Hi Sébastien, the problem doesn't seem to be only the kmer values, because I've in the meantime successfully assembled some things with higher kmer-values (125 for most of the MiSeq data). I have the suspicion that this could be connected to the problem with the amount of cores, at which the assembly fails *dunno*.
Still, the version: ./Ray -version Ray version 2.3.0 License for Ray: GNU General Public License version 3 RayPlatform version: 2.0.0 License for RayPlatform: GNU Lesser General Public License version 3 MAXKMERLENGTH: 201 Maximum coverage depth stored by CoverageDepth: 4294967295 MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes FORCE_PACKING = n ASSERT = n HAVE_LIBZ = n HAVE_LIBBZ2 = n PROFILER_COLLECT = n MINIRANKS = y CLOCK_GETTIME = n __linux__ = y _MSC_VER = n __GNUC__ = y RAY_32_BITS = n RAY_64_BITS = y MPI standard version: MPI 2.1 MPI library: Open-MPI 1.4.3 Compiler: GNU gcc/g++ 4.6.3 MPI I/O: n ________________________________________ From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca] Sent: Monday, January 06, 2014 11:19 PM To: Hornung, Bastian Cc: denovoassembler-users@lists.sourceforge.net Subject: Re: [Denovoassembler-users] largest kmer-value? On 20/11/13 08:09 AM, Hornung, Bastian wrote: > hhmm...any other compilation flags used? > I've only changed the maximum kmer length, maybe something else is different? > Hi Bastian, I tried to reproduce the issue by building Ray with MAXKMERLENGTH=96 and I tried "-k 49" and "-k 51" on some MiSeq data (E. coli). I did not reproduce the issue. You said that compiled new versions with a way higher kmer-value (200, 500). Can you provide the output of "Ray -version" with the executable you are using ? > Bastian > ________________________________________ > From: Tan, Yifang [yifang....@nrc-cnrc.gc.ca] > Sent: Monday, November 18, 2013 4:00 PM > To: Sébastien Boisvert; Hornung, Bastian > Cc: denovoassembler-users@lists.sourceforge.net > Subject: RE: [Denovoassembler-users] largest kmer-value? > > 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. 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