On 05/09/13 07:53 AM, 陈嘉鹏 wrote: > Dear Boisvert: > > I found ray use same command for single genome assembly and metagenomics > assembly. But how does ray know the data is metagenomics or single genome > sample? >
Hello, Ray 2 (2.0.0, 2.1.0, 2.2.0) is an improvement over the older Ray 1 in the sense that the algorithms are generalized to work on both genomes and metagenomes. In our paper http://genomebiology.com/2012/13/12/R122 , we explained how we did it. You can read more about that in the Materials and methods. Ray Meta is really just a workflow for metagenome assembly provided by the Ray 2.x.y series. Also, Ray Communities allows you to profile gene ontologies and taxons in your sample. This is also part of Ray 2. > > 2013/9/5 陈嘉鹏 <[email protected] <mailto:[email protected]>> > > Our cluster administrator says: Seems it is caused by the library file > libdl.a. It should be fixed now. > This is the only thing I know. > > > 2013/9/4 Sébastien Boisvert <[email protected] > <mailto:[email protected]>> > > On 04/09/13 05:22 AM, 陈嘉鹏 wrote: > > Dear author: > > We have solved this problem, but still have other problems. > > But you don't need to think about my last email. > > Hello, > > Just out of curiosity, what was the problem during the compilation of > Ray > that produced " undefined reference to `__dlopen'" ? > > And how did you solve it ? > > > > > Thanks > > > > > > > > 2013/9/4 陈嘉鹏 <[email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>>> > > > > Dear Boisvert: > > > > Thanks very much for developing MPI meta assembler. Our > cluster has only this choice. I used below command to compile: > > make PREFIX=/disk/rdisk08/jiapchen/bin/Ray-v2.2.0/ray-build > > > > But I got error message below: > > > > > /share/apps/mvapich2-1.6/lib/libibverbs.a(src_libibverbs_la-init.o): In > function `load_driver': > > (.text+0xc7): warning: Using 'dlopen' in statically linked > applications requires at runtime the shared libraries from the glibc version > used for linking > > /share/apps/mvapich2-1.6/lib/libdl.a(dlopen.o): In function > `dlopen': > > (.text+0x5): undefined reference to `__dlopen' > > /share/apps/mvapich2-1.6/lib/libdl.a(dlclose.o): In function > `dlclose': > > (.text+0x1): undefined reference to `__dlclose' > > /share/apps/mvapich2-1.6/lib/libdl.a(dlsym.o): In function > `dlsym': > > (.text+0x5): undefined reference to `__dlsym' > > /share/apps/mvapich2-1.6/lib/libdl.a(dlerror.o): In function > `dlerror': > > (.text+0x1): undefined reference to `__dlerror' > > collect2: ld returned 1 exit status > > make: *** [Ray] Error 1 > > > > I know the reason may be in our cluster, but I don't have hint > after some google search. So could you please give me any ideas? > > > > Thank you very much, > > Jiapeng > > RA in City University of Hong Kong > > > > > > > > > > -- > > Jiapeng Chen, Research Assistant > > # School of Energy and Environment > > # City University of Hong Kong > > Shatin, N.T. HK China > > Cell phone: +852-4789219 > > > > > -- > Jiapeng Chen, Research Assistant > # School of Energy and Environment > # City University of Hong Kong > Shatin, N.T. HK China > Cell phone: +852-4789219 > > > > > -- > Jiapeng Chen, Research Assistant > # School of Energy and Environment > # City University of Hong Kong > Shatin, N.T. HK China > Cell phone: +852-4789219 ------------------------------------------------------------------------------ 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=58041391&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
