[wgs-assembler-users] ovlstore our of memory

[Quan, X. <x....@im...>]

Hi

I am running my job to assembly Illumina and 454 reads. After running runCA 7.0 my job was killed in the ovlstore stage due to out of memory.
"/apps/wgs/7.0/wgs-7.0/Linux-amd64/bin/overlapStore  -c /ax3-savolainenlab/analysis/Plants/Genomics/Celera/fullrun1/Howea.ovlStore.BUILDING  -g /ax3-savolaine
nlab/analysis/Plants/Genomics/Celera/fullrun1/Howea.gkpStore  -i 0 -M 655360 -L /ax3-savolainenlab/analysis/Plants/Genomics/Celera/fullrun1/Howea.ovlStore.li
st  > /ax3-savolainenlab/analysis/Plants/Genomics/Celera/fullrun1/Howea.ovlStore.err 2>&1
=>> PBS: job killed: mem 1014599844kb exceeded limit 1006632960kb
"

Is it possible to set a memory limit which ovlstore will not exceed? "ovlStoreMemory" is currently set as 655360 and seems doesn't work.
And am I able to resume the job from the ovlstore stage rather than run from the beginning? It really took very long time to finish the overlapper stage.

Thanks very much!



Dr. Xueping Quan
Imperial College London