[mira_talk] Re: exiting mira without error message
- From: Chris Hoefler <hoeflerb@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 15 May 2014 13:32:37 -0500
Just FYI, you will need a lot more than 16 Gb to error-correct and assemble
your reads. If you can get access to a high memory machine (or a cluster)
that would be best. What is your expected genome size? What is your
post-filter median read length and yield?
Best,
Chris
On Thu, May 15, 2014 at 11:04 AM, Chenling Antelope <
chenlingantelope@xxxxxxxxx> wrote:
> THANKS Bastien and Andrej :)
>
>
> 2014-05-15 0:26 GMT-07:00 Andrej Benjak <abenjak@xxxxxxxxx>:
>
> Hi Chenling,
>>
>> For correcting PacBio reads and/or de novo assemblies you can use the
>> SMRT portal. As an alternative to the PIA local installation, you can
>> download the PacBio virtual machine with the SMRT portal installed and
>> configured (not the latest version, but almost):
>>
>> https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/SMRT-Analysis-Virtual-Machine-Install
>>
>>
>> Cheers,
>> Andrej
>>
>>
>>
>> On 05/15/2014 09:02 AM, Bastien Chevreux wrote:
>>
>> On 15 May 2014, at 2:55 , Chenling Antelope <chenlingantelope@xxxxxxxxx>
>> <chenlingantelope@xxxxxxxxx> wrote:
>>
>> Thanks Bastien for the answer!
>> However I am currently unable to correct my reads because I lack the glib
>> version required by celera.
>>
>> Then you should get that from somewhere :-)
>>
>>
>> Also, I used miramem to estimate the RAM required, which is a lot smaller
>> than my actual RAM 16G
>>
>> miramem does not know about PacBio reads yet, especially not about the
>> worst memory eater for that scenario: the Smith-Waterman overlapper.
>>
>>
>> Is there something else I can do to trouble shoot?
>>
>> You could try to remove all reads >= 10kb (or 9kb, 8kb, etc.) to save
>> memory at the overlap stage.
>>
>> But again: it makes absolutely no sense to currently use MIRA with
>> non-corrected PacBio reads. These simply contain too much crap which MIRA is
>> not prepared for. You will get “something” as result, but it will be total
>> nonsense.
>>
>> B.
>>
>>
>>
>>
>>
>>
>
--
Chris Hoefler, PhD
Postdoctoral Research Associate
Straight Lab
Texas A&M University
2128 TAMU
College Station, TX 77843-2128
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