7c371e97e282fccecaf3cc8e0109c69a36a9caf3
hiram
  Mon Jun 12 12:57:28 2023 -0700
completed liftOver to GCA_001624675.1 no redmine

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index 7246231..165a7ef 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -18707,32 +18707,31 @@
         -target2Bit=/hive/data/genomes/mm10/mm10.2bit \
         -targetSizes=/hive/data/genomes/mm10/chrom.sizes \
  -query2Bit=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.2bit \
  -querySizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.chrom.sizes \
         -ooc=/hive/data/genomes/mm10/jkStuff/mm10.11.ooc \
          mm10 GCA_001624675.1
 
     time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -target2Bit=/hive/data/genomes/mm10/mm10.2bit \
         -targetSizes=/hive/data/genomes/mm10/chrom.sizes \
  -query2Bit=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.2bit \
  -querySizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.chrom.sizes \
         -ooc=/hive/data/genomes/mm10/jkStuff/mm10.11.ooc \
          mm10 GCA_001624675.1) > doLiftOverToGCA_001624675.1.log 2>&1
-XXX - running - Fri Jan 20 15:07:05 PST 2023
-    # real    190m50.501s
+    # real    160m19.129s
 
     # see if the liftOver menus function in the browser from mm10
     #    to GCA_001624675.1
 
 ##############################################################################
 # LIFTOVER TO mm10 (DONE - 2023-01-20 - Hiram)
     ssh hgwdev
     # going to need an ooc for this GenArk hub
     cd  /hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1
     time blat GCA_001624675.1_NOD_ShiLtJ_v1.2bit /dev/null /dev/null -tileSize=11 \
       -makeOoc=GCA_001624675.1_NOD_ShiLtJ_v1.11.ooc -repMatch=1000
 
 # Wrote 13801 overused 11-mers to GCA_001624675.1_NOD_ShiLtJ_v1.11.ooc
 # real    0m29.753s
 
@@ -18742,33 +18741,32 @@
         -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
  -target2Bit=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.2bit \
  -targetSizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.chrom.sizes \
         -query2Bit=/hive/data/genomes/mm10/mm10.2bit \
         -querySizes=/hive/data/genomes/mm10/chrom.sizes \
         -ooc=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.11.ooc \
          GCA_001624675.1 mm10
     time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
  -target2Bit=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.2bit \
  -targetSizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.chrom.sizes \
         -query2Bit=/hive/data/genomes/mm10/mm10.2bit \
         -querySizes=/hive/data/genomes/mm10/chrom.sizes \
         -ooc=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.11.ooc \
          GCA_001624675.1 mm10) > doLiftOverToMm10.log 2>&1
-XXX running Fri Jan 20 14:46:36 PST 2023
 
-    # real    244m28.766s
+    # real    193m24.137s
 
     # see if the liftOver menus function in the browser from mm10
     #    to GCA_001624675.1
 
 ##############################################################################
 # FANTOM5 refs #21605 (2023-06-09 Gerardo)
 cd /hive/data/outside/
 mkdir fantom5
 cd fantom5
 hubClone -download https://fantom.gsc.riken.jp/5/datahub/hub.txt
 cd /gbdb/mm10
 mkdir fantom5
 cd fantom5
 # Making symlinks for big files
 for file in $(ls /hive/data/outside/fantom5/riken_f5/mm10/*.b*) ; do ln -s $file; done