Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.96
retrieving revision 1.97
diff -b -B -U 4 -r1.96 -r1.97
--- src/hg/makeDb/doc/hg19.txt	7 Apr 2010 17:42:44 -0000	1.96
+++ src/hg/makeDb/doc/hg19.txt	9 Apr 2010 15:24:24 -0000	1.97
@@ -8823,8 +8823,9 @@
 
 
 #######################################################################
 # felCatV17e Cat BLASTZ/CHAIN/NET (DONE  - 2010-03-22 - Chin)
+# Rerun the complete doBlastzChainNet.pl (2010-04-07 -Chin)
     screen # use a screen to manage this multi-day job
     mkdir /hive/data/genomes/hg19/bed/lastzFelCatV17e.2010-03-22
     cd /hive/data/genomes/hg19/bed/lastzFelCatV17e.2010-03-22
 
@@ -8864,9 +8865,9 @@
     # then continue
     # with:
 
     time nice -n +19 doBlastzChainNet.pl -verbose=2 \
-	`pw`/DEF \
+	`pwd`/DEF \
         -continue=download  -syntenicNet -noDbNameCheck \
 	-chainMinScore=3000 -chainLinearGap=medium \
 	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
         > download.log 2>&1 &
@@ -8876,19 +8877,32 @@
     # make it time independent and indicate that it is really done
     cd /hive/data/genomes/hg19/bed 
     ln -s  lastzFelCatV17e.2010-03-22 lastz.felCatV17e
 
+#  04/07 re-reun the  doBlastzChinNet.pl steps with screen
+    cd /hive/data/genomes/hg19/bed/lastzFelCatV17e.2010-03-22
+ 
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+        `pwd`/DEF \
+        -syntenicNet -noDbNameCheck \
+        -chainMinScore=3000 -chainLinearGap=medium \
+        -workhorse=hgwdev -smallClusterHub=pk -bigClusterHub=swarm \
+        > do.log 2>&1 &
+    #    real    423m7.683s
+
+
     # Swap
     mkdir /hive/data/genomes/felCatV17e/bed/blastz.hg19.swap
     cd /hive/data/genomes/felCatV17e/bed/blastz.hg19.swap
+
     time nice -n +19 doBlastzChainNet.pl -verbose=2 \
 	/hive/data/genomes/hg19/bed/lastzFelCatV17e.2010-03-22/DEF \
 	-swap -syntenicNet -noDbNameCheck \
-	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
+	-workhorse=hgwdev -smallClusterHub=pk -bigClusterHub=swarm \
 	-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
-    #	real    120m42.991s
+    #   real    200m43.245s
     cat fb.felCatV17e.chainHg19Link.txt 
-    #	2030475813 bases of 2752505800 (73.768%) in intersection
+    #   1211702270 bases of 1990635005 (60.870%) in intersection
 
 #####################################################################
 # susScr2 Pig BLASTZ/CHAIN/NET (DONE - 2010-03-26,27 - Hiram)
     screen # use a screen to manage this multi-day job

