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

MarkDuplicatesSpark Follow

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    I'm trying to use MarkDuplicatesSpark on WGS files of approx. 130Go,

    I've set spark.local.dir and --tmp-dir to a RAM disk to avoid very long memory access (I don't have a large SSD, and scratch is on a NFS mount of HDD),

    On a slurm cluster with a server of 128CPUs + 1To of RAM I get an error "out of disk space" (RAM-disk),

    Is it normal? It looks like MarkDuplicatesSpark needs more than 1To of temporary files

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