImpl.write(Unknown Source)

    at java.nio.channels.Channels.writeFullyImpl(Unknown Source)

    at java.nio.channels.Channels.writeFully(Unknown Source)

    at java.nio.channels.Channels.access$000(Unknown Source)

    at java.nio.channels.Channels$1.write(Unknown Source)

    at sun.nio.cs.StreamEncoder.writeBytes(Unknown Source)

    at sun.nio.cs.StreamEncoder.implWrite(Unknown Source)

    at sun.nio.cs.StreamEncoder.write(Unknown Source)

    at java.io.OutputStreamWriter.write(Unknown Source)

    at java.io.BufferedWriter.flushBuffer(Unknown Source)

    at java.io.BufferedWriter.write(Unknown Source)

    at java.io.Writer.write(Unknown Source)

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

    at com.dmtavt.fragpipe.tabs.TabRun.on(TabRun.java:309)

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

    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

    at java.lang.reflect.Method.invoke(Unknown Source)

    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.cmd.ProcessBuilderInfo.lambda$toRunnable$0(ProcessBuilderInfo.java:96)

    at java.util.concurrent.CompletableFuture$AsyncRun.run(Unknown Source)

    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)

    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)

    at java.lang.Thread.run(Unknown Source)

    Suppressed: java.nio.channels.ClosedChannelException: null

        at sun.nio.ch.FileChannelImpl.ensureOpen(Unknown Source)

        at sun.nio.ch.FileChannelImpl.write(Unknown Source)

        at java.nio.channels.Channels.writeFullyImpl(Unknown Source)

        at java.nio.channels.Channels.writeFully(Unknown Source)

        at java.nio.channels.Channels.access$000(Unknown Source)

        at java.nio.channels.Channels$1.write(Unknown Source)

        at sun.nio.cs.StreamEncoder.writeBytes(Unknown Source)

        at sun.nio.cs.StreamEncoder.implClose(Unknown Source)

        at sun.nio.cs.StreamEncoder.close(Unknown Source)

        at java.io.OutputStreamWriter.close(Unknown Source)

        at java.io.BufferedWriter.close(Unknown Source)

        at com.dmtavt.fragpipe.tabs.TabRun.saveLogToFile(TabRun.java:355)

        ... 16 common frames omitted
fcyu commented 3 years ago

Right, the error message says

Not enough memory allocated to MSFragger.
If running using FragPipe: in MSFragger tab, increase the amount of memory allocated using RAM (Gb) parameter. If your computer does not have enough memory, use “Split database” option (requires python; see Configuration page of FragPipe). Set “Split database” parameter to 2. If the program continues to crash, gradually increase the “Split database” value (e.g. to 4, then to 8, etc.) until the program runs successfully.
Alternatively, or in combination with the “Split database” option, consider the following options: reduce the number of variable modifications specified; reduce the range of allowed peptide length (from 7-50 to e.g. 7-35).

Best,

Fengchao