b43571b81e045dc6658483bdbe790a5557bf1fa4
hiram
  Fri Jan 20 15:08:22 2023 -0800
trying an experiment blat same species to GCA_001624675.1_NOD_ShiLtJ_v1 to see if it is different than the lastz result refs #30492

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index 632e98a..5a74738 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -18623,78 +18623,142 @@
     \
    -target2bit="/hive/data/genomes/asmHubs/GCA/001/624/535/GCA_001624535.1/GCA_001624535.1.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/GCA/001/624/535/GCA_001624535.1/GCA_001624535.1.chrom.sizes.txt" \
    GCA_001624535.1 mm10) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	93m42.796s
 
     sed -e 's/^/    # /;' fb.GCA_001624535.1.chainRBest.Mm10.txt
     # 2255354454 bases of 2588619290 (87.126%) in intersection
 
 
 real	1211m31.498s
 user	0m1.396s
 sys	0m1.411s
-##############################################################################
 
 ##############################################################################
-# LIFTOVER TO GCA_001632575.1_C3H_HeJ_v1 (WORKING - 2023-01-19 - Hiram)
+# LIFTOVER TO GCA_001632575.1_C3H_HeJ_v1 (DONE - 2023-01-19 - Hiram)
     ssh hgwdev
     mkdir /hive/data/genomes/mm10/bed/blat.GCA_001632575.1.2023-01-19
     cd /hive/data/genomes/mm10/bed/blat.GCA_001632575.1.2023-01-19
     doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
         -debug -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/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.2bit \
  -querySizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.chrom.sizes \
         -ooc=/hive/data/genomes/mm10/jkStuff/mm10.11.ooc \
          mm10 GCA_001632575.1
     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/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.2bit \
  -querySizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.chrom.sizes \
         -ooc=/hive/data/genomes/mm10/jkStuff/mm10.11.ooc \
          mm10 GCA_001632575.1) > doLiftOverToGCA_001632575.1.log 2>&1
-XXX - running - Thu Jan 19 12:32:47 PST 2023
+    # real    190m50.501s
 
     # see if the liftOver menus function in the browser from mm10
     #    to GCA_001632575.1
 
 ##############################################################################
-# LIFTOVER TO mm10 (WORKING - 2023-01-19 - Hiram)
+# LIFTOVER TO mm10 (DONE - 2023-01-19 - Hiram)
     ssh hgwdev
     # going to need an ooc for this GenArk hub
     cd  /hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1
     time blat GCA_001632575.1_C3H_HeJ_v1.2bit /dev/null /dev/null -tileSize=11 \
       -makeOoc=GCA_001632575.1_C3H_HeJ_v1.11.ooc -repMatch=1000
 # Wrote 14128 overused 11-mers to GCA_001632575.1_C3H_HeJ_v1.11.ooc
 # real    0m46.685s
 
 
     mkdir /hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/trackData/blat.mm10.2023-01-19
     cd /hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/trackData/blat.mm10.2023-01-19
     doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
         -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
  -target2Bit=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.2bit \
  -targetSizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.chrom.sizes \
         -query2Bit=/hive/data/genomes/mm10/mm10.2bit \
         -querySizes=/hive/data/genomes/mm10/chrom.sizes \
         -ooc=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.11.ooc \
          GCA_001632575.1 mm10
     time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
  -target2Bit=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.2bit \
  -targetSizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.chrom.sizes \
         -query2Bit=/hive/data/genomes/mm10/mm10.2bit \
         -querySizes=/hive/data/genomes/mm10/chrom.sizes \
         -ooc=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.11.ooc \
          GCA_001632575.1 mm10) > doLiftOverToMm10.log 2>&1
-XXX - running - Thu Jan 19 12:32:47 PST 2023
+
+    # real    244m28.766s
 
     # see if the liftOver menus function in the browser from mm10
     #    to GCA_001632575.1
 
 ##############################################################################
+# LIFTOVER TO GCA_001624675.1_C3H_HeJ_v1 (DONE - 2023-01-20 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/mm10/bed/blat.GCA_001624675.1.2023-01-20
+    cd /hive/data/genomes/mm10/bed/blat.GCA_001624675.1.2023-01-20
+    doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
+        -debug -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
+
+    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
+
+    # 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
+
+    mkdir /hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/trackData/blat.mm10.2023-01-20
+    cd /hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/trackData/blat.mm10.2023-01-20
+    doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
+        -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
+
+    # see if the liftOver menus function in the browser from mm10
+    #    to GCA_001624675.1
+
+##############################################################################