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.