Hi Christopher, you can increase the JVM memory options via the job_conf.xml file for a particular tool.
Hope this helps, Bjoern Am 06.07.2017 um 13:05 schrieb Previti: > Dear all, > I seemly have a java issue (out of memory) when trying to construct a > picard index for the rat (rn6) genome build using the > picard_index_builder_data_manager. > This is strange because other, bigger genomes have not presented any > problems... > > Does anybody have any suggestions? > > Cheers, > Christopher Previti > > Fatal error: Exit code 1 () > [Thu Jul 06 08:26:48 UTC 2017] picard.sam.CreateSequenceDictionary > REFERENCE=/opt/galaxy/galaxy/database/jobs_directory/000/978/dataset_1974_files/rn6.fa > OUTPUT=rn6.dict TRUNCATE_NAMES_AT_WHITESPACE=true > NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false > VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 > CREATE_INDEX=false CREATE_MD5_FILE=false > GA4GH_CLIENT_SECRETS=client_secrets.json > [Thu Jul 06 08:26:48 UTC 2017] Executing as > gal...@xgs-node071.xgs.dkfz-heidelberg.de on Linux 3.10.0-514.el7.x86_64 > amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 2.7.1-SNAPSHOT > [Thu Jul 06 08:26:49 UTC 2017] picard.sam.CreateSequenceDictionary done. > Elapsed time: 0.03 minutes. > Runtime.totalMemory()=1051721728 > To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp > Exception in thread "main" java.lang.OutOfMemoryError: Java heap space > at > htsjdk.samtools.reference.FastaSequenceFile.readSequence(FastaSequenceFile.java:151) > at > htsjdk.samtools.reference.FastaSequenceFile.nextSequence(FastaSequenceFile.java:81) > at > picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:156) > at > picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:137) > at > picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208) > at > picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) > at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105) > Error building index. > > > > > > > > -- > *Dr. Christopher Previti* > Genomics and Proteomics Core Facility > High Throughput Sequencing (W190) > Bioinformatician > > German Cancer Research Center (DKFZ) > Foundation under Public Law > Im Neuenheimer Feld 580 > 69120 Heidelberg > Germany > Room: B2.102 (INF580/TP3) > Phone: +49 6221 42-4434 > > christopher.prev...@dkfz.de <http://www.dkfz.de/> > www.dkfz.de <http://www.dkfz.de/> > > Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta > VAT-ID No.: DE143293537 > > Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die > Personen bestimmt, an die sie adressiert ist. > Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte > Informationen enthalten. Sollten Sie nicht > der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den > Absender und löschen Sie die Mitteilung. > Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist > untersagt. > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
