(Please use the list) On 21/10/13 02:53 PM, Gomez, Andres M wrote: > Thanks much for your response. > > 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. > > Does this mean I have to download every fasta file present in each > bacterial genome? >
You can fetch all of them with one single command using something like wget -r ftp://ftp.ncbi.nlm.nih.gov/genomes/HUMAN_MICROBIOM/Bacteria -r stands for "recursive" > > > > Andres Gomez > Institute for Genomic Biology > Animal Science Department > University of Illinois at Urbana-Champaign > e-mail: amgo...@illinois.edu > Office +1 217 298 6014 > Cell +1217 418 0438 > > > > > > > On 10/21/13 1:44 PM, "Sébastien Boisvert" <sebastien.boisver...@ulaval.ca> > wrote: > >> 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
