Hey,
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) ?
Second, when I run the unified genotyper, I get the following error:
[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)
I assume, changing the java heap size will solve the problem. But how can I do
it in galaxy ?
Thanks for your help!
Jan
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