Using large amazon instance 

Trying to do an interval join of SNPs as output from pileup 120,000 regions(5.5Mb) with with snp135Common 12,000,000(425Mb) and get the following errors. The goal is to pickup rs id's for known SNPs in the list of SNPs. 

Is this a memory issue? 

I was able to do the operation against chr1 as a test. Thought about chaining the outputs and doing against a file for each chromosome to make smaller files but then I have a mess where rs id's are in different columns.