I am trying to run UG across just over 2,200 individuals (exome sequencing). I have successfully done this on our computing cluster with just over 1,000 samples without issues (apart from having to get the limit on no. of open files (ulimit) increased).
I got another increase in ulimit to allow me to run UG on the larger set. However, our IO is being pushed over the edge with the 2,200 input samples. I have two questions:
Would appreciate any advice you would have on getting this to run on this size of data. Thanks!