e29a2749a1dd0fc28c17cd45270edbf151cbd532
hiram
  Wed Oct 13 10:11:15 2021 -0700
per user request rheMac2 and rheMac10 chainNet to macFas5 refs #28318

diff --git src/hg/makeDb/doc/macFas5/lastzRuns.txt src/hg/makeDb/doc/macFas5/lastzRuns.txt
index 2deb73c..64dcc24 100644
--- src/hg/makeDb/doc/macFas5/lastzRuns.txt
+++ src/hg/makeDb/doc/macFas5/lastzRuns.txt
@@ -136,16 +136,117 @@
     cd /hive/data/genomes/papHam1/bed/blastz.macFas5.swap
 
     time (doBlastzChainNet.pl -verbose=2 \
       /hive/data/genomes/macFas5/bed/lastzPapHam1.2014-05-15/DEF \
      -chainMinScore=5000 -chainLinearGap=medium \
         -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
              -swap -syntenicNet) > do.log 2>&1
     #  real    619m9.663s
 
     cat fb.papHam1.chainMacFas5Link.txt 
     # 2522131870 bases of 2741849051 (91.987%) in intersection
 
     time (doRecipBest.pl -buildDir=`pwd` papHam1 macFas5) > rbest.log 2>&1
     # real    244m37.728s
 
-#########################################################################
+##############################################################################
+# LASTZ Crab-eating macaque MacFas5 vs. Rhesus RheMac2
+#	(DONE - 2021-10-12 - hiram)
+
+    cd /cluster/home/hiram/kent/src/hg/makeDb/doc/macFas5
+
+    time (~/kent/src/hg/utils/automation/pairLastz.sh macFas5 rheMac2 \
+      primate primate) > macFas5.rheMac2.log 2>&1 &
+    #	real	366m28.349s
+    #	user	0m1.422s
+    #	sys	0m1.082s
+
+    # the following make doc is in that log file, copied here:
+
+    mkdir /hive/data/genomes/macFas5/bed/lastzRheMac2.2021-10-12
+    cd /hive/data/genomes/macFas5/bed/lastzRheMac2.2021-10-12
+
+    printf '# Rhesus RheMac2 vs. Crab-eating macaque MacFas5
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+BLASTZ_T=2
+BLASTZ_O=600
+BLASTZ_E=150
+BLASTZ_M=254
+BLASTZ_K=4500
+BLASTZ_Y=15000
+BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
+#       A     C     G     T
+# A    90  -330  -236  -356
+# C  -330   100  -318  -236
+# G  -236  -318   100  -330
+# T  -356  -236  -330    90
+
+# TARGET: Crab-eating macaque MacFas5
+SEQ1_DIR=/hive/data/genomes/macFas5/macFas5.2bit
+SEQ1_LEN=/hive/data/genomes/macFas5/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: Rhesus RheMac2
+SEQ2_DIR=/hive/data/genomes/rheMac2/rheMac2.2bit
+SEQ2_LEN=/hive/data/genomes/rheMac2/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/macFas5/bed/lastzRheMac2.2021-10-12
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -verbose=2 `pwd`/DEF -syntenicNet \
+        -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	158m45.932s
+
+    sed -e 's/^/    # /;' fb.macFas5.chainRheMac2Link.txt
+    # 2614119665 bases of 2803866698 (93.233%) in intersection
+    sed -e 's/^/    # /;' fb.macFas5.chainSynRheMac2Link.txt
+    # 2604737022 bases of 2803866698 (92.898%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+       \
+        macFas5 rheMac2) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	77m6.953s
+
+    sed -e 's/^/    # /;' fb.macFas5.chainRBest.RheMac2.txt
+    # 2596696673 bases of 2803866698 (92.611%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/rheMac2/bed/blastz.macFas5.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -swap -verbose=2 \
+    /hive/data/genomes/macFas5/bed/lastzRheMac2.2021-10-12/DEF -swapDir=`pwd` \
+  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1
+
+    grep -w real swap.log | sed -e 's/^/    # /;'
+    # real	76m2.171s
+
+    sed -e 's/^/    # /;' fb.rheMac2.chainMacFas5Link.txt
+    # 2600572513 bases of 2646704109 (98.257%) in intersection
+    sed -e 's/^/    # /;' fb.rheMac2.chainSynMacFas5Link.txt
+    # 2595637716 bases of 2646704109 (98.071%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
+    \
+    \
+   rheMac2 macFas5) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	54m32.803s
+
+    sed -e 's/^/    # /;' fb.rheMac2.chainRBest.MacFas5.txt
+    # 2596730835 bases of 2646704109 (98.112%) in intersection
+
+
+##############################################################################