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Print Reads Memory Problem: Tried adding -xmx argument

leslie.oldfieldleslie.oldfield TorontoMember
edited August 2015 in Ask the GATK team


I am having trouble getting print reads to run successfully. I keep getting the error that there is not enough memory and to try the xmx JVM command.. but I already have used this. I've read various threads saying to use a tmp directory and even with that it is not working. Any ideas? Thanks for your assistance and below is the script I use:

java -Xmx8g -Djava.io.tmpdir=/oicr/data/archive/projects/PCSI/PCSI_MR/leslie/tmp -jar /oicr/local/analysis/sw/gatk/GenomeAnalysisTK-3.4-0/GenomeAnalysisTK.jar -T PrintReads -R ./hg19/Genomic/references/fasta/hg19.fa -I ./Ag/Ag_rg_sorted_split.bam -BQSR ./Ag/Ag_bqsr_data.table -o ./Ag/Ag_processed.bam

Note: When I try to use -Xmv16g I get the error:

Error occurred during initialization of VM
Could not reserve enough space for 16777216KB object heap



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