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archive:bioinformatic_tools:ray [2010/05/20 21:11] jstjohn |
archive:bioinformatic_tools:ray [2015/07/28 06:26] ceisenhart ↷ Page moved from bioinformatic_tools:ray to archive:bioinformatic_tools:ray |
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===Assembly 1=== | ===Assembly 1=== | ||
===Assembly 2=== | ===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==== | ====Slug Assembly==== | ||
===Assembly 1=== | ===Assembly 1=== |