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=====Ray Assembler===== wget from ray site compiled normally See the [[http://denovoassembler.sourceforge.net/|ray wiki]] for further documentation and usage examples. ====Pog Assembly==== ===Assembly 1=== ===Assembly 2=== To generate a fresh machinefile, and execute ray over that machinefile parallelizing over nodes first and slots second: <code> /campus/BME235/bin/genMach >machinefile /campus/BME235/bin/mpirun -machinefile machinefile -x PATH=/campus/BME235/bin:$PATH -loadbalance --bynode -np 32 Ray \ -s /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff \ -s /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff \ -s /campusdata/BME235/data/Pog/sanger/PogSanger.fa \ -s /campusdata/BME235/data/Pog/sanger/sequences-3-19-2010.fa \ -s /campusdata/BME235/data/Pog/sanger/sequences-3-2-2010.fa \ -o slugRay2.fa </code> Resulting assembly: <code> 2508055 bases (0 N's 2508055 real 2508055 upper 0 lower) in 1392 sequences in 1 files Total size: mean 1801.8 sd 1627.0 min 124 (contig-480007) max 12656 (contig-1280008) media n 1347 N count: mean 0.0 sd 0.0 U count: mean 1801.8 sd 1627.0 L count: mean 0.0 sd 0.0 %0.00 masked total, %0.00 masked real </code> ====Slug Assembly==== ===Assembly 1=== On kolossus: <code> mpirun -np 25 -x LD_LIBRARY_PATH=/scratch/jstjohn/lib -machinefile machinefile /scratch/jstjohn/Ray-0.0.7/Ray -p /scratch/galt/bananaSlug/slug_1.fastq /scratch/galt/bananaSlug/slug_2.fastq -s /scratch/galt/bananaSlug/GCLL8Y406.fastq -s /scratch/galt/bananaSlug/GAZ7HUX02.fastq -s /scratch/galt/bananaSlug/GAZ7HUX03.fastq -s /scratch/galt/bananaSlug/GAZ7HUX04.fastq -a SLUG.amos -o slugRay1.fa ************************************************** This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions; see "gpl-3.0.txt" for details. ************************************************** Ray Copyright (C) 2010 Sébastien Boisvert, Jacques Corbeil, François Laviolette http://denovoassembler.sf.net/ AssemblyEngine: Ray 0.0.7 NumberOfRanks: 25 MPILibrary: Open-MPI 1.4.1 OperatingSystem: Linux LoadPairedEndReads Left sequences: /scratch/galt/bananaSlug/slug_1.fastq Right sequences: /scratch/galt/bananaSlug/slug_2.fastq Average length: auto Standard deviation: auto LoadSingleEndReads Sequences: /scratch/galt/bananaSlug/GCLL8Y406.fastq LoadSingleEndReads Sequences: /scratch/galt/bananaSlug/GAZ7HUX02.fastq LoadSingleEndReads Sequences: /scratch/galt/bananaSlug/GAZ7HUX03.fastq LoadSingleEndReads Sequences: /scratch/galt/bananaSlug/GAZ7HUX04.fastq Preparing AMOS file SLUG.amos Loading /scratch/galt/bananaSlug/slug_1.fastq </code>
