src/hg/makeDb/doc/canFam2.txt 1.28

Index: src/hg/makeDb/doc/canFam2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/canFam2.txt,v
retrieving revision 1.27
retrieving revision 1.28
diff -b -B -U 4 -r1.27 -r1.28
--- src/hg/makeDb/doc/canFam2.txt	12 Feb 2010 23:44:52 -0000	1.27
+++ src/hg/makeDb/doc/canFam2.txt	16 Feb 2010 04:47:43 -0000	1.28
@@ -3071,11 +3071,20 @@
 	-verbose=2 `pwd`/DEF \
 	-syntenicNet -chainMinScore=3000 -chainLinearGap=medium \
 	-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
 	> do.log 2>&1 &
-XXX - running Fri Feb 12 14:42:59 PST 2010
+    #	real    1988m5.805s
+    cat fb.canFam2.chainCalJac3Link.txt 
+    #	1363307334 bases of 2384996543 (57.162%) in intersection
 
-    time nice -n +19 doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
-	-stop=load -chainMinScore=3000 \
-	-chainLinearGap=medium -bigClusterHub=pk > do.log 2>&1 &
-    #	real    897m58.156s
-#########################################################################
+    mkdir /hive/data/genomes/calJac3/bed/blastz.canFam2.swap
+    cd /hive/data/genomes/calJac3/bed/blastz.canFam2.swap
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/canFam2/bed/lastzCalJac3.2010-02-12/DEF \
+	-swap -syntenicNet \
+	-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+	-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+    #	real    129m56.144s
+    cat fb.calJac3.chainHg19Link.txt 
+    #	1397333116 bases of 2752505800 (50.766%) in intersection
+
+#####################################################################