On 21/10/13 02:34 PM, Gomez, Andres M wrote: > Dear All > > After using meta-velvet unsuccessfully in my sequences I decided to give Ray > a try. Main problem with meta-velvet was that it was not detecting any peaks > in many of my samples. Now running Ray, I have this warning message : > "you should increase the number of Ranks because the number of reads per > rank is high" > Is this referring to my kmer length? I set it up to 75 (my illumina pair end > reads are 150 bp).
Ray is a distributed software that runs better on many cores, and possibly many machines. > The code I ran was: > $ mpiexec Ray –k 75 –i G_shuffled.fastq –search > ftp://ftp.ncbi.nlm.nih.gov/genomes/HUMAN_MICROBIOM/Bacteria/ -o Ray_test The number of ranks with this command is 1 (the default). Assuming you are using a machine with many cores or a cluster, you can set the number of ranks with "-n 32" where 32 is the number of ranks desired. mpiexec -n 32 Ray -k 75 -i G_shuffled.fastq -search ftp://ftp.ncbi.nlm.nih.gov/genomes/HUMAN_MICROBIOM/Bacteria/ -o Ray_test The -search option requires a directory. I suppose that in your case "ftp://ftp.ncbi.nlm.nih.gov/genomes/HUMAN_MICROBIOM/Bacteria"; is an address and not a directory. Therefore, Ray will just skip this as it is invalid. > Thanks in advance for any clues. I am really new in metagenomic analysis. > > Andres > > > ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
