[mira_talk] Re: Mira-2.9.46

Bastien Chevreux a écrit :

I have tested Mira-2.9.46 on this machine:


So you could get it compiled?


[...]
i have a core dumped:
[...]
Out of memory detected, exception message is: std::bad_alloc


You had me sweating for a minute: that's not a core dump, bud a perfectly 
controlled abortion of the program once the OS had no more spare memory.

Core dumps are different beasts: they're showed 'as such' on the command line 
and are due to (severe) bugs in the code.


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 ofyour
assembly project.


Actually I was not joking when I wrote "the last 1000 lines": the lines you 
sent just give me a status on the memory usage but I have no clue where that happened and 
what could be the reason. Please resend the log (the complete one is even better).

Regards,
  Bastien




i have re-run my analysis with this command:
bin/mira -project=ESTUR -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 

and now it works fine.
elapsed time: 14 hours.
In the result i obtain 44817 contigs and 164208 singulets whereas with Mira-2.9.43 i was obtained 52254 contigs and 145984 singulets using the same command. 
I send you here the last 1000 lioens of the log file.
i think version 2.9.46 use more memory than 2.9.43 and if others people work at the same time, the program crash and generate a dumped core. 

Laurent --

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