86ae147ac68707dcb81a697e5e45f4619465097e
hiram
  Tue Feb 16 08:52:47 2021 -0800
completed lastz/chain/net to mm10 mm39 hg38 for rn7 release refs #26682

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index bd58490..bf86c85 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -18112,15 +18112,80 @@
     #	real    51m16.400s
 
     cat fb.calJac4.chainMm10Link.txt
     #	882506277 bases of 2859817025 (30.859%) in intersection
     cat fb.calJac4.chainSynMm10Link.txt
     #   831171319 bases of 2859817025 (29.064%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev calJac4 mm10 \
       -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
     # real    308m53.845s
 
     cat fb.calJac4.chainRBest.Mm10.txt
     # 833789913 bases of 2859817025 (29.155%) in intersection
 
 ##############################################################################
+# LASTZ Rat rn7 (DONE - 2021-02-15 - Hiram)
+    mkdir /hive/data/genomes/mm10/bed/lastzRn7.2021-02-15
+    cd /hive/data/genomes/mm10/bed/lastzRn7.2021-02-15
+
+    printf '# rat vs mouse
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+# TARGET: Mouse Mm10
+SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit
+SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+
+# QUERY: Rat Rn7
+SEQ2_DIR=/hive/data/genomes/rn7/rn7.2bit
+SEQ2_LEN=/hive/data/genomes/rn7/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=500
+
+BASE=/hive/data/genomes/mm10/bed/lastzRn7.2021-02-15
+TMPDIR=/dev/shm
+' > DEF
+
+    #	establish a screen to control this job
+    screen -S mm10Rn7
+    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
+	-syntenicNet \
+	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+	-chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 &
+    #   real    245m21.728s
+
+    sed -e 's/^/    # /;' fb.mm10.chainRn7Link.txt
+    # 1896928045 bases of 2652783500 (71.507%) in intersection
+    sed -e 's/^/    # /;' fb.mm10.chainSynRn7Link.txt
+    # 1787142074 bases of 2652783500 (67.369%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+	 mm10 rn7) > rbest.log 2>&1 &
+    # real    578m13.711s
+
+    sed -e 's/^/    # /;' fb.mm10.chainRBest.Rn7.txt
+    # 1753198266 bases of 2652783500 (66.089%) in intersection
+
+    mkdir /hive/data/genomes/rn7/bed/blastz.mm10.swap
+    cd /hive/data/genomes/rn7/bed/blastz.mm10.swap
+    time (doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/mm10/bed/lastzRn7.2021-02-15/DEF \
+	-swap -syntenicNet \
+	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+	-chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1
+    #	real    112m36.899s
+
+    sed -e 's/^/    # /;' fb.rn7.chainMm10Link.txt
+    # 1853300495 bases of 2626580772 (70.559%) in intersection
+    sed -e 's/^/    # /;' fb.rn7.chainSynMm10Link.txt
+    # 1762899567 bases of 2626580772 (67.118%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+	rn7 mm10) > rbest.log 2>&1
+    # real    599m24.766s
+
+    sed -e 's/^/    # /;' fb.rn7.chainRBest.Mm10.txt 
+    # 1753558422 bases of 2626580772 (66.762%) in intersection
+
+##############################################################################