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/rheMac10/lastzRuns.txt src/hg/makeDb/doc/rheMac10/lastzRuns.txt
index f3b5f67..c8b66a2 100644
--- src/hg/makeDb/doc/rheMac10/lastzRuns.txt
+++ src/hg/makeDb/doc/rheMac10/lastzRuns.txt
@@ -51,16 +51,116 @@
 	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
     #	real    61m59.379s
 
     cat fb.rn6.chainRheMac10Link.txt
     #   938991388 bases of 2729860805 (34.397%) in intersection
     cat fb.rn6.chainSynRheMac10Link.txt
     #	873546846 bases of 2729860805 (32.000%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
 	rn6 rheMac10) > rbest.log 2>&1
     # real    358m51.937s
 
     cat fb.rn6.chainRBest.RheMac10.txt
     #	861947799 bases of 2729860805 (31.575%) in intersection
 
-#########################################################################
+##############################################################################
+# LASTZ Rhesus RheMac10 vs. Crab-eating macaque MacFas5
+#	(DONE - 2021-10-12 - hiram)
+
+    cd /cluster/home/hiram/kent/src/hg/makeDb/doc/rheMac10
+    time (~/kent/src/hg/utils/automation/pairLastz.sh rheMac10 macFas5 \
+      primate primate) > rheMac10.macFas5.log 2>&1 &
+    #	real	422m56.515s
+    #	user	0m1.550s
+    #	sys	0m1.626s
+
+    # the following make doc is in that log file, copied here:
+
+    mkdir /hive/data/genomes/rheMac10/bed/lastzMacFas5.2021-10-12
+    cd /hive/data/genomes/rheMac10/bed/lastzMacFas5.2021-10-12
+
+    printf '# Crab-eating macaque MacFas5 vs. Rhesus RheMac10
+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: Rhesus RheMac10
+SEQ1_DIR=/hive/data/genomes/rheMac10/rheMac10.2bit
+SEQ1_LEN=/hive/data/genomes/rheMac10/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: Crab-eating macaque MacFas5
+SEQ2_DIR=/hive/data/genomes/macFas5/macFas5.2bit
+SEQ2_LEN=/hive/data/genomes/macFas5/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/rheMac10/bed/lastzMacFas5.2021-10-12
+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	188m26.969s
+
+    sed -e 's/^/    # /;' fb.rheMac10.chainMacFas5Link.txt
+    # 2784170031 bases of 2936892733 (94.800%) in intersection
+    sed -e 's/^/    # /;' fb.rheMac10.chainSynMacFas5Link.txt
+    # 2760382026 bases of 2936892733 (93.990%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+       \
+        rheMac10 macFas5) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	96m55.151s
+
+    sed -e 's/^/    # /;' fb.rheMac10.chainRBest.MacFas5.txt
+    # 2728786009 bases of 2936892733 (92.914%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/macFas5/bed/blastz.rheMac10.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -swap -verbose=2 \
+    /hive/data/genomes/rheMac10/bed/lastzMacFas5.2021-10-12/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	71m1.507s
+
+    sed -e 's/^/    # /;' fb.macFas5.chainRheMac10Link.txt
+    # 2739714634 bases of 2803866698 (97.712%) in intersection
+    sed -e 's/^/    # /;' fb.macFas5.chainSynRheMac10Link.txt
+    # 2729711862 bases of 2803866698 (97.355%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
+    \
+    \
+   macFas5 rheMac10) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	66m32.559s
+
+    sed -e 's/^/    # /;' fb.macFas5.chainRBest.RheMac10.txt
+    # 2730109619 bases of 2803866698 (97.369%) in intersection
+
+##############################################################################
+