---------------------------------------- > From: plat...@sbcglobal.net > To: sebastien.boisver...@ulaval.ca > Date: Thu, 21 Aug 2014 10:47:37 -0400 > Subject: Re: [Denovoassembler-users] Ray assembler > > Hi Seb >
Hi Adrian, > I know you're no longer actively developing Ray, but as a long-time > enthusiast for Ray I'd be happy to buy you a beer (or two) I don't drink beer. > at the next conference we're both at if you'd be able to make the warning > about running Ray with a Kmer longer than the supported value in > the compilation more explicit (perhaps make it an assertion failure). > I really have concerns that people are missing this and running with much > lower Kmers than they think they are (it can happen in other assemblers too > of course, but most give a more > obvious warning). This change would go there: https://github.com/sebhtml/ray/blob/master/code/Mock/Parameters.cpp#L899 Sure, adding an assertion would violently kill the job. But it would be preferable to cleanly shutdown the ranks. > > All the best. > > Adrian > > Adrian Platts > McGill > > On Aug 21, 2014, at 10:11 AM, Sébastien Boisvert > <sebastien.boisver...@ulaval.ca> wrote: > >> You need to recompile Ray with MAXKMERLENGTH=something larger than 32. >> >> ---------------------------------------- >>> From: eforoo...@nigeb.ac.ir >>> To: sebastien.boisver...@ulaval.ca >>> Date: Thu, 21 Aug 2014 05:30:58 -0400 >>> Subject: Ray assembler >>> >>> >>> hello dear Sébastien, >>> I am a phd student and I'm trying to assemble a bacterial genome (illumina >>> reads) using Ray and soapdenovo. But I get a confusing result from Ray. I >>> mean I run Ray on my data with different k parameter(31 51 75) but the >>> result is almost identical! Is this OK with Ray? >>> Here is my command line >>> >>> mpiexec -n 10 Ray -p Serratia_marcescens_450_10_71.fq >>> Serratia_marcescens_450_10_72.fq -o Serratia_marcescens_450_10_7_k31 -k 31 >>> >>> thanks in advance and best regards >>> esmail foroozan >> >> ------------------------------------------------------------------------------ >> Slashdot TV. >> Video for Nerds. Stuff that matters. >> http://tv.slashdot.org/ >> _______________________________________________ >> Denovoassembler-users mailing list >> Denovoassembler-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce. Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
