2bc6c95b6b5139093990edbceb2e75ae101d3035
hiram
  Fri Jan 20 15:10:28 2023 -0800
completed blat same species to GCF_016772045.1_ARS-UI_Ramb_v2.0 refs #30517

diff --git src/hg/makeDb/doc/oviAri1.txt src/hg/makeDb/doc/oviAri1.txt
index e6da5f7..1f2a649 100644
--- src/hg/makeDb/doc/oviAri1.txt
+++ src/hg/makeDb/doc/oviAri1.txt
@@ -741,31 +741,31 @@
         -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -target2Bit=/hive/data/genomes/oviAri1/oviAri1.2bit \
         -targetSizes=/hive/data/genomes/oviAri1/chrom.sizes \
  -query2Bit=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.2bit \
  -querySizes=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.chrom.sizes \
         -ooc=/hive/data/genomes/oviAri1/jkStuff/oviAri1.11.ooc \
          oviAri1 GCF_016772045.1
     time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -target2Bit=/hive/data/genomes/oviAri1/oviAri1.2bit \
         -targetSizes=/hive/data/genomes/oviAri1/chrom.sizes \
  -query2Bit=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.2bit \
  -querySizes=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.chrom.sizes \
         -ooc=/hive/data/genomes/oviAri1/jkStuff/oviAri1.11.ooc \
          oviAri1 GCF_016772045.1) > doLiftOverToGCF_016772045.1.log 2>&1
-XXX - running - Thu Jan 19 13:08:03 PST 2023
+    # real    149m54.568s
 
     # see if the liftOver menus function in the browser from oviAri1
     #    to GCF_016772045.1
 
 ##############################################################################
 # LIFTOVER TO oviAri1 (WORKING - 2023-01-19 - Hiram)
     ssh hgwdev
     # going to need an ooc for this GenArk hub
     cd  /hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0
 
     # what is the 'real' size of this genome (without gaps):
     head -1 *.faSize.txt
 # 2628146905 bases (42000 N's 2628104905 real 1396540621 upper 1231564284 lower)
 #    in 142 sequences in 1 files
     # note the 'real' size is 2628104905
@@ -789,21 +789,21 @@
         -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
  -target2Bit=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.2bit \
  -targetSizes=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.chrom.sizes \
         -query2Bit=/hive/data/genomes/oviAri1/oviAri1.2bit \
         -querySizes=/hive/data/genomes/oviAri1/chrom.sizes \
         -ooc=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.11.ooc \
          GCF_016772045.1 oviAri1
     time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
  -target2Bit=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.2bit \
  -targetSizes=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.chrom.sizes \
         -query2Bit=/hive/data/genomes/oviAri1/oviAri1.2bit \
         -querySizes=/hive/data/genomes/oviAri1/chrom.sizes \
         -ooc=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.11.ooc \
          GCF_016772045.1 oviAri1) > doLiftOverToOviAri1.log 2>&1
-XXX - running - Thu Jan 19 13:08:03 PST 2023
+    # real    55m5.324s
 
     # see if the liftOver menus function in the browser from oviAri1
     #    to GCF_016772045.1
 
 ##############################################################################