Re: [wgs-assembler-users] Time of running for overlap stage

[Walenz, B. <bw...@jc...>]

Hi-

Without details, I can’t really say what expected is.  It depends on genome properties (repeats, duplications), configuration (kmer size, threshold), read properties (number of reads, quality), and, of course, the amount of hardware you have.  I’d be unhappy with one week of wall clock too.

It is (sadly) easy to badly configure overlapper so that it runs forever.  Can you share your spec?  Hardware?  Are you willing to share details of genome and reads?

b


On 8/14/12 10:01 AM, "Quan, Xueping" <x....@im...> wrote:

Hi

I am running hybrid assembling using celera assembler version 7.0 for my genome (3.5gb) and wondering what's the normal expected time to finish. I started the assemle job one week ago and it is still on the overlap stage.

Thanks!

Xueping

Dr. Xueping Quan
Research Associate in BioInformatics
Imperial College London
Tel: +44(0)207 594 17 80
email:x....@im...
Personal:http://www3.imperial.ac.uk/people/x.quan
Group:  www3.imperial.ac.uk/savolainenlab <https://exchange.imperial.ac.uk/ecp/Customize/www3.imperial.ac.uk/savolainenlab>