[mira_talk] Re: exiting mira without error message
- From: Chenling Antelope <chenlingantelope@xxxxxxxxx>
- To: mira_talk <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 15 May 2014 11:53:55 -0700
Hi Chris,
My genome is about 1.4 Mb, and I have 28245 reads with median length ~2000.
I am really inexperienced with pacbio, so could you clarify what you mean
by filter? (I am assembling a parasite genome from sequencing results from
whole organism by pulling out reads with homology with a closely related
genome and then extracting those reads.)
Best,
Chenling
2014-05-15 11:32 GMT-07:00 Chris Hoefler <hoeflerb@xxxxxxxxx>:
> 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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