archive:bioinformatic_tools:ray
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archive:bioinformatic_tools:ray [2010/05/20 21:11] jstjohn |
archive:bioinformatic_tools:ray [2010/05/20 21:17] jstjohn |
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| ===Assembly 1=== | ===Assembly 1=== | ||
| ===Assembly 2=== | ===Assembly 2=== | ||
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| + | 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==== | ====Slug Assembly==== | ||
| ===Assembly 1=== | ===Assembly 1=== | ||
archive/bioinformatic_tools/ray.txt · Last modified: 2015/07/28 06:26 by ceisenhart
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