[mira_talk] denovo assembly runs out of memory
- From: "Andreas Petzold" <andpet@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 12 Jun 2009 16:53:37 +0200
Hi Bastien,
currently we are trying to assemble the genome of a pathogenic plant
fungus (est. genome size 50 Mbp) and despite 64 GB RAM available mira
(version 2.9.43-45) still runs out of memory.
Our input consists of ~ 2,7 mio 454 titanium reads and 7900 paired
fosmidends generated by Sanger technology. Mira crashes already during
pass 1 (when writing the repeat_resolve files).
Our parameters:
-job=denovo,genome,accurate,454,sanger
-GE:pro=Rhsecalis
-SK:not=4:bph=16:hss=8:mhpr=100:pr=80
-AL:mrs=80:ms=50:mo=80
-CO:np=Rhsecalis
-ED:ace=1
-LR:fo=0
SANGER_SETTINGS
-LR:mxti=0
-GE:uti=1:tismin=27000:tismax=45000
To us it seems that the crash happens at the graph phase so maybe we have
to much spurious overlaps. Could they somehow be reduced ? Should we
adjust the parameters ?
Furthermore we have access to a 64bit Itanium cluster with 146 GB RAM (os:
linux). Is there a possibility to provide a fitting binary so that we can
use mira on this cluster ?
Thanks and best regards,
Andreas
--
Andreas Petzold
Genome Analysis
Fritz Lipmann Institute
Beutenbergstrasse 11, D-07745 Jena
voice : ++49-3641-656038
fax : ++49-3641-656038
email : andpet@xxxxxxxxxxxxxx
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