Hi: We're trying to assemble a genome with Ray. We have a couple of Illumina pair-end lines and a ocuple of Illumina mate-pairs. Ray seems to finish OK, but there's a lot of files missing in the output directory. I'm missing at least Scaffolds.fasta and OutputNumbers.txt. Am I doing something wrong? Here you have some information about the run.
Ray information: Ray version 2.1.0 License for Ray: GNU General Public License version 3 RayPlatform version: 1.1.0 License for RayPlatform: GNU Lesser General Public License version 3 MAXKMERLENGTH: 32 KMER_U64_ARRAY_SIZE: 1 Maximum coverage depth stored by CoverageDepth: 4294967295 MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes FORCE_PACKING = n ASSERT = n HAVE_LIBZ = n HAVE_LIBBZ2 = n CONFIG_PROFILER_COLLECT = n CONFIG_CLOCK_GETTIME = n __linux__ = y _MSC_VER = n __GNUC__ = y RAY_32_BITS = n RAY_64_BITS = y MPI standard version: MPI 2.1 MPI library: Open-MPI 1.6.1 Compiler: GNU gcc/g++ 4.3.4 [gcc-4_3-branch revision 152973] Ray command: mpiexec -n 100 Ray \ -k \ 39 \ -p \ /mnt/scratch/users/comav_gen_upv/jblanca/zucchini/reads/cleaned/mucu16.mp_3k.1.fastq \ /mnt/scratch/users/comav_gen_upv/jblanca/zucchini/reads/cleaned/mucu16.mp_3k.2.fastq \ -p \ /mnt/scratch/users/comav_gen_upv/jblanca/zucchini/reads/cleaned/mucu16.mp_7k.1.fastq \ /mnt/scratch/users/comav_gen_upv/jblanca/zucchini/reads/cleaned/mucu16.mp_7k.2.fastq \ -p \ /mnt/scratch/users/comav_gen_upv/jblanca/zucchini/reads/cleaned/mucu16.pe1.1.fastq \ /mnt/scratch/users/comav_gen_upv/jblanca/zucchini/reads/cleaned/mucu16.pe1.2.fastq \ -p \ /mnt/scratch/users/comav_gen_upv/jblanca/zucchini/reads/cleaned/mucu16.pe2.1.fastq \ /mnt/scratch/users/comav_gen_upv/jblanca/zucchini/reads/cleaned/mucu16.pe2.2.fastq \ -o \ /mnt/scratch/users/comav_gen_upv/jblanca/zucchini/assembly/ray39/ Rank 0 wrote /mnt/scratch/users/comav_gen_upv/jblanca/zucchini/assembly/ray39//RayCommand.txt k-mer length: 31 tail -n 5 of stdout: Rank 44: gathering scaffold links [53/1618] [1/17653] Rank 44: assembler memory usage: 1860568 KiB Rank 90: gathering scaffold links [13/1394] [16374/16374] (completed) Rank 90: assembler memory usage: 1876488 KiB Rank 44: gathering scaffold links [53/1618] [10001/17653] Rank 44: assembler memory usage: 1860568 KiB stderr is empty. ls of output dir: Contigs.fasta FilePartition.txt LibraryStatistics.txt RayCommand.txt CoverageDistributionAnalysis.txt Library0.txt NetworkTest.txt RayPlatform_Version.txt CoverageDistribution.txt Library1.txt NumberOfSequences.txt RayVersion.txt degreeDistribution.txt Library2.txt ParallelPaths.txt SeedLengthDistribution.txt ElapsedTime.txt Library3.txt Plugins SequencePartition.txt Let me know if you need any extra information. Best regards, -- Jose M. Blanca Postigo Instituto Universitario de Conservacion y Mejora de la Agrodiversidad Valenciana (COMAV) Universidad Politecnica de Valencia (UPV) Edificio CPI (Ciudad Politecnica de la Innovacion), 8E 46022 Valencia (SPAIN) Tlf.:+34-96-3877000 (ext 88473) ------------------------------------------------------------------------------ How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
