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

>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