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Indel Realignment die for no enough memory in RNAseq

I have 2 samples of RNAseq with 10 million PE reads for each and read length of 81 bp.
indelRealigner gave me this error

ERROR MESSAGE: There was a failure because you did not provide enough memory to run this program. See the -Xmx JVM argument to adjust the maximum heap size provided to Java

I increased the heap size to 78g. One sample was done successful but the 2nd sample are still giving the same error.
I tried to use down sampling but still the same error

Here is my code:

java -Xmx78g -jar $GATK/GenomeAnalysisTK.jar \
-T IndelRealigner \
-R $gatk_ref \
-I $sample \
-targetIntervals gatk.intervals \
-nWayOut '.realigned.bam' \
-known $indels \
-model USE_SW \
-LOD 0.4 \
-dcov 1000

Any advice will be truly appreciated.
Thank you

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    I'm afraid that's a limitation of the algorithm compute requirements. Running Smith-Waterman on 1000-read deep data uses a huge amount of memory. I can only recommend using lower dcov settings or not using USE_SW. Or give the program more memory of course, if that's available to you. But honestly I think it's overkill to run IR this way.

  • drtamermansourdrtamermansour USAMember

    Thank you for your answer.
    Unfortunately I can not increase the memory. Also I am working with horses where known variants are limited and I have to use the USE_SW.

    I think lowering the dcov will affect the efficiency of downstream variant calling step. With the new HaplotypeCaller, it might be better to ignore the whole IR step rather than risking the variant calling, Am I right??

    Can I decrease the --maxReadsInMemory? if yes, what is your recommendation for the value I should use.

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