Hi Sébastien,
I currently don't have the information regarding the distribution of the
taxa in the pooled metagenome.
In case that the abundance doesn't follow some kind of a power law
distribution, would it
affect the duration or correctness of the assembly ?
Thanks,
Goor
2013/11/8 Sébastien Boisvert <[email protected]>
> On 08/11/13 03:40 AM, Goor Sasson wrote:
>
>> Hi Sebastien & Adrian,
>>
>> The Blacklight we consider to use is the one at Urbana Illinois
>> university.
>> (http://help.igb.illinois.edu/Biocluster#Cluster_Specifications).
>> A rough estimation for the the total genome size is at least 5000 genomes.
>> Hopes that these details can shed some light.
>>
>
> Do you expect some sort of power law distribution ?
>
>
> To summarize, you have one sample with 2.5 Gigabases of Illumina data
> (probably one lane or something like that).
> And that contains roughly 5000 bacterial genomes.
>
> Is that correct ?
>
>
> Also, the next version (2.3.1) will include a patch that will lower the
> memory usage.
> see https://github.com/sebhtml/ray/issues/210
>
>
>> Thanks,
>> Goor
>>
>>
>> 2013/11/6 Sébastien Boisvert <[email protected] <mailto:
>> [email protected]>>
>>
>>
>> On 06/11/13 09:49 AM, Goor Sasson wrote:
>>
>> Dear Mailing-List,
>>
>>
>> Hi,
>>
>>
>>
>> I've chosen to use Ray Meta in order to assemble reads from a
>> pooled metagenome that contains 2.5g of illumina (HiSeq2500) paired-end
>> reads
>> (read length 100bp, totalling ~250g bp).
>> I need an gross estimation for the predicted execution time. The
>> computational platform is a Blacklight platform with ~400 cores (Xeon
>> X7542) with 2TB RAM.
>>
>>
>> Is it this Blacklight: http://www.psc.edu/index.php/_
>> _computing-resources/blacklight <http://www.psc.edu/index.php/
>> computing-resources/blacklight> ?
>>
>>
>> What is the interconnect (the network) ?
>>
>>
>> Thanks
>>
>>
>> As Adrian Pelin pointed out, it depends a lot of the genomic content
>> of your metagenome.
>>
>> In our paper http://genomebiology.com/2012/__13/12/R122 <
>> http://genomebiology.com/2012/13/12/R122> , we used 128 machines each
>> with 8 cores
>>
>> (Xeon X5560). Each machine had 24 GiB of RAM memory, so that was
>> around 3 TiB of distributed memory.
>> It took ~15 hours to assemble metagenome containing 1000 bacterial
>> genomes (power law abundances)
>> + human contaminations. Note that this 15 hours included also the
>> taxonomic profiling and so on.
>> Doing only an assembly will be shorter in time.
>>
>> Obviously, a test that you can you before going for the whole thing
>> is:
>>
>>
>> mpiexec -n 400 Ray -test-network-only -o NetworkTest-1
>>
>>
>> Then, check the measured latency in NetworkTest-1/NetworkTest.txt
>>
>>
>>
>> ---Sébastien
>>
>>
>>
>
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