When I compiled MAXKMERLENGTH=256 was used. So far I've tried highest kmer=127 with Ray2.2.0 and 2.3.0. No problem was detected with kmer setting.
Yifang _________________________________________________ National Research Council Canada 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Conseil national de recherches Canada Institut de biotechnologie des plantes 110 place Gymnasium, Saskatoon (SK) S7N 0W9 Government of Canada | Gouvernement du Canada yifang....@nrc-cnrc.gc.ca; Tel/Tél: (306) 975-5279 | Fax/Télécopieur: (306) 975-4839 _________________________________________________ ________________________________________ From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca] Sent: Friday, November 15, 2013 12:00 PM To: Hornung, Bastian Cc: denovoassembler-users@lists.sourceforge.net Subject: Re: [Denovoassembler-users] largest kmer-value? On 15/11/13 05:37 AM, Hornung, Bastian wrote: > Hi @all, > > I wonder what's the highest kmer-value, which ray can utilize. > I know that by default it's 30something. > I've compiled now versions with a way higher kmer-value (200, 500), because I > have MiSeq data with a read length of 250. > But I somehow get crashes, if I get higher than a certain kmer-value. > I began testing with 99, which doesn't work, 55 doesn't work either, 44 works > (I know, should be uneven, was my mistake), so I'm curious what's the highest > value. > And should it not work with more? Why do I get a segmentation fault with > higher values? > I personnally used MAXKMERLENGTH=96 on some of our local MiSeq data (read length is 150 I think). And it worked as far as I remember. What message are you getting ? seb > Best regards, > > Bastian > > > ------------------------------------------------------------------------------ > DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps > OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access > Free app hosting. Or install the open source package on any LAMP server. > Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! > http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ------------------------------------------------------------------------------ DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
