Re: [Denovoassembler-users] error in running Ray with communities...need help

Hello, The command was mpiexec --hostfile /home/openmpi-1.6.5/hosts.txt Ray -s navy/_Meta_Small.fastq -o /home/rayOutputMPI_again/ -search scripts/NCBI-Taxonomy/NCBI-taxonomy/NCBI-Finished-Bacterial-Genomes/ -with-taxonomy scripts/NCBI-Taxonomy/NCBI-taxonomy/Genome-to-Taxon.tsv scripts/NC

Re: [Denovoassembler-users] error in running Ray with communities...need help

On 07/11/13 11:18 AM, Tyx, Robert (CDC/ONDIEH/NCEH) wrote: > Hello > > I’m new to Ray, and was hoping someone can help me with this error. We can > get Ray to produce contigs and scaffolds and that worked fine. Then we > installed the optional stuff for Ray Communities to work, but it is giving

Re: [Denovoassembler-users] GeneOntology search mode

On 08/11/13 01:31 PM, JC Grenier wrote: > Yes, I have those programs. I'll erase everything and redo it completely. How > much time is it suppose to take? I would say around 1 hour including downloads. > > > 2013/11/8 Sébastien Boisvert > > > On 08/11/

Re: [Denovoassembler-users] maximum read length for ray

On 08/11/13 11:54 AM, Rob Egan wrote: > Hi Sébastien, > Correct, the contigs are not paired, but the error occurred after the 'Step' > summary for Estimation of outer distances for paired reads. I'm not sure > what step it was trying to perform when the Bus error happens. > I think this is simi

Re: [Denovoassembler-users] GeneOntology search mode

Yes, I have those programs. I'll erase everything and redo it completely. How much time is it suppose to take? 2013/11/8 Sébastien Boisvert > On 08/11/13 11:41 AM, JC Grenier wrote: > >> Hi there, >> >> > Hi, > > > I got a couple of question for you today. If I want to get the >> information a

Re: [Denovoassembler-users] GeneOntology search mode

On 08/11/13 11:41 AM, JC Grenier wrote: > Hi there, > Hi, > I got a couple of question for you today. If I want to get the information > about the Biological Abundance and the GeneOntology Terms in the same > analysis, how should I proceed? If I'm putting two search terms in the > command line

Re: [Denovoassembler-users] CoverageDistribution Analysis

On 07/11/13 05:03 AM, Habib Rijzaani wrote: > Hi Seb, (Please use the mailing list, to subscribe: https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ) > > I just used Ray for my small dataset with relatively high coverage reads. I > just wondering if the Coverage distribution an

Re: [Denovoassembler-users] Execution Time Estimation

On 08/11/13 03:40 AM, Goor Sasson wrote: > Hi Sebastien & Adrian, > > The Blacklight we consider to use is the one at Urbana Illinois university. > (http://help.igb.illinois.edu/Biocluster#Cluster_Specifications). > A rough estimation for the the total genome size is at least 5000 genomes. > Hope

[Denovoassembler-users] GeneOntology search mode

Hi there, I got a couple of question for you today. If I want to get the information about the Biological Abundance and the GeneOntology Terms in the same analysis, how should I proceed? If I'm putting two search terms in the command line, would it be alright and detect automatically where to look

Re: [Denovoassembler-users] Memory Limitations in RAY

On 07/11/13 08:27 PM, Munish Mehta wrote: > Hi Seb, (Please use the mailing list, to subscribe: https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ) > > I am using RAY to do a denovo assembly of Cane Toad (Bufo Marinus). > We are using IBM Blue Gene/Q system. (65,536 PowerPC base

Re: [Denovoassembler-users] Execution Time Estimation

Hi Sebastien & Adrian, The Blacklight we consider to use is the one at Urbana Illinois university. (http://help.igb.illinois.edu/Biocluster#Cluster_Specifications). A rough estimation for the the total genome size is at least 5000 genomes. Hopes that these details can shed some light. Thanks, Go