2eb7675b61bc79306e6ec54839140d2b40b31bf5
hiram
  Mon May 24 12:19:29 2021 -0700
canFam6 dog Tasha browser completed refs #27546

diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt
index c400232..d5d4d62 100644
--- src/hg/makeDb/doc/hg38/lastzRuns.txt
+++ src/hg/makeDb/doc/hg38/lastzRuns.txt
@@ -13170,15 +13170,89 @@
 
 time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
 -target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \
 $query $target) >> rbest.log 2>&1
 grep -w real rbest.log | sed -e 's/^/    # /;'
     # real    463m23.874s
 
 sed -e 's/^/    # /;' fb.${query}.chainRBest.${Target}.txt
     # 1281096559 bases of 2869914396 (44.639%) in intersection
 
 # Complete run time for all the swap operation:
     # real    554m2.489s
 
 ##############################################################################
+# LASTZ human/hg38 vs. boxer/Tasha/canFam6
+#	(DONE - 2021-05-17 - Hiram)
+
+    mkdir /hive/data/genomes/hg38/bed/lastzCanFam6.2021-05-17
+    cd /hive/data/genomes/hg38/bed/lastzCanFam6.2021-05-17
+
+    printf '# human vs. dog (boxer Tasha)
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+BLASTZ_M=254
+
+# TARGET: human hg38
+SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
+SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
+SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
+SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
+SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
+SEQ1_CHUNK=40000000
+SEQ1_LIMIT=20
+SEQ1_LAP=10000
+
+# QUERY: boxer Tasha/canFam6
+SEQ2_DIR=/hive/data/genomes/canFam6/canFam6.2bit
+SEQ2_LEN=/hive/data/genomes/canFam6/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=20
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg38/bed/lastzCanFam6.2021-05-17
+TMPDIR=/dev/shm
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl `pwd`/DEF \
+        -verbose=2 -chainMinScore=3000 -chainLinearGap=medium \
+          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+            -syntenicNet) > do.log 2>&1
+    # real    589m47.086s
+
+    sed -e 's/^/    # /;' fb.hg38.chainCanFam6Link.txt
+    # 1529157815 bases of 3110768607 (49.157%) in intersection
+
+    sed -e 's/^/    # /;' fb.hg38.chainSynCanFam6Link.txt
+    # 1468477892 bases of 3110768607 (47.206%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+	hg38 canFam6) > rbest.log 2>&1 &
+    # real    389m44.734s
+
+    sed -e 's/^/    # /;' fb.hg38.chainRBest.CanFam6.txt
+    # 1406453581 bases of 3110768607 (45.212%) in intersection
+
+    # and for the swap:
+    mkdir /hive/data/genomes/canFam6/bed/blastz.hg38.swap
+    cd /hive/data/genomes/canFam6/bed/blastz.hg38.swap
+
+    time (doBlastzChainNet.pl -verbose=2 \
+      /hive/data/genomes/hg38/bed/lastzCanFam6.2021-05-17/DEF \
+        -swap -chainMinScore=3000 -chainLinearGap=medium \
+          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+            -syntenicNet) > swap.log 2>&1
+    #  real    84m5.076s
+
+    sed -e 's/^/    # /;' fb.canFam6.chainHg38Link.txt
+    # 1435515352 bases of 2312743346 (62.070%) in intersection
+    sed -e 's/^/    # /;' fb.canFam6.chainSynHg38Link.txt
+    # 1400962536 bases of 2312743346 (60.576%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+	canFam6 hg38) > rbest.log 2>&1 &
+    # real    270m7.152s
+
+    sed -e 's/^/    # /;' fb.canFam6.chainRBest.Hg38.txt
+    # 1406634909 bases of 2312743346 (60.821%) in intersection
+
+############################################################################