Dear Börn,

Sorry for the late response but thanks!

I'll look into it,

Christopher

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/>

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