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compomics / searchgui

Highly adaptable common interface for proteomics search and de novo engines
http://compomics.github.io/projects/searchgui.html
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Error: Map failed #311

Closed ssybbc closed 3 years ago

ssybbc commented 3 years ago

Hello,

I have been trying to use searchgui to search previous data and hunting for new modifications that possibly hidden in those spectrum. I was using a GUI of version 4.1.0 for Windows. The error message were as below:

Wed Aug 25 23:30:47 EDT 2021 Importing spectrum files. Wed Aug 25 23:30:47 EDT 2021 Importing spectrum file A-GluC-7-F005884.dat-pride.pride.mgf Wed Aug 25 23:31:55 EDT 2021 Error: Map failed Wed Aug 25 23:31:55 EDT 2021 An error occurred while running SearchGUI. Please contact the developers. Wed Aug 25 23:31:55 EDT 2021 The search or processing did not finish properly!

Wed Aug 25 23:31:55 EDT 2021 Searching Canceled!

I am wondering what I could do to rescue this. It seems like it is the software problem instead of search engine thing.

Thanks, Siyuan

------------------------------------------------------------------

SearchGUI 4.1.0 Report File

#

Originally saved by: siyua @ DESKTOP-2Q7HJSN

on: 25 Aug 2021, 23:31

as: SearchGUI Report 2021-08-25 23.31.55.html

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Wed Aug 25 23:30:47 EDT 2021 Importing spectrum files. Wed Aug 25 23:30:47 EDT 2021 Importing spectrum file A-GluC-7-F005884.dat-pride.pride.mgf Wed Aug 25 23:31:55 EDT 2021 Error: Map failed Wed Aug 25 23:31:55 EDT 2021 An error occurred while running SearchGUI. Please contact the developers. Wed Aug 25 23:31:55 EDT 2021 The search or processing did not finish properly!

Wed Aug 25 23:31:55 EDT 2021 Searching Canceled!

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General Search Parameters

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ENZYME0=Glu-C, Specific, 2 missed cleavages FIXED_MODIFICATIONS=Carbamidomethylation of C VARIABLE_MODIFICATIONS=Dimethylation of R,Methylation of R,Oxidation of M REFINEMENT_FIXED_MODIFICATIONS=Carbamidomethylation of C REFINEMENT_VARIABLE_MODIFICATIONS= PRECURSOR_MASS_TOLERANCE=15.0 PRECURSOR_MASS_TOLERANCE_UNIT=ppm FRAGMENT_MASS_TOLERANCE=0.02 FRAGMENT_MASS_TOLERANCE_UNIT=Da PPM_TO_DA_CONVERSION_REF_MASS=2000.0 FORWARD_FRAGMENT_ION_TYPE=b FRAGMENT_ION_TYPE_2=y PRECURSOR_CHARGE_LOWER_BOUND=2 PRECURSOR_CHARGE_UPPER_BOUND=4 ISOTOPIC_CORRECTION_LOWER_BOUND=0 ISOTOPIC_CORRECTION_UPPER_BOUND=1

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OMSSA Specific Parameters

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EVALUE_CUTOFF=100.0 MAXIMUM_HITLIST_LENGTH=10 PRECURSOR_ELIMINATION=false PRECURSOR_SCALING=true MINIMAL_PEPTIDE_SIZE=8 MAXIMAL_PEPTIDE_SIZE=30 PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS=3 CHARGE_ESTIMATION=true OUTPUT_TYPE=OMX MEMORY_MAPPED_SEQUENCES=false MASS_TO_CONSIDER_EXACT_NEUTRON_MASS=1446.94 LOW_INTENSITY_CUTOFF=0.0 HIGH_INTENSITY_CUTOFF=0.2 INTENSITY_INCREMENT=5.0E-4 SINGLE_CHARGE_WINDOW_WIDTH=27 DOUBLE_CHARGE_WINDOW_WIDTH=14 SINGLE_CHARGE_WINDOW_NPEAKS=2 DOUBLE_CHARGE_WINDOW_NPEAKS=2 MAX_HITS_PER_SPECTRUM_PER_CHARGE=30 MIN_ANNOTATED_INTENSE_PEAKS=6 MIN_ANNOTATED_PEAKS=2 MIN_PEAKS=4 CLEAVE_TERMINAL_METHIONINE=true MAX_MZ_LADDERS=128 MAX_FRAGMENT_CHARGE=2 FRACTION_PEAKS_FOR_CHARGE_1_ESTIMATION=0.95 AUTO_DETERMINE_CHARGE_ONE=true SEARCH_POSITIVE_IONS=true MIN_PERCURSORS_PER_SPECTRUM=1 FORWARD_FRAGMENTS_FIRST=false REWIND_FRAGMENTS=true FRAGMENTS_PER_SERIES=100 CORRELATION_CORRECTION_SCORE=true CONSECUTIVE_ION_PROBABILITY=0.5 ITERATIVE_SEARCH_SEQUENCE_EVALUE=0.0 ITERATIVE_SEARCH_SPECTRUM_EVALUE=0.01 ITERATIVE_SEARCH_REPLACEMENT_EVALUE=0.0

