src/hg/makeDb/doc/canFam2.txt 1.26
1.26 2010/01/25 19:16:11 hiram
panda aligned to dog,rat,mouse,human,opossum pig aligned to mouse,human,opossum,cow bosTau4 to rn4, rabbit to rat,mouse,opossum,guineaPig
Index: src/hg/makeDb/doc/canFam2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/canFam2.txt,v
retrieving revision 1.25
retrieving revision 1.26
diff -b -B -U 4 -r1.25 -r1.26
--- src/hg/makeDb/doc/canFam2.txt 20 Sep 2009 17:16:42 -0000 1.25
+++ src/hg/makeDb/doc/canFam2.txt 25 Jan 2010 19:16:11 -0000 1.26
@@ -2981,4 +2981,67 @@
svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2009-09-13
see doc/builds.txt for specific details.
############################################################################
+# ailMel1 Panda alignment (DONE - 2010-01-19 - Hiram)
+ mkdir /hive/data/genomes/canFam2/bed/lastzAilMel1.2010-01-19
+ cd /hive/data/genomes/canFam2/bed/lastzAilMel1.2010-01-19
+
+ cat << '_EOF_' > DEF
+# Dog vs. Panda
+# parameters from the Panda paper supplemental where they describe
+# their lastz parameters
+BLASTZ_K=2200
+BLASTZ_Y=3400
+BLASTZ_L=6000
+BLASTZ_H=2000
+BLASTZ_C=2
+BLASTZ_T=2
+
+# our usual M
+BLASTZ_M=50
+
+# TARGET: Dog canFam2
+SEQ1_DIR=/scratch/data/canFam2/nib
+SEQ1_LEN=/scratch/data/canFam2/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Horse
+SEQ2_DIR=/scratch/data/ailMel1/ailMel1.2bit
+SEQ2_LEN=/scratch/data/ailMel1/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LIMIT=50
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/canFam2/bed/lastzAilMel1.2010-01-19
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -workhorse=hgwdev -noLoadChainSplit -verbose=2 -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+ # interrupted by storm induced power failures, finish cat step,
+ # then continuing under tornado watch:
+ time doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -continue=chainRun -workhorse=hgwdev -noLoadChainSplit \
+ -smallClusterHub=pk -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > chain.log 2>&1 &
+ # real 102m27.429s
+ cat fb.canFam2.chainAilMel1Link.txt
+ # 1785774721 bases of 2384996543 (74.875%) in intersection
+
+ mkdir /hive/data/genomes/ailMel1/bed/blastz.canFam2.swap
+ cd /hive/data/genomes/ailMel1/bed/blastz.canFam2.swap
+ time doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/canFam2/bed/lastzAilMel1.2010-01-19/DEF \
+ -swap -noLoadChainSplit -workhorse=hgwdev -bigClusterHub=pk \
+ -smallClusterHub=pk -chainMinScore=3000 -chainLinearGap=medium \
+ > swap.log 2>&1 &
+ # real 89m3.603s
+ cat fb.ailMel1.chainCanFam2Link.txt
+ # 1774362211 bases of 2225124764 (79.742%) in intersection
+
+############################################################################