El 06/06/13 14:09, Pier-Luc Plante escribió: > 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.
I'll try with a shorter kmer. Recompiling is not trivial because I'm not the admin of the machine. > Are you sure Ray is not still running? Yes, it is not in the queue any more. > What are the last lines of the ElapsedTime.txt file? *** Step: Generation of contigs Date: Wed Jun 5 22:39:19 2013 Elapsed time: 16 seconds Since beginning: 1 days, 13 hours, 57 minutes, 28 seconds *** > How many reads do you have? NumberOfSequences: 48856732 NumberOfSequences: 48856732 NumberOfSequences: 21534182 NumberOfSequences: 21534182 NumberOfSequences: 203748499 NumberOfSequences: 203748499 NumberOfSequences: 165831130 NumberOfSequences: 165831130 Best regards, Jose Blanca > > 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, >> > > -- 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