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MetaMorpheus Specific Parameters

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MIN_PEPTIDE_LENGTH=8 MAX_PEPTIDE_LENGTH=30 SEARCH_TYPE=Classic NUM_PARTITIONS=1 DISSOCIATION_TYPE=HCD MAX_MODS_FOR_PEPTIDE=2 INITIATOR_METHIONINE_BEHAVIOR=Variable SCORE_CUTOFF=5.0 USE_DELTA_SCORE=false FRAGMENTATION_TERMINUS=Both MAX_FRAGMENTATION_SIZE=30000.0 MIN_ALLOWED_INTERNAL_FRAGMENT_LENGTH=0 MASS_DIFF_ACCEPTOR_TYPE=OneMM WRITE_MZID=true WRITE_PEPXML=false USE_PROVIDED_PRECURSOR=true DO_PREC_DECONVOLUTION=true DECONVOLUTION_INT_RATIO=3.0 DECONVOLUTION_MASS_TOL=4.0 DECONVOLUTION_MASS_TOL_TYPE=PPM TRIM_MS1_PEAKS=false TRIM_MSMS_PEAKS=true NUM_PEAKS_PER_WINDOWS=200 MIN_ALLOWED_INT_RATIO_TO_BASE_PEAK=0.01 WINDOW_WITH_THOMPSON=null NUM_WINDOWS=null NORMALIZE_PEAKS_ACROSS_ALL_WINDOWS=false MOD_PEPTIDES_ARE_DIFFERENT=false NO_ONE_HIT_WONDERS=false SEARCH_TARGET=true DECOY_TYPE=None MAX_MOD_ISOFORMS=1024 MIN_VARIANT_DEPTH=1 MAX_HETROZYGOUS_VARIANTS=4 RUN_GPTM=false GPTMS=Common Biological, Common Artifact, Metal

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X!Tandem Specific Parameters

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DYNAMIC_RANGE=100.0 NUMBER_OF_PEAKS=50 MIN_FRAG_MASS=200.0 MIN_NUMBER_OF_PEAKS=5 NOISE_SUPPRESSION=NO PARENT_MONOISOTOPIC_MASS_ISOTOPE_ERROR=YES MIN_PREC_MASS=500.0 PROTEIN_QUICK_ACETYL=YES QUICK_PYROLIDONE=YES PROTEIN_PTM_COMPLEXITY=6.0 STP_BIAS=NO REFINE=YES REFINE_SEMI=NO REFINE_POINT_MUTATIONS=NO REFINE_SPECTRUM_SYNTHESIS=YES REFINE_UNANTICIPATED_CLEABAGES=YES REFINE_SNAPS=YES REFINE_MAX_EVALUE=0.01 POTENTIAL_MODIFICATIONS_FOR_FULL_REFINEMENT=NO EVALUE_CUTOFF=0.01 SKYLINE_PATH= OUTPUT_RESULTS=all OUTPUT_PROTEINS=YES OUTPUT_SEQUENCES=NO OUTPUT_SPECTRA=YES OUTPUT_HISTOGRAMS=NO

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PepNovo+ Specific Parameters

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HIT_LIST_LENGTH=10 CORRECT_PRECURSOR_MASS=false DISCARD_LOW_QUALITY_SPECTRA=true FRAGMENTATION_MODEL=CID_IT_TRYP GENERATE_QUERY=false

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Andromeda Specific Parameters

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MIN_PEPTIDE_LENGHT_NO_ENZYME=8 MAX_PEPTIDE_LENGHT_NO_ENZYME=30 MAX_PEPTIDE_MASS=4600.0 NUMBER_SPECTRUM_MATCHES=10 MAX_PTMS=5 FRAGMENTATION_METHOD=CID WATER_LOSS=true AMMONIA_LOSS=true SEQUENCE_DEPENDENT_NEUTRAL_LOSS=true EQUAL_IL=false FRAGMENT_ALL=false EMPERICAL_CORRECTION=true HIGHER_CHARGE=true MAX_COMBINATIONS=250 TOP_PEAKS=8 TOP_PEAKS_WINDOW=100 DECOY_MODE=none

