Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

SelectVariants and IndexFeatureFile run into OutOfMemoryError at java.io.ByteArrayOutputStream.hugeCapacity(ByteArrayOutputStream.java:123)

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    Bhanu Gandham

    Hi,

     

    You are using a very old version of GATK. Can you please try the latest version GATKv4.1.6.0 and let us know if the issue persists.

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    Yen On Chan

    Hi Bhanu,

    I updated GATK to the latest version today and ran the command below. However, I am still getting the same error. 

    gatk --java-options "-Xmx490g -Xms400g -Djava.io.tmpdir=/data/yenc/datasets/gVCF/tmp" IndexFeatureFile -I input.g.vcf.gz

     

    Yen On Chan

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    Bhanu Gandham

    Hi,

    I wonder if you facing this issue because you set the Xms value very high. Can you try to run it without the Xms value and lowering the Xmx as well?

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