On 10/06/13 02:43 AM, Jose Blanca wrote: > > 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.
You probably exceeded the allocated time by the scheduler of the machine. > >> 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 > Maybe you need to throw more cores at this large number of reads. > 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, >>> >> >> > > ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
