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MarkDuplicatesSpark: consider adding --conf 'spark.local.dir=./tmp #6

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cgpu opened this issue Dec 9, 2019 · 0 comments

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cgpu commented Dec 9, 2019

This ensures that spark is dumping its temp files onto a fast disk (the main local-disk that you requested) and not the boot disk (which is guaranteed to be both slow and small).

https://gatkforums.broadinstitute.org/gatk/discussion/23441/markduplicatespark-is-slower-than-normal-markduplicates

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