[mira_talk] Re: exiting mira without error message

  • From: Andrej Benjak <abenjak@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 15 May 2014 09:26:31 +0200

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> 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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