On 04/09/13 02:32 AM, Hornung, Bastian wrote: > Thanks for the answer :). > > Why has the download then not been updated with the patch o_O?
Stable releases are thoroughly tested before being distributed. The next stable release (version 2.3.0) will include these and other improvements as well. > 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? You need to apply each patch one after the other. That should work. > > 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 > ------------------------------------------------------------------------------ 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
