src/hg/makeDb/doc/bosTau4.txt 1.22
1.22 2010/01/25 19:16:14 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/bosTau4.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/bosTau4.txt,v
retrieving revision 1.21
retrieving revision 1.22
diff -b -B -U 4 -r1.21 -r1.22
--- src/hg/makeDb/doc/bosTau4.txt 16 Dec 2009 23:43:36 -0000 1.21
+++ src/hg/makeDb/doc/bosTau4.txt 25 Jan 2010 19:16:14 -0000 1.22
@@ -1827,4 +1827,65 @@
pushd /usr/local/apache/htdocs/goldenPath/bosTau4/liftOver/
md5sum bosTau4ToBosTauMd3.over.chain.gz >> md5sum.txt
popd
+#########################################################################
+# susScr1 Pig BLASTZ/CHAIN/NET (WORKING - 2010-01-21 - Hiram)
+ screen # use a screen to manage this multi-day job
+ mkdir /hive/data/genomes/bosTau4/bed/lastzSusScr1.2010-01-21
+ cd /hive/data/genomes/bosTau4/bed/lastzSusScr1.2010-01-21
+
+ cat << '_EOF_' > DEF
+# Pig vs. Cow
+BLASTZ_M=50
+
+# TARGET: Cow BosTau4
+SEQ1_DIR=/scratch/data/bosTau4/bosTau4.2bit
+SEQ1_LEN=/scratch/data/bosTau4/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=100
+
+# QUERY: Pig SusScr1
+SEQ2_DIR=/scratch/data/susScr1/susScr1.2bit
+SEQ2_LEN=/scratch/data/susScr1/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/bosTau4/bed/lastzSusScr1.2010-01-21
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << this line keeps emacs coloring happy
+
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -noLoadChainSplit -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ -chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+ # real 3811m31.428s
+ # failed
+XXX - running Thu Jan 21 14:49:43 PST 2010
+
+ time nice -n +19 $HOME/kent/src/hg/utils/automation/doBlastzChainNet.pl \
+ `pwd`/DEF -verbose=2 \
+ -bigClusterHub=memk -chainMinScore=3000 -chainLinearGap=medium \
+ -syntenicNet > do.log 2>&1
+
+#########################################################################
+# lastz swap Rat Rn4 (DONE - 2010-01-22 - Hiram)
+ # original run
+ cd /cluster/data/rn4/bed/blastzBosTau4.2010-01-19
+ cat fb.rn4.chainBosTau4Link.txt
+ # 649931321 bases of 2571531505 (25.274%) in intersection
+
+ mkdir /cluster/data/bosTau4/bed/blastz.rn4.swap
+ cd /cluster/data/bosTau4/bed/blastz.rn4.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /cluster/data/rn4/bed/blastzBosTau4.2010-01-19/DEF \
+ -noLoadChainSplit -workhorse=hgwdev -smallClusterHub=memk \
+ -bigClusterHub=pk -chainMinScore=3000 -chainLinearGap=medium \
+ -swap -syntenicNet > swap.log 2>&1 &
+ # real 77m18.645s
+ cat fb.bosTau4.chainRn4Link.txt
+ # 664253901 bases of 2731830700 (24.315%) in intersection
+
+#########################################################################