[khmer] speed up partitioning?

C. Titus Brown ctb at msu.edu
Tue Feb 18 20:16:51 PST 2014


great idea!

On Wed, Feb 19, 2014 at 03:15:49PM +1100, Torsten Seemann wrote:
> Cedar
> 
> 
> > > My problem is that it's been running for about a month now, using 90% of
> > memory, and 4600% cpu. In other words, it appears to be using available
> > resources. If I read the output (pasted below) correctly, I can expect to
> > see 6566 partitions. After a month, it is working on partition 2178, so I'm
> > only 1/3 of the way through.
> >
> 
> My suggestion is to run "sga preqc" on the reads to get an idea if there is
> anything unusual about your data set:
> 
> https://groups.google.com/forum/#!msg/sga-users/95dTwpJCARU/oKoq54EZqKwJ
> 
> Torsten
> 
> 
> > The computer I'm using has 48 cores (AMD 6176 2.3Ghz) and 256GB ram.
> >
> 
> PS. We have similar: 64 cores (AMD 6272 2.1 Ghz) and 512GB RAM :-)
> 
> -- 
> 
> *--Dr Torsten Seemann--Victorian Bioinformatics Consortium, Monash
> University, AUSTRALIA*
> 
> *--Life Sciences Computation Centre, VLSCI, Parkville, AUSTRALIA
> --http://www.bioinformatics.net.au/ <http://www.bioinformatics.net.au/>*

-- 
C. Titus Brown, ctb at msu.edu




More information about the khmer mailing list