[mira_talk] Re: mira_talk Digest V3 #54
- From: Stefano Ghignone <stefano.ghignone@xxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Mar 2010 10:23:15 +0100
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:
Total skims taken: 66287
Filtering forward skims.
Localtime: Mon Mar 15 10:14:50 2010
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
Done.
Done.
Filtering complement skims.
Localtime: Mon Mar 15 10:14:50 2010
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
Done.
Done all filtering.
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Pre-assembly alignment search for read extension and / or vector clipping:
Making alignments.
Ouch, out of memory detected.
========================== Memory self assessment
==============================
Running in 64 bit mode.
========================== Memory self assessment
==============================
Running in 64 bit mode.
stefano
On 03/14/2010 07:08 AM, FreeLists Mailing List Manager wrote:
Re: mira 3.0.1 crashes in mapping mode
--
Dr. Stefano Ghignone
Istituto per la Protezione delle Piante, Sez. Torino - CNR
c/o Dpt. Plant Biology, University of Turin
V.le P.A. Mattioli, 25
I-10125 Turin
Italy
Phone: +39 011 6502927 ext. 48
Fax: +39 011 6705962
e-mail: stefano.ghignone@xxxxxxxx
MSN: ste.ghi@xxxxxxxxxxx
http://www.bioveg.unito.it
http://www.sppadbase.com
http://www.dinamycode.it/
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