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MS Amanda Specific Parameters

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SEARCH_DECOY=false REPORT_BOTH_BEST_HITS_FOR_TD=true INSTRUMENT_ID=b, y MONOISOTOPIC=true MAX_RANK=10 PERFORM_DEISOTOPING=true MAX_MODIFICATIONS=3 MAX_VARIABLE_MODIFICATIONS=4 MAX_MODIFICATIONS_SITES=6 MAX_NEUTRAL_LOSSES=1 MAX_NEUTRAL_LOSSES_PER_MODIFICATION=2 MIN_PEPTIDE_LENGTH=8 MAX_PEPTIDE_LENGTH=30 MAX_LOADED_PROTEINS=100000 MAX_LOADED_SPECTRA=2000 OUTPUT_FORMAT=csv

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MS-GF+ Specific Parameters

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SEARCH_DECOY=false INSTRUMENT_ID=3 FRAGMENTATION_ID=3 PROTOCOL_ID=0 MIN_PEP_LENGTH=8 MAX_PEP_LENGTH=30 NUMBER_SPECTRUM_MATCHES=10 ADDITIONAL_OUTPUT=false NUMBER_OF_TOLERABLE_TERMINI=2 MAX_NUMBER_MODIFICATIONS=2 NUMBER_TASKS=null

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DirecTag Specific Parameters

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TIC_CUTOFF_PERCENTAGE=100.0 MAX_PEAK_COUNT=100 NUM_INTENSITY_CLASSES=3 ADJUST_PRECURSOR_MASS=false MIN_PRECUSOR_ADJUSTMENT=-0.5 MAX_PRECUSOR_ADJUSTMENT=1.5 PRECUSOR_ADJUSTMENT_STEP=0.1 NUM_CHARGE_STATES=3 OUTPUT_SUFFIX= USE_CHARGE_STATE_FROM_MS=true DUPLICATE_SPECTRA=true DEISOTOPING_MODE=0 ISOTOPE_MZ_TOLERANCE=0.25 COMPLEMENT_MZ_TOLERANCE=0.1 TAG_LENGTH=4 MAX_DYNAMIC_MODS=2 MAX_TAG_COUNT=10 INTENSITY_SCORE_WEIGHT=1.0 MZ_FIDELITY_SCORE_WEIGHT=1.0 COMPLEMENT_SCORE_WEIGHT=1.0

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Comet Specific Parameters

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NUMBER_SPECTRUM_MATCHES=10 MAX_VARIABLE_MODS=10 REQUIRE_VARIABLE_MODS=false MIN_PEAKS=10 MIN_PEAKS_INTENSITY=0.0 REMOVE_PRECURSOR=0 REMOVE_PRECURSOR_TOLERANCE=1.5 LOWER_CLEAR_MZ_RANGE=0.0 UPPER_CLEAR_MZ_RANGE=0.0 ENZYME_TYPE=2 ISOTOPE_CORRECTION=1 MIN_PRECURSOR_MASS=600.0 MAX_PRECURSOR_MASS=5000.0 MIN_PEP_LENGTH=8 MAX_PEP_LENGTH=30 MAX_FRAGMENT_CHARGE=3 REMOVE_METHIONINE=false BATCH_SIZE=0 THEORETICAL_FRAGMENT_IONS_SUM_ONLY=false FRAGMENT_BIN_OFFSET=0.01

USE_SPARSE_MATRIX=true OUTPUT_FORAMT=PepXML PRINT_EXPECT_SCORE=true

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MyriMatch Specific Parameters

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MIN_PEP_LENGTH=8 MAX_PEP_LENGTH=30 NUMBER_SPECTRUM_MATCHES=10 TIC_CUTOFF_PERCENTAGE=0.98 MAX_DYNMIC_MODS=2 MIN_TERMINI_CLEAVAGES=2 MIN_PRECURSOR_MASS=600.0 MAX_PRECURSOR_MASS=5000.0 USE_SMART_PLUS_THREE_MODEL=false COMPUTE_XCORR=false NUM_INTENSITY_CLASSES=3 CLASS_SIZE_MULTIPLIER=2 NUM_BATCHES=50 FRAGMENTATION_RULE=CID MAX_PEAK_COUNT=300 OUTPUT_FORMAT=mzIdentML

