[mira_talk] Re: Mira-2.9.46

Hello everyone,

same thing happened here.
Machine:

Dell Precision T3400
CPU Q9550 @2830 Mhz
Memory 8GB RAM
OS Ubuntu Jaunty
Kernel 2.6.28-13-generic, GCC version 4.3.3

Test data set were 581082 454 Titanium reads (EST)
mira --project=Atta --job=denovo,est,normal,454 -SK:mnr=on -SK:not=1 454_SETTINGS -LR:mxti=no -CL:qc=no
Same command passed without problems with mira 2.9.43. Idiot that I am I started a new assembly with memory-use limiting options without saving the logfile. 

Hope this help a bit,
Ewald


I have tested Mira-2.9.46 on this machine:

- Dell PowerEdge 2600
- CPU: 2x Intel Xeon @ 3200Mhz
- Memory: 4GB RAM
- OS: Linux Debian / Debian release 4.1.2-25
- Kernel: 2.6.26-2-686
- gcc version 4.1.3


test use a set of data(435000 454-Titanium reads)
the command use is:
mira -project=test -job=denovo,est,normal,454 -SK:mnr=yes -SK:nrr=4 -GE:not=2 -CO:asir=yes -CO:mr 454_SETTINGS -AL:mrs=80:egp=yes:egpl=reject_codongaps:megpp=100 -LR:mxti=no -CO:rodirs=10 -AL:mo=60 -CL:cpat=yes 

i have a core dumped:


--------------------------------------------------------------------------------

Information on current assembly object:

AS_readpool: 434802 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 1644694204 (1.5 GiB)

Memory used in assembly structures:
Eff. Size Free cap. LostByAlign AS_writtenskimhitsperid: 434802 2 MiB 0 B 0 B AS_skim_edges: 0 12 B 0 B 0 B AS_adsfacts: 0 49 MiB 49 MiB 0 B AS_confirmed_edges: 0 98 MiB 98 MiB 0 B AS_permanent_overlap_bans: 434802 10 MiB 0 B 0 B AS_readhitmiss: 0 12 B 0 B 0 B AS_readhmcovered: 0 12 B 0 B 0 B AS_count_rhm: 0 12 B 0 B 0 B AS_weakestOvercallDelVote: 0 12 B 0 B 0 B AS_weakestOvercallCoverage: 0 12 B 0 B 0 B AS_clipleft: 434802 2 MiB 0 B 0 B AS_clipright: 434802 2 MiB 0 B 0 B AS_used_ids: 0 425 KiB 425 KiB 2 B AS_multicopies: 434802 425 KiB 0 B 2 B AS_hasmcoverlaps: 434802 425 KiB 0 B 2 B AS_maxcoveragereached: 434802 2 MiB 0 B 0 B AS_coverageperseqtype: 0 12 B 0 B 0 B AS_istroublemaker: 434802 425 KiB 0 B 2 B AS_isdebris: 434802 425 KiB 0 B 2 B AS_needalloverlaps: 434802 425 KiB 14 B 0 B AS_readsforrepeatresolve: 0 20 B 0 B 0 B AS_allrmbsok: 0 12 B 0 B 0 B AS_probablermbsnotok: 0 12 B 0 B 0 B AS_weakrmbsnotok: 0 12 B 0 B 0 B AS_readmaytakeskim: 0 20 B 0 B 0 B AS_numskimoverlaps: 0 12 B 0 B 0 B AS_numleftextendskims: 0 12 B 0 B 0 B AS_rightextendskims: 0 12 B 0 B 0 B AS_skimleftextendratio: 0 12 B 0 B 0 B AS_skimrightextendratio: 0 12 B 0 B 0 B 
Total: 1818950584 (1.7 GiB)

================================================================================
Out of memory detected, exception message is: std::bad_alloc


If you have questions on why this happened, please send the last 1000
lines of the output log to the author (together with a short summary of your 
assembly project.

Abort (core dumped)


Laurent --






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