[mira_talk] Re: exiting mira without error message
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 15 May 2014 09:02:05 +0200
On 15 May 2014, at 2:55 , Chenling Antelope <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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