[mira_talk] Re: mira_talk Digest V3 #54
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Mar 2010 21:35:06 +0100
On Montag 15 März 2010 Stefano Ghignone wrote:
> Bastien,
> mira version 3.0.3 doesn't give the reported error, even if it goes out
> of memory (as well as v. 3.0.0) on the same dataset used (mapping mode)
>
> These are the parameters used:
> >mira -project=CaGg -job=mapping,genome,normal,sanger,454
> -highlyrepetitive -GE:not=3 -LR:mxti=yes -AS:urd=no:sd=yes
> -SB:lb=yes:bft=fasta -SK:not=3:mnr=yes:nrr=7:mhpr=500:mmhr=1 -OUT:ora=yes
>
> and these are the last lines of the log file:
> [...]
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): std::bad_alloc
> Ouch, out of memory detected.
The other log you sent me tells me your machine has 4 GiB RAM. The command
line you took sets a few options which might be pretty memory hungry. Try your
original command, adding these settings:
-DP:ure=no
SANGER_SETTINGS -CL:pvlc=no
454_SETTINGS -CL:pvlc=no
Which reminds me that I should configure MIRA not to use pvlc when pec is on.
Regards,
Bastien
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
