On 05/12/11 12:37 AM, Zhengshuang Hua wrote: > Hi, > I'm doing assembly of a metagenome of a non reference organism. Our > dataset is about 250G. I'm so glad to find the software Ray which can > assemble in parallel. The version which I used is Ray_1.7. I run it on > a cluster with 18 nodes(216 cores in total) But when I execute the Ray > program. I find there is no output named contig.fasta when the job > finished. The command is : > mpirun -np 216 /parastor/users/shuws/software/ray_1.7/Ray -k 79 -p > /parastor/users/shuws/data/soil_metagenome/1107KHS-0021/Soil_DNA_1.fastq > /parastor/users/shuws/data/soil_metagenome/1107KHS-0021/Soil_DNA_2.fastq > -write-contig-paths -write-seeds -write-extensions -o Ray_assemble_v1_7_2 >
What is the peak coverage in CoverageDistributionAnalysis.txt ? The standard output presumably contains something like 'Assembly panic: no peak coverage observed, please lower the k-mer length'. We are presently working on méta-Ray -- modifications to enable Ray on massive metagenomics datasets. > All files i get is listed below: > CoverageDistributionAnalysis.txt > CoverageDistribution.txt > MessagePassingInterf > MessagePassingInterface.txt > MessagePassingInterfP > NetworkTest.txt > NumberOfSequences.txt > RayCommand.txt > RayVersion.txt > SequencePartition.txt > I don't know why it has such problem. See above. > I saw the standard error file with nothing in it. Also, standard > output file have no useful information about the job which I run. > Without any error information, I don't know what to do. So, can you > help me about the question or give me some advice? Try to lower the k-mer length (let's say 31). > Thanks very much! > > > Hua > Zhengshuang ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
