[mira_talk] Re: Lots of contigs, then segmentation fault
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 4 Jun 2011 17:33:50 +0200
On Thursday 02 June 2011 17:37:17 Egon Ozer wrote:
> [...]
> There are a few minor differences after the skim:
> [...]
> There's further divergence in the output after this:
> [...]
> There are some more differences in the block loading outputs after that, a
> lot of which I'm assuming is due to mira not being able to use memory
> management on OSX.
> [...]
> After that both log files go through "Filtering forward skims" and
> "Filtering complement skims." After the next step, "Aligning possible
> forward matches," there are really divergent "Alignment stats":
> [...]
> Does any of this help you to figure out why OSX is going off the rails?
> Any thoughts would be appreciated. Thanks.
Hi Egon,
you're on the right track regarding this: what you did was exactly what I
planned to do, albeit a bit differently. I have two hypotheses atm, one being
the memory management, the other differences in file handling.
Please fetch
http://www.chevreux.org/tmp/mira_3.2.1.17ood_dev_linux-gnu_x86_64_static.tar.bz2
and
http://www.chevreux.org/tmp/mira_3.2.1.17ood_dev_darwin10.7.0_x86_64_static.tar.bz2
and run it on both your Linux server and on your Mac. Don't panic: this version
cannot be used for assembly per se and will abort all by itself after the
first SKIM, it won't even assemble contigs, so it should be through quickly.
Important: please use the same command line for both machines *AND* be sure to
include
-GE:not=1
somewhere after the "--job=" definition. This will make MIRA use just one
processor and have (hopefully) exactly the same output. Shouldn't take too long
I suppose.
Also, please redirect the output of MIRA to a file (e.g.
"log_assembly_linux.txt" respectively "log_assembly_mac.txt").
After the the runs:
- I'd like to have both "log_assembly*" files
- please do a "ls -lR" for both the Linux and the Mac run and also send me that
output.
(via mail pleaee, no need to clog the mailing list)
B.
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