7d0bd2b7d089f94c9a8260c417246d4dbfce2523
mspeir
  Sat Mar 29 18:51:22 2025 -0700
adding make docs for several lastz runs from the last 6 months or so

diff --git src/hg/makeDb/doc/rheMac10/lastzRuns.txt src/hg/makeDb/doc/rheMac10/lastzRuns.txt
index d70a6cc514e..f287339960b 100644
--- src/hg/makeDb/doc/rheMac10/lastzRuns.txt
+++ src/hg/makeDb/doc/rheMac10/lastzRuns.txt
@@ -1,267 +1,369 @@
 ##############################################################################
 # LASTZ Rat rn6 (DONE - 2020-10-20 - Hiram)
     mkdir /hive/data/genomes/rheMac10/bed/lastzRn6.2020-10-20
     cd /hive/data/genomes/rheMac10/bed/lastzRn6.2020-10-20
 
     printf '# rat vs rhesus
 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
 # 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
 
 # QUERY: Rat Rn6
 SEQ2_DIR=/hive/data/genomes/rn6/rn6.2bit
 SEQ2_LEN=/hive/data/genomes/rn6/chrom.sizes
 SEQ2_CHUNK=20000000
 SEQ2_LAP=0
 SEQ2_LIMIT=500
 
 BASE=/hive/data/genomes/rheMac10/bed/lastzRn6.2020-10-20
 TMPDIR=/dev/shm
 ' > DEF
 
     #	establish a screen to control this job
     screen -S rheMac10Rn6
     time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
 	-syntenicNet \
 	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
 	-chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 &
     #   real    278m29.024s
 
     cat fb.rheMac10.chainRn6Link.txt
     #	901231172 bases of 2936892733 (30.687%) in intersection
     cat fb.rheMac10.chainSynRn6Link.txt
     #   854008376 bases of 2936892733 (29.079%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
 	rheMac10 rn6) > rbest.log 2>&1 &
     # real    293m29.540s
 
     cat fb.rheMac10.chainRBest.Rn6.txt
     #	860406990 bases of 2936892733 (29.297%) in intersection
 
     mkdir /hive/data/genomes/rn6/bed/blastz.rheMac10.swap
     cd /hive/data/genomes/rn6/bed/blastz.rheMac10.swap
     time (doBlastzChainNet.pl -verbose=2 \
 	/hive/data/genomes/rheMac10/bed/lastzRn6.2020-10-20/DEF \
 	-swap -syntenicNet \
 	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
 	-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
 
 ##############################################################################
 # LASTZ Rhesus RheMac10 vs. Baboon PapAnu2
 #    (DONE - 2022-03-17 - Jairo Navarro)
 
     mkdir /hive/data/genomes/rheMac10/bed/lastzPapAnu2.2022-03-09
     cd /hive/data/genomes/rheMac10/bed/lastzPapAnu2.2022-03-09
 
     printf '# Baboon PapAnu2 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: Baboon PapAnu2
 SEQ2_DIR=/hive/data/genomes/papAnu2/papAnu2.2bit
 SEQ2_LEN=/hive/data/genomes/papAnu2/chrom.sizes
 SEQ2_CHUNK=20000000
 SEQ2_LAP=0
 SEQ2_LIMIT=500
 
 BASE=/hive/data/genomes/rheMac10/bed/lastzPapAnu2.2022-03-09
 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/^/    # /;'
 
     sed -e 's/^/    # /;' fb.rheMac10.chainPapAnu2Link.txt
     # 2661233289 bases of 2936892733 (90.614%) in intersection
     sed -e 's/^/    # /;' fb.rheMac10.chainSynPapAnu2Link.txt
     # 2637780437 bases of 2936892733 (89.815%) in intersection
 
     time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
        \
        \
         rheMac10 papAnu2) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	92m15.570s
 
     sed -e 's/^/    # /;' fb.rheMac10.chainRBest.PapAnu2.txt
     # 2603944831 bases of 2936892733 (88.663%) in intersection
 
