Java memory requirements for Picard index?
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 galaxy@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.previti@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.
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 galaxy@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.previti@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.
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Dear Börn, Sorry for the late response but thanks! I'll look into it, Christopher On 07/07/2017 06:36 PM, Björn Grüning wrote:
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 galaxy@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.previti@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/
-- *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.previti@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.
participants (2)
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Björn Grüning -
Previti