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  • SRMA memory leak

    Hi friends
    Was anybody successful using SRMA? I have tried it with the RANGE option sa well, and it has worked for chr1, but I get the error with chr2.. Here is the error (RAM we have is 140GB) after that srcript is hanging:


    [Wed Mar 02 09:28:35 CET 2011] srma.SRMA INPUT=[camergdup.bam] OUTPUT=[casrmachr2.bam] REFERENCE=/project/erasys1/ngs/ca/hg19.fa RANGE=chr2:1-243199373 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/ot VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
    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: 2752469 (last chr2:231988063-231988112)Exception in thread "Thread-84" java.lang.OutOfMemoryError: Java heap space
    at java.util.PriorityQueue.<init>(Unknown Source)
    at srma.Graph.addNode(Graph.java:161)
    at srma.Graph.addSAMRecord(Graph.java:120)

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