Hello, I'm currently putting together a workflow for WGS (Illumina 30x) variant calling (HaplotypeCaller) using GATK 3.2 on our local SGE grid. I was wondering whether there is any speedup with redirecting -Djava.io.tmpdir to scratch space on the local node? Which steps are I/O intensive and could potentially benefit from this? Currently the bottleneck seems to be IndelRealigner which takes ~14hrs. Thank you.
When trying to run the UnifiedGenotyper, I keep getting the following
ERROR MESSAGE: There was a failure because temporary file /tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub7040175770023361502.tmp could not be found while running the GATK with more than one thread. Possible causes for this problem include: your system's open file handle limit is too small, your output or temp directories do not have sufficient space, or just an isolated file system blip
About the suggested causes: * The system's open file handle limit is set to 4827982, I doubt that this is exhausted. * On the /tmp/ file system, there is 200GB of free space; each GATK run seems to use less that 1/1000 of that. * I have no idea what a file system blip would be, but apparently it occurs every time I run the UnifiedGenotyper. Any idea why this would be, and how it could be avoided?
Or could there be still a different reason for the error?