[mira_talk] Re: Regarding Time-estimate of mira
- From: Ganga Jeena <ganga.jeena@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 6 Jan 2011 11:14:40 +0530
Happy New Year Michael,
For a genomic 454 data in accurate mode, My program din't proceed with the
contig formation since twwo days for million reads.
How should I go about it?
wd splitting the data further to lesser number of reads for assembly in mira
and then contigs into cap3 for further assembly a better idea ?
Regards,
Ganga Jeena
On Wed, Dec 22, 2010 at 1:49 AM, bio5yz <bio5yz@xxxxxxxxxxxxxx> wrote:
> Not sure if this is helpful, but I made a recent 3.5 million 454 assembly
> (~350 bp ave length) that took 10 days. This was a transcriptome assembly at
> accurate setting.
> Our system also has 512 GB memory, 4 hexacore processors (I believe).
> Number of processors doesn't seem to affect the assembly too much, as I
> believe it is only parrallelized during the skimming process. NFS is a bad
> idea; my first run stalled and had to be killed. Is your run log file 500
> GB or the log directory in the assembly folder?
>
> Michael
>
>
>
> On Tue, Dec 21, 2010 at 3:09 AM, Ganga Jeena <ganga.jeena@xxxxxxxxx>wrote:
>
>> I have to do this assembly for 8 million reads454 in master-node/home
>> within 230 GB space. How should I work it?
>> The log file generated is already 500 GB.
>> Is there some way | option to avoid log file generation and other
>> non-result files ?
>> Regards,
>> Ganga Jeena
>>
>>
>>
>> On Tue, Dec 21, 2010 at 10:22 AM, Ganga Jeena <ganga.jeena@xxxxxxxxx>wrote:
>>
>>
>>>
>>> ---------- Forwarded message ----------
>>> From: Bastien Chevreux <bach@xxxxxxxxxxxx>
>>> Date: Mon, Dec 20, 2010 at 11:54 PM
>>> Subject: [mira_talk] Re: Regarding Time-estimate of mira
>>> To: mira_talk@xxxxxxxxxxxxx
>>>
>>>
>>> On Montag 20 Dezember 2010 Ganga Jeena wrote:
>>> > I am trying to do assembly of 8 million reads with mira
>>> > Configuration of system is as follows:
>>> > 512 GB RAM
>>> > 8 hexa-core processors
>>> >
>>> > miramem gives me a memory estimate of 66.6 GB.
>>> > How to get the time-estimate for assembly of data on my system.
>>>
>>>
>>> It is impossible to estimate the time needed, there are too many
>>> sequencing
>>> project depending variables which make things absolutely unpredictable.
>>>
>>> Sorry, you'll have to try it out with your data.
>>>
>>> B.
>>>
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>>>
>>
>
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