Hi,
I am getting the following error while using smra.
How much should I specify for MAX_HEAP_SIZE?
I am getting the following error while using smra.
Code:
java -jar /srma/srma-0.1.6/srma-0.1.6.jar I=KLM_sorted.bam O=KLM_sorted_smra.bam R=/Genome/hg18/hg18.fa VALIDATION_STRINGEN CY=SILENT [Thu Jun 24 16:12:12 SGT 2010] srma.SRMA INPUT=KLM_sorted.bam OUTPUT=KLM_sorted_smra.bam REFERENCE=/Genome/hg18/hg18.fa VALIDATION_STRINGENCY=SILENT OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=3 MAXIMUM_TOTAL_COVERAGE=100 CORRECT_BASES=false USE_SEQUENCE_QUALITIES=true QUIET_STDERR=false MAX_HEAP_SIZE=8192 MAX_QUEUE_SIZE=65536 NUM_THREADS=1 TMP_DIR=/tmp/userrig VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 Allele coverage cutoffs: coverage: 1 minimum allele coverage: 0 coverage: 2 minimum allele coverage: 0 coverage: 3 minimum allele coverage: 0 coverage: 4 minimum allele coverage: 1 coverage: 5 minimum allele coverage: 1 coverage: 6 minimum allele coverage: 1 coverage: 7 minimum allele coverage: 2 coverage: 8 minimum allele coverage: 2 coverage: 9 minimum allele coverage: 3 coverage: >9 minimum allele coverage: 3 Records processsed: 65534 (last chr10:1904158-1904236) Exception in thread "Thread-2" java.lang.OutOfMemoryError: Java heap space [Thu Jun 24 16:16:07 SGT 2010] srma.SRMA done. Runtime.totalMemory()=954466304 Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.util.LinkedList.addBefore(LinkedList.java:795) at java.util.LinkedList.add(LinkedList.java:215) at srma.ThreadPoolLinkedList.add(ThreadPoolLinkedList.java:19) at srma.SRMA.processToAddToGraphList(SRMA.java:485) at srma.SRMA.doWork(SRMA.java:272) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150) at srma.SRMA.main(SRMA.java:94)
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