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pNovo+ Specific Parameters

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NUMBER_PEPTIDES=10 LOWER_PRECURSOR_MASS=300 UPPER_PRECURSOR_MASS=5000 ACTIVATION_TYPE=HCD

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Tide Specific Parameters

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MIN_PEP_LENGTH=6 MAX_PEP_LENGTH=30 MIN_PRECURSOR_MASS=200.0 MAX_PRECURSOR_MASS=7200.0 MAX_VARIABLE_MODIFICATIONS_PER_TYPE_PER_PEPTIDE=2 MAX_VARIABLE_MODIFICATIONS_PER_PEPTID=255 DECOY_FORMAT=none KEEP_TERMINAL_AMINO_ACIDS=NC DECOY_SEED=1 OUTPUT_FOLDER_NAME=crux-output PRINT_PEPTIDES=false VERBOSITY=30 MONOISOTOPIC_PRECURSOR=true CLIP_NTERM_METHIONINE=false DIGESTION_TYPE=full-digest COMPUTE_SP_SCORE=false NUMBER_SPECTRUM_MATCHES=10 COMPUTE_EXACT_P_VALUES=false MIN_SPECTRUM_MZ=0.0 MAX_SPECTRUM_MZ=null MIN_SPECTRUM_PEAKS=20 SPECTRUM_CHARGES=all REMOVE_PRECURSOR=false REMOVE_PRECURSOR_TOLERANCE=1.5 PRINT_PROGRESS_INDICATOR_SIZE=1000 USE_FLANKING_PEAKS=false USE_NEUTRAL_LOSS_PEAKS=false MZ_BIN_WIDTH=0.02 MZ_BIN_OFFSET=0.0 CONCATENATE_TARGET_DECOY=false STORE_SPECTRA_FILE_NAME=null TEXT_OUTPUT=true SQT_OUTPUT=false PEPXML_OUTPUT=false MZID_OUTPUT=false PERCOLATOR_OUTPUT=false

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Novor Specific Parameters

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FRAGMENTATION=HCD MASS_ANALYZER=FT

hbarsnes commented 3 years ago

Can you share the SearchGUI log file? You'll find it via the Help menu > Bug Report. It will hopefully tell us a bit more about why the mgf file cannot be parsed correctly.

ssybbc commented 3 years ago

Hi hbarnes

Thanks for swift response! Please see below for the log file.

jshortcut.dll loaded via tmp generated pathname: C:\Users\siyua\AppData\Local\Temp\jshortcut-1011991475722907883.dll java.io.IOException: Map failed at sun.nio.ch.FileChannelImpl.map(Unknown Source) at com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader.(CmsFileReader.java:141) at com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler.register(MsFileHandler.java:154) at eu.isas.searchgui.SearchHandler$SearchWorker.doInBackground(SearchHandler.java:2528) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Caused by: java.lang.OutOfMemoryError: Map failed at sun.nio.ch.FileChannelImpl.map0(Native Method) ... 10 more java.io.IOException: Map failed at sun.nio.ch.FileChannelImpl.map(Unknown Source) at com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader.(CmsFileReader.java:141) at com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler.register(MsFileHandler.java:154) at eu.isas.searchgui.SearchHandler$SearchWorker.doInBackground(SearchHandler.java:2528) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Caused by: java.lang.OutOfMemoryError: Map failed at sun.nio.ch.FileChannelImpl.map0(Native Method) ... 10 more

hbarsnes commented 3 years ago

It seems like the parsing of the mgf file is running out of memory. May I ask how big the mgf file is? You can also try increasing the memory you provide to SearchGUI via the Edit > Java Settings > Memory option. (Please also make sure that you are using a 64 bit version of Java, as otherwise the amount of memory Java can use is more limited.)

ssybbc commented 3 years ago

The mgf file is 294 MB and yes the java was 32 bit. I will re-install a 64 bit java and give it a shot.

ssybbc commented 3 years ago

Thanks. I changed the java to 64-bit and it worked perfect.

On Thu, Aug 26, 2021 at 12:07 PM Harald Barsnes @.***> wrote:

It seems like the parsing of the mgf file is running out of memory. May I ask how big the mgf file is? You can also try increasing the memory you provide to SearchGUI via the Edit > Java Settings > Memory option. (Please also make sure that you are using a 64 bit version of Java, as otherwise the amount of memory Java can use is more limited.)

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