Thanks for the answer :). Why has the download then not been updated with the patch o_O? Will applying this patch invalidate the other patch for the PacBio data, which I've applied, or is that one also included in the mentioned link?
Bastian ________________________________________ From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca] Sent: Tuesday, September 03, 2013 4:33 PM To: denovoassembler-users@lists.sourceforge.net Subject: Re: [Denovoassembler-users] Critical exception: The system is out of memory, returned NULL. Requested -168128560 bytes of type RAY_MALLOC_TYPE_BLOOM_FILTER On 02/09/13 03:57 AM, Hornung, Bastian wrote: > Hi @ all, > > guess I have again a sort of technical problem. > I get the error message in the subject line when I try to run my current > assembly (after roughly 10 minutes). > I've first run an assembly with ray, with 3 datasets and a kmer size of 33. > Now, I'm again doing the same, but I load additionally a set of PCR fragments > via -s in the assembly (30 fragments, shortest 112 bp, longest ~1.6 kb), and > the assembly begins to crash. > Same happens when I try to load some FLX data into it (obviously more data), > but that one works on smaller kmer size (only tested with 21, currently it's > running with 27). > The machine, on which the assembly is running, has in total 256 GB RAM, and > currently there's more than 200 of it free, and there's also more than enough > hard disk space (80 GB in the home partition, 800 in the working partition), > so I can't see why it should fail at allocating memory :/. > Any idea what could be going on? > Hello, This is a known bug in Ray 2.2.0. The problem was fixed 5 months ago: https://github.com/sebhtml/ray/commit/3bf06597ed21c6d72cf172884aa1708f37828347 You can apply this patch on Ray 2.2.0 with these commands: $ wget http://sourceforge.net/projects/denovoassembler/files/Ray-v2.2.0.tar.bz2 $ tar -xjf Ray-v2.2.0.tar.bz2 $ cd Ray-v2.2.0/ $ wget https://github.com/sebhtml/ray/commit/3bf06597ed21c6d72cf172884aa1708f37828347.patch $ patch -p1 < 3bf06597ed21c6d72cf172884aa1708f37828347.patch # apply other patches, if any After that, you can build Ray as usual. Sébastien > Best regards, > > Bastian > > > ------------------------------------------------------------------------------ > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! > Discover the easy way to master current and previous Microsoft technologies > and advance your career. Get an incredible 1,500+ hours of step-by-step > tutorial videos with LearnDevNow. Subscribe today and save! > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ------------------------------------------------------------------------------ Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
