[wgs-assembler-users] cgw running single core?

[mathog <ma...@ca...>]

Hi,

I have been running a bunch of MaSuRCA jobs, testing how well it does 
with different simulated library combinations on simulated homozygous 
and heterozgyous (4% difference) genomes using only Illumina data.  The 
homozygous ones finish in about 8 hours. The one heterozygous one to 
complete to date took 29 hours. Almost all of the extra time was spent 
with cgw running single threaded, or at least it hovers at just around 
100% CPU, which is pretty low on a 46 core machine.  So the issue seems 
to be in the (modified) wgs assembler, not in the steps that MaSuRCA 
runs before that.  An earlier experiment with real(ly bad) data saw cgw 
run for 29 _days_ before MaSuRCA crashed - almost all of that as cgw 
running on one core.

Is there a way to speed cgw up?  Some command line switch which has been 
omitted or set incorrectly? Here is the cgw command on the diploid test 
that is running now (which is currently showing 6 hours of cumulative 
CPU time, and has 8.4G resident):

/opt/MaSuRCA/CA/Linux-amd64/bin/cgw -j 1 -k 5 -r 5 -s 2 -z -P 2 -B 
167006 -m 100 -g 
/home/mathog/wgs_project/do_masurca_diploid/CA/genome.gkpStore -t 
/home/mathog/wgs_project/do_masurca_diploid/CA/genome.tigStore -o 
/home/mathog/wgs_project/do_masurca_diploid/CA/7-0-CGW/genome

The "diploid" genome in this experiment is C elegans, with one wild type 
copy and one mutated copy.

Thanks,

David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech