Hi, you are using a k (39) bigger than the maximum k-mer length (32) but it is probably not the source of the problem. You can solve this by recompiling Ray using the MAXKMERLENGTH option. Your assembly is not finished yet and that's why some files are missing. Are you sure Ray is not still running? What are the last lines of the ElapsedTime.txt file? How many reads do you have?
Pier-Luc Plante Le 2013-06-06 02:52, Jose Blanca a écrit : > 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 Here is the max k-mer length: > 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 \ The k-mer length you have used > -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, > ------------------------------------------------------------------------------ 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
