c6768809fed768591851aa1547d1f5e867727a2f
hiram
  Wed Jul 29 12:41:26 2020 -0700
liftOvers from canFam5 to Fam3 Fam4 and vs. vs. refs #25917

diff --git src/hg/makeDb/doc/canFam3.txt src/hg/makeDb/doc/canFam3.txt
index 93db850..c89c85b 100644
--- src/hg/makeDb/doc/canFam3.txt
+++ src/hg/makeDb/doc/canFam3.txt
@@ -1009,30 +1009,47 @@
     time (doBlastzChainNet.pl -verbose=2 \
 	/hive/data/genomes/canFam3/bed/lastzXenTro9.2017-04-05/DEF \
 	-swap -syntenicNet \
 	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
 	-chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1
     # real    11m49.432s
 
     cat fb.xenTro9.chainCanFam3Link.txt
     #	45357837 bases of 1369865365 (3.311%) in intersection
 
     time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` xenTro9 canFam3) \
       > rbest.log 2>&1
     # real    131m41.477s
 
 ##############################################################################
+# LIFTOVER TO canFam5 (DONE - 2020-07-28 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/canFam3/bed/blat.canFam5.2020-07-28
+    cd /hive/data/genomes/canFam3/bed/blat.canFam5.2020-07-28
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -ooc=/hive/data/genomes/canFam3/jkStuff/canFam3.11.ooc \
+         canFam3 canFam5
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -ooc=/hive/data/genomes/canFam3/jkStuff/canFam3.11.ooc \
+         canFam3 canFam5) > doLiftOverToCanFam5.log 2>&1
+    # real    316m50.048s
+
+    # see if the liftOver menus function in the browser from canFam3 to canFam5
+
+##############################################################################
 # LIFTOVER TO canFam4 (DONE - 2020-04-02 - Hiram)
     ssh hgwdev
     mkdir /hive/data/genomes/canFam3/bed/blat.canFam4.2020-04-02
     cd /hive/data/genomes/canFam3/bed/blat.canFam4.2020-04-02
     doSameSpeciesLiftOver.pl -verbose=2 \
         -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/canFam3/jkStuff/canFam3.11.ooc \
          canFam3 canFam4
     time (doSameSpeciesLiftOver.pl -verbose=2 \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/canFam3/jkStuff/canFam3.11.ooc \
          canFam3 canFam4) > doLiftOverToCanFam4.log 2>&1
     # real    1264m58.309s
 
     # see if the liftOver menus function in the browser from canFam3 to canFam4