[mira_talk] Re: megahubs ?

Hello,

And mira indeed thought that the memory requirements would explode, it
stopped.
"Loading skim hits from disk (will need approximately 156.0 GiB RAM)
...Ouch, out of memory detected."

Is there a setting I can use, so I can assemble this thing ?

With kind regards,
Jan


On Sat, Feb 28, 2009 at 22:20, Jan van Haarst <jan@xxxxxxxxxxxxx> wrote:

> Hello Bastien,
>
> I just started the assembly with "-SKIM:max_megahub_ratio=1" , and I'll
> track the memory usage.
> I'll let you know how it goes.
>
> Right now we aren't sure of the size of this genome, Newbler and Celera
> Assembler come to differing sizes, that's why I'm trying Mira to give me the
> definitive answer :-)
>
> Dag,
> Jan
>
> On Sat, Feb 28, 2009 at 21:59, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>
>> On Saturday 28 February 2009 Jan van Haarst wrote:
>> > What should I do to get the assembly to finish ?
>> > 0.5 % of bad reads doesn't sound that bad, does it ?
>>
>> Hello Jan,
>>
>> no, it doesn't. I suppose that the megahubs detected come more from the
>> fact
>> you have an eukaryote than from remaining vector adaptor sequences.
>>
>> Set the allowed megahub ratio to 1.0, that should allow you to continue.
>>
>> If I did my math right, you seem to have something like a 40 to 45 MB
>> organism
>> ... or 70 to 80MB if the main bulk of your reads is Titanium instead of
>> FLX.
>> Please note that I had mixed feedback from users regarding eukaryotes of
>> this
>> size, seems like MIRA sometimes explodes in memory consumption for these
>> (I'm
>> working on it).
>>
>> Regards,
>>  Bastien
>>
>>
>> --
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>
>
>
> --
> Dag,
> Jan
>



-- 
Dag,
Jan

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