I know, the GATK-tools is considered to be in alpha status, but maybe someone can help me. First, is there a documentation on which dependencies where to put (just to confirm I've done it correctly) ?
[Wed May 25 15:57:04 CEST 2011] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/var/folders/gr/grLYUw45FFS4KKMXzK5R6++++TI/-Tmp-/tmp7m3sg0/gatk_input.fasta OUTPUT=/var/folders/gr/grLYUw45FFS4KKMXzK5R6++++TI/-Tmp-/tmp7m3sg0/dict6511818973877179087.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 TMP_DIR=/var/folders/gr/grLYUw45FFS4KKMXzK5R6++++TI/-Tmp-/ngs2 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed May 25 15:57:04 CEST 2011] net.sf.picard.sam.CreateSequenceDictionary done.
Runtime.totalMemory()=129957888
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at net.sf.picard.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:178)
at net.sf.picard.reference.IndexedFastaSequenceFile.getSequence(IndexedFastaSequenceFile.java:157)
at net.sf.picard.reference.IndexedFastaSequenceFile.nextSequence(IndexedFastaSequenceFile.java:234)
at net.sf.picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:133)
at net.sf.picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:113)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165)
at org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSource.(ReferenceDataSource.java:131)
at org.broadinstitute.sting.gatk.AbstractGenomeAnalysisEngine.openReferenceSequenceFile(AbstractGenomeAnalysisEngine.java:577)
at org.broadinstitute.sting.gatk.AbstractGenomeAnalysisEngine.initializeDataSources(AbstractGenomeAnalysisEngine.java:318)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:90)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:97)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:244)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)