From qconf the hard and soft vmem limits are set to 2G and also set to consumable.
How about trying changes as per Zayeds suggestion and request an increased memory limit limit in the qsub. I think you may need to do this for both the hard and soft limit as well "h_vmem=14g s_vmem=14g". You should set the limit at 2-3G higher than the index file size.
Could you try this with a 2 node MPI job. If it works for a 2 node job but fails when you request more nodes it is likely that SGE doesn't understand about shared memory, you might be able to correct for this by changing vmem to non-consumable in qconf.
There's also the possibility of running multi-threaded slaves so you use -c8 or similar on NovoalignMPI and then start just one 8 threaded job on each server. This requires the PE to be set up correctly. I haven't set up a PE like this but there are quite a few examples of this on the internet.