src/hg/makeDb/doc/danRer6.txt 1.8

Index: src/hg/makeDb/doc/danRer6.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/danRer6.txt,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 4 -r1.7 -r1.8
--- src/hg/makeDb/doc/danRer6.txt	6 Aug 2009 22:13:19 -0000	1.7
+++ src/hg/makeDb/doc/danRer6.txt	18 Sep 2009 22:15:32 -0000	1.8
@@ -824,6 +824,25 @@
     ln -s /hive/data/genomes/danRer6/danRer6.2bit /usr/local/apache/htdocs/goldenPath/danRer6/bigZips/
     vi README
     md5sum danRer6.2bit >> /usr/local/apache/htdocs/goldenPath/danRer6/bigZips/md5sum.txt
 
+#######################################################################
+# LASTZ/CHAIN/NET swap tetNig2 (DONE - 2009-09-15,18 - Hiram)
+    # original alignment to tetNig2
+    cd /hive/data/genomes/tetNig2/bed/lastzDanRer6.2009-09-15
+    cat fb.tetNig2.chainDanRer6Link.txt 
+    #	70626082 bases of 302314788 (23.362%) in intersection
 
+    #	and the swap to here, danRer6:
+    mkdir /hive/data/genomes/danRer6/bed/blastz.tetNig2.swap
+    cd /hive/data/genomes/danRer6/bed/blastz.tetNig2.swap
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/tetNig2/bed/lastzDanRer6.2009-09-15/DEF \
+	-swap -tRepeats=windowmaskerSdust \
+	-noLoadChainSplit -chainMinScore=2000 -chainLinearGap=medium \
+	-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+	> swap.log 2>&1 &
+    #	real    26m40.310s
+    cat fb.danRer6.chainTetNig2Link.txt 
+    #	93349443 bases of 1506896106 (6.195%) in intersection
 
+#######################################################################