Memory problem with HaplotypeCaller -L


I´m using HaplotypeCaller program spliting by chromosomes in sheep genome.

On 22 chromosomes the process has been completed correctly, but on the others there have been several errors. The next paragraph is the command used for all 158 samples. We use nodes of 16 cores (-ntc 16) and 32 Gb of memory RAM.

java -Xmx28g -jar /home/dpaule_1/COMUNES/WGS_software/gatk/3.8.0/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/dpaule_1/
COMUNES/reference_genome/reference_genome_Oar-v3.1-r90_toVariantCalling/Ovis_aries_v3.1-r90.fa -L 9 -I /home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AFS32_SRR501853/AFS32_SRR50
1853_recal_reads.bam -I /home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AFS33_SRR501871/AFS33_SRR501871_recal_reads.bam -I /home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AU
MEHM000000000001/AUMEHM000000000001_recal_reads.bam -I
/home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AUMEHM000000000002/AUMEHM000000000002_recal_reads.bam -I /home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AUMEHM000000000003/AUMEHM000000000003_recal_reads.bam -I /home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AUMEHM000000000004/AUMEHM000000000004_recal_reads.bam -I

ERROR MESSAGE: An error occurred because you did not provide enough memory to run this program. You can use the -Xmx argument (before the -jar argument) to adjust the maximum heap size provided to Java. Note that this is a JVM argument, not a GATK argument.

Best Answers


  • Hi SkyWarrior,

    Thank you for the answer. I can not run GATK without -ntc, because we are trying to reduce the analysis time as much as possible. But we will prove it as a last resort.

    Thank you for everything.


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