Hello,
This is very nice !
Which MPI library did you use ? (Open-MPI, MPICH2, or MVAMPICH2 or other)
I am glad to see that the virtual router in RayPlatform is utilized !
Mates should help in the graph traversal too, not just in the scaffolding.
Sébastien
On 05/10/12 12:02 AM, Louis Letourneau wrote:
> The question of how long does it take to assemble X specie comes up often.
> I thought I would share my experience and some results.
>
> A ~2.7G genome.
> 4 different librairies of the same individual
> 1 lane of hiseq each (lots of molecule diversity)
>
> I have mates but didn't put them in, will scaffold with something else.
> Although I will rerun with the mates to see how Ray fairs latter.
>
> 2025 cores (distributed mpi), on 85 nodes
> cput=1044:55:24,walltime=43:53:52
>
> Ray settings:
> -read-write-checkpoints ${RAY_WORK_DIR}/checkpoints \
> -show-memory-usage \
> -route-messages \
> -connection-type polytope \
> -routing-graph-degree 88 \
>
> Output :
> Contigs >= 100 nt
> Number: 3287924
> Total length: 2959541162
> Average: 900
> N50: 8158
> Median: 119
> Largest: 175227
> Contigs >= 500 nt
> Number: 588712
> Total length: 2588045901
> Average: 4396
> N50: 9851
> Median: 1860
> Largest: 175227
> Scaffolds >= 100 nt
> Number: 3256053
> Total length: 2964597718
> Average: 910
> N50: 8758
> Median: 119
> Largest: 175227
> Scaffolds >= 500 nt
> Number: 559885
> Total length: 2594461126
> Average: 4633
> N50: 10569
> Median: 1931
> Largest: 175227
>
> I'm very happy with the result!
>
> Louis
>
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