Did a subtract first to get a known list of rs SNPs that will be found in the tumor SNPs. That ran without error. Doing a join of the subtracted list of rs SNPs and the tumor SNPs.

So something different in the join code then in the subtract code.

From: Scooter Willis <hwillis@scripps.edu>
Date: Wednesday, October 31, 2012 5:42 PM
To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: Join version 1.0.0 error

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.

71: Join on data 38 and data 36
0 bytes
An error occurred running this job: /opt/sge/default/spool/execd/ip-10-191-53-90/job_scripts/14: line 13: 5517 Killed python /mnt/galaxyTools/galaxy-central/tools/new_operations/gops_join.py /mnt/galaxyData/files/000/dataset_75.dat /mnt/galaxyData/files/000/dataset_77.dat