     ### and for the swap
 
     cd /hive/data/genomes/papAnu2/bed/blastz.rheMac10.swap
 
    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -swap -verbose=2 \
     /hive/data/genomes/rheMac10/bed/lastzPapAnu2.2022-03-09/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/^/    # /;'
 
     sed -e 's/^/    # /;' fb.papAnu2.chainRheMac10Link.txt
     # 2643316405 bases of 2893250291 (91.361%) in intersection
     sed -e 's/^/    # /;' fb.papAnu2.chainSynRheMac10Link.txt
 
     cd /hive/data/genomes/papAnu2/bed/blastz.rheMac10.swap
 
    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -swap -verbose=2 \
     /hive/data/genomes/rheMac10/bed/lastzPapAnu2.2022-03-09/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	70m47.109s
 
     sed -e 's/^/    # /;' fb.papAnu2.chainRheMac10Link.txt
     # 2643316405 bases of 2893250291 (91.361%) in intersection
     sed -e 's/^/    # /;' fb.papAnu2.chainSynRheMac10Link.txt
     # 2615443297 bases of 2893250291 (90.398%) in intersection
 \    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
     \
     \
    papAnu2 rheMac10) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	109m15.780s
 
     sed -e 's/^/    # /;' fb.papAnu2.chainRBest.RheMac10.txt
     # 2607952215 bases of 2893250291 (90.139%) in intersection
 
 ##############################################################################
+# LASTZ Rhesus RheMac10 vs. Cow BosTau9
+#    (DONE - 2025-03-23 - mspeir)
+
+    mkdir /hive/data/genomes/rheMac10/bed/lastzBosTau9.2025-03-23
+    cd /hive/data/genomes/rheMac10/bed/lastzBosTau9.2025-03-23
+
+    printf '# Cow BosTau9 vs. Rhesus RheMac10
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+
+# 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: Cow  bosTau9
+SEQ2_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit
+SEQ2_LEN=/hive/data/genomes/bosTau9/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/rheMac10/bed/lastzBosTau9.2025-03-23
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -verbose=2 `pwd`/DEF -syntenicNet \
+        -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	796m10.530s
+
+    sed -e 's/^/    # /;' fb.rheMac10.chainBosTau9Link.txt
+    # 1345771048 bases of 2936892733 (45.823%) in intersection
+    sed -e 's/^/    # /;' fb.rheMac10.chainSynBosTau9Link.txt
+    # 1293982344 bases of 2936892733 (44.060%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+       \
+        rheMac10 bosTau9) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	229m21.039s
+
+    sed -e 's/^/    # /;' fb.rheMac10.chainRBest.BosTau9.txt
+    # 1282431413 bases of 2936892733 (43.666%) in intersection
+
+##############################################################################
+# LASTZ Rhesus RheMac10 vs. Horse EquCab3
+#    (DONE - 2025-03-23 - mspeir)
+
+    mkdir /hive/data/genomes/rheMac10/bed/lastzEquCab3.2025-03-23
+    cd /hive/data/genomes/rheMac10/bed/lastzEquCab3.2025-03-23
+
+    printf '# Horse EquCab3 vs. Rhesus RheMac10
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+
+# 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: Horse  equCab3
+SEQ2_DIR=/hive/data/genomes/equCab3/equCab3.2bit
+SEQ2_LEN=/hive/data/genomes/equCab3/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/rheMac10/bed/lastzEquCab3.2025-03-23
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -verbose=2 `pwd`/DEF -syntenicNet \
+        -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	757m43.917s
+
+    sed -e 's/^/    # /;' fb.rheMac10.chainEquCab3Link.txt
+    # 1631389178 bases of 2936892733 (55.548%) in intersection
+    sed -e 's/^/    # /;' fb.rheMac10.chainSynEquCab3Link.txt
+    # 1576810063 bases of 2936892733 (53.690%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+       \
+        rheMac10 equCab3) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	230m53.590s
+
+    sed -e 's/^/    # /;' fb.rheMac10.chainRBest.EquCab3.txt
+    # 1553000153 bases of 2936892733 (52.879%) in intersection
+
+##############################################################################