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Memory setting issue in CNV calling pipeline step 2: SVAltAlign


I failed in running CNV calling step 2: SVAltAlign, probably because of the memory setting issue.
Even though the "-lsfMemLimit 128" is specified in the command, which is:

"java -Xmx128g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVAltAlign.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-genomeMaskFile ${cwd}/Homo_sapiens_assembly38.mask.101.fasta \
-vcf ${vcf} \
-R ${ref} \
-I ${bam_list} \
-md ${metadata_dir} \
-jobLogDir ${log_dir} \
**-lsfMemLimit 128 **

The error message is:

"ERROR 16:28:28,640 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10'
INFO 16:28:28,710 QGraph - 35 Pend, 0 Run, 1 Fail, 3 Done"

It seems the "-lsfMemLimit 128" parameter is not passed to java command, which is still "-Xmx2048".

How could I fix this issue?


Issue · Github
by Sheila

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Peter, I've moved your question to the GenomeStrip forum since this is not our domain. @bhandsaker may be able to help you.

  • bhandsakerbhandsaker Member, Broadie, Moderator

    Two responses:
    First, with modern sequencing data you should not be using SVAltAlign, there is no need for this step. Consider it deprecated.
    Second, your specific question is about -lsfMemLimit. This controls the total memory request to LSF for your job. If you want to increase the maximum java heap size, use -memLimit.
    Also note that -lsfMemLimit only applies to LSF7. If you are not using LSF7, use -jobNative to control your job settings such as memory reservation if you need to override the defaults.

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