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/canFam4/initialBuild.txt src/hg/makeDb/doc/canFam4/initialBuild.txt
index 628a83b..699c226 100644
--- src/hg/makeDb/doc/canFam4/initialBuild.txt
+++ src/hg/makeDb/doc/canFam4/initialBuild.txt
@@ -885,30 +885,47 @@
 
     # XXX 2019-11-20 - ready for this after genbank runs
 
     featureBits -enrichment canFam4 refGene ncbiRefSeq 
  # refGene 0.402%, ncbiRefSeq 3.148%, both 0.402%, cover 99.90%, enrich 31.73x
     featureBits -enrichment canFam4 ncbiRefSeq refGene
  # ncbiRefSeq 3.148%, refGene 0.402%, both 0.402%, cover 12.76%, enrich 31.73x
 
     featureBits -enrichment canFam4 ncbiRefSeqCurated refGene
  # ncbiRefSeqCurated 0.401%, refGene 0.402%, both 0.400%, cover 99.66%, enrich 247.79x
 
     featureBits -enrichment canFam4 refGene ncbiRefSeqCurated
  # refGene 0.402%, ncbiRefSeqCurated 0.401%, both 0.400%, cover 99.33%, enrich 247.79x
 
 #########################################################################
+# LIFTOVER TO canFam5 (DONE - 2020-07-28 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/canFam4/bed/blat.canFam5.2020-07-28
+    cd /hive/data/genomes/canFam4/bed/blat.canFam5.2020-07-28
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -ooc=/hive/data/genomes/canFam4/jkStuff/canFam4.11.ooc \
+         canFam4 canFam5
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -ooc=/hive/data/genomes/canFam4/jkStuff/canFam4.11.ooc \
+         canFam4 canFam5) > doLiftOverToCanFam5.log 2>&1
+    # real    286m56.444s
+
+    # see if the liftOver menus function in the browser from canFam4 to canFam5
+
+#########################################################################
 # LIFTOVER TO canFam3 (DONE - 2020-04-02 - Hiram)
     ssh hgwdev
     mkdir /hive/data/genomes/canFam4/bed/blat.canFam3.2020-04-02
     cd /hive/data/genomes/canFam4/bed/blat.canFam3.2020-04-02
     doSameSpeciesLiftOver.pl -verbose=2 \
         -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/canFam4/jkStuff/canFam4.11.ooc \
          canFam4 canFam3
     time (doSameSpeciesLiftOver.pl -verbose=2 \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/canFam4/jkStuff/canFam4.11.ooc \
          canFam4 canFam3) > doLiftOverToCanFam3.log 2>&1
     # real    1100m17.743s
 
     # see if the liftOver menus function in the browser from canFam4 to canFam3
@@ -918,31 +935,31 @@
 #	After getting a blat server assigned by the Blat Server Gods,
     ssh hgwdev
 
     hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
 	VALUES ("canFam4", "blat1b", "17904", "1", "0"); \
 	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
 	VALUES ("canFam4", "blat1b", "17905", "0", "1");' \
 	    hgcentraltest
     #	test it with some sequence
 
 ############################################################################
 ## reset default position to gene: CDH2 upon recommendation from Kerstin
 ##  (DONE - 2020-06-22 - Hiram)
 
     ssh hgwdev
-    hgsql -e 'update dbDb set defaultPos="chr7:60744942-60958801"
+    hgsql -e 'update dbDb set defaultPos="chr7:60683331-61003907"
 	where name="canFam4";' hgcentraltest
 
 ##############################################################################
 # crispr whole genome (DONE - 2020-04-09 - Hiram)
     mkdir /hive/data/genomes/canFam4/bed/crisprAll
     cd /hive/data/genomes/canFam4/bed/crisprAll
 
     # the large shoulder argument will cause the entire genome to be scanned
     # this takes a while for a new genome to get the bwa indexing done
     time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 -stop=ranges \
     canFam4 genscan -shoulder=250000000 -tableName=crisprAll \
     -fileServer=hgwdev \
     -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
       -workhorse=hgwdev) > ranges.log 2>&1
     # real    1m16.539s
@@ -1035,31 +1052,30 @@
     # when clean, check in:
     git commit -m 'adding rules for canFam4 refs #25279' all.joiner
     git push
     # run up a 'make alpha' in hg/hgTables to get this all.joiner file
     # into the hgwdev/genome-test system
 
     cd /hive/data/genomes/canFam4
     time (makeDownloads.pl canFam4) > downloads.log 2>&1
     #  real    16m11.233s
 
     #   now ready for pushQ entry
     mkdir /hive/data/genomes/canFam4/pushQ
     cd /hive/data/genomes/canFam4/pushQ
  time ($HOME/kent/src/hg/utils/automation/makePushQSql.pl -redmineList canFam4) > canFam4.pushQ.sql 2> stderr.out
     # real    15m2.385s
-XXXX
 
     # remove the tandemDups and gapOverlap from the file list:
     sed -i -e "/tandemDups/d" redmine.canFam4.table.list
     sed -i -e "/Tandem Dups/d" redmine.canFam4.releaseLog.txt
     sed -i -e "/gapOverlap/d" redmine.canFam4.table.list
     sed -i -e "/Gap Overlaps/d" redmine.canFam4.releaseLog.txt
 
     #   check for errors in stderr.out, some are OK, e.g.:
   # WARNING: canFam4 does not have ucscToRefSeq
   # WARNING: hgwdev does not have /gbdb/canFam4/ncbiRefSeq/ncbiRefSeqVersion.txt
   # WARNING: hgwdev does not have /gbdb/canFam4/ncbiRefSeq/ncbiRefSeqOther.bb
   # WARNING: hgwdev does not have /gbdb/canFam4/ncbiRefSeq/ncbiRefSeqOther.ix
   # WARNING: hgwdev does not have /gbdb/canFam4/ncbiRefSeq/ncbiRefSeqOther.ixx
   # WARNING: hgwdev does not have /gbdb/canFam4/ncbiRefSeq/seqNcbiRefSeq.rna.fa
   # WARNING: canFam4 does not have seq