[mira_talk] Re: exiting mira without error message
- From: Chenling Antelope <chenlingantelope@xxxxxxxxx>
- To: mira_talk <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 15 May 2014 09:04:50 -0700
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.
>
>
>
>
>
>
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