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Nesvilab / MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
https://msfragger.nesvilab.org
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JVM stated with 0 GB memory #127

Closed Romi112 closed 3 years ago

Romi112 commented 3 years ago

Hi, I am trying to test msfragger open searches within philosopher in Fragpipe but am getting the following error: (I'm new to github and posting stuff, still hope you find all the info you need to help me)

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

Version info: FragPipe version 14.0 MSFragger version 3.1.1 Philosopher version 3.4.13 (build 1611589727)

LCMS files: Experiment/Group: 

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v14.0ui state cache

crystalc.run-crystalc=false
database.db-path=D\:\\JEG\\2021-02-03-decoys_Ref_uniprot-proteome_cRAP.fasta.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\Users\\Admin\\Desktop\\OLD\\FragPipe-14.0\\MSFragger-3.1.1\\MSFragger-3.1.1\\MSFragger-3.1.1.jar
fragpipe-config.bin-philosopher=C\:\\Users\\Admin\\Desktop\\fragpipe\\lib\\..\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\Admin\\anaconda3\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=true
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=1
ionquant.minisotopes=1
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=false
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=0
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=40
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=-200
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=200
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021464,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 0.000000,site_06,false,1; 0.000000,site_07,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
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=--keepold --static --em 1 --nions b --mods STY\:79.966331,M\:15.9949 --minprob 0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.diag_ions=
ptmshepherd.glyco_mode=false
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_background=4
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=false
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
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\\Admin\\Desktop\\JEGTEST
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=15

WorkspaceCleanInit [Work dir: C:\Users\Admin\Desktop\JEGTEST] C:\Users\Admin\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:42:35] Executing Workspace v3.4.13
INFO[11:42:35] Removing workspace
INFO[11:42:35] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\Users\Admin\Desktop\JEGTEST] C:\Users\Admin\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:42:35] Executing Workspace v3.4.13
INFO[11:42:35] Creating workspace
INFO[11:42:35] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MsFragger [Work dir: C:\Users\Admin\Desktop\JEGTEST] C:\Users\Admin\Desktop\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx249G C:\Users\Admin\Desktop\OLD\FragPipe-14.0\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar C:\Users\Admin\Desktop\JEGTEST\fragger.params D:\JEG\Gelfree_BU\RAW\G1.raw MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, JVM started with 0 GB memory Checking database... Checking D:\JEG\Gelfree_BU\RAW\G1.raw...

****MAIN SEARCH**** Checking database... Parameters: num_threads = 15 database_name = D:\JEG\2021-02-03-decoys-B.t._Ref_uniprot-proteome UP000001414_cRAP.fasta.fas decoyprefix = rev precursor_mass_lower = -200.0 precursor_mass_upper = 200.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 0 write_calibrated_mgf = false isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_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 = 40 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 = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Number of unique peptides of length 7: 47435 of length 8: 46618 of length 9: 44573 of length 10: 43569 of length 11: 42579 of length 12: 41507 of length 13: 39169 of length 14: 37814 of length 15: 36649 of length 16: 34868 of length 17: 33269 of length 18: 31867 of length 19: 31207 of length 20: 29301 of length 21: 27947 of length 22: 26638 of length 23: 24995 of length 24: 23340 of length 25: 22186 of length 26: 21110 of length 27: 19903 of length 28: 18772 of length 29: 17087 of length 30: 16232 of length 31: 14958 of length 32: 13975 of length 33: 12927 of length 34: 12157 of length 35: 11091 of length 36: 10586 of length 37: 9537 of length 38: 8991 of length 39: 8250 of length 40: 7610 In total 868717 peptides. java.lang.reflect.InvocationTargetException 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 com.simontuffs.onejar.Boot.run(Boot.java:340) at com.simontuffs.onejar.Boot.main(Boot.java:166) Caused by: java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at edu.umich.andykong.msfragger.M.a(Unknown Source) at edu.umich.andykong.msfragger.K.a(Unknown Source) at edu.umich.andykong.msfragger.m.a(Unknown Source) at edu.umich.andykong.msfragger.B.(Unknown Source) at edu.umich.andykong.msfragger.MSFragger.b(Unknown Source) at edu.umich.andykong.msfragger.MSFragger.main(Unknown Source) ... 6 more Caused by: java.lang.OutOfMemoryError: Java heap space Picked up _JAVA_OPTIONS: -Xmx512M Process 'MsFragger' finished, exit code: 1 Process returned non-zero exit code, stoppingMsFragger move pepxml C:\Users\Admin\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\Admin\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\JEG\Gelfree_BU\RAW\G1.pepXML C:\Users\Admin\Desktop\JEGTEST\G1.pepXML


Cancelling 10 remaining tasks
Processing interrupted, stopping MsFragger move pepxml

**Im not familiar with java and cant tell, if its a problem with the java installation or msfragger. Hopefully someone of you know´s what's going on.

Best 
Romi**
fcyu commented 3 years ago

I guess this is because there is not much free memory available in your computer.

Best,

Fengchao

Romi112 commented 3 years ago

In fact, I have 256 GB of DDR3 memory in this computer. I also changed the global RAM settings from 0 to higher values, but as expected this has no effect on the JVM startup memory (it is 0 GB in my runs).

fcyu commented 3 years ago

There are C:\Users\Admin\Desktop\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx249G C:\Users\Admin\Desktop\OLD\FragPipe-14.0\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar C:\Users\Admin\Desktop\JEGTEST\fragger.params and Picked up _JAVA_OPTIONS: -Xmx512M in your log, which indicates that your configuration limits the usage of the memory. Can you check if your system has the global JAVA_OPTIONS?

Best,

Fengchao