efd88f6acfb7fc2bfcf6b15583aa8bc35a8540c9
gperez2
  Mon Feb 28 12:12:48 2022 -0800
bosTau9  vs. bosTau5  lastz/chain/net run for user, refs #28943

diff --git src/hg/makeDb/doc/bosTau9/lastzRuns.txt src/hg/makeDb/doc/bosTau9/lastzRuns.txt
new file mode 100644
index 0000000..9ac6182
--- /dev/null
+++ src/hg/makeDb/doc/bosTau9/lastzRuns.txt
@@ -0,0 +1,95 @@
+#########################################################################
+# LASTZ Cow BosTau9 vs. Cow BosTau5 (DONE - 2022-02-25 - Gerardo)
+
+# should be able to run this from anywhere, this time it was run from:
+    cd kent/src/hg/utils/automation
+
+  time (~/kent/src/hg/utils/automation/pairLastz.sh \
+        bosTau9 bosTau5 mammal mammal) \
+           > bosTau9_bosTau5_20220225_secondTime.log 2>&1 &
+  # check the total time
+grep -w real  bosTau9_bosTau5_20220225_secondTime.log  | tail -1 | sed -e 's/^/    # /;'
+    # real      675m26.699s
+#########################################################################
+# LASTZ Cow BosTau9 vs. Cow BosTau5
+#    (DONE - 2022-02-25 - Gerardo)
+
+    mkdir /hive/data/genomes/bosTau9/bed/lastzBosTau5.2022-02-18
+    cd /hive/data/genomes/bosTau9/bed/lastzBosTau5.2022-02-18
+
+    printf '# Cow BosTau5 vs. Cow BosTau9
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+
+# TARGET: Cow BosTau9
+SEQ1_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit
+SEQ1_LEN=/hive/data/genomes/bosTau9/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: Cow BosTau5
+SEQ2_DIR=/hive/data/genomes/bosTau5/bosTau5.2bit
+SEQ2_LEN=/hive/data/genomes/bosTau5/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/bosTau9/bed/lastzBosTau5.2022-02-18
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -verbose=2 `pwd`/DEF -syntenicNet \
+        -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	543m53.934s
+
+    sed -e 's/^/    # /;' fb.bosTau9.chainBosTau5Link.txt
+    # 2595387173 bases of 2715853792 (95.564%) in intersection
+    sed -e 's/^/    # /;' fb.bosTau9.chainSynBosTau5Link.txt
+    # 2560256591 bases of 2715853792 (94.271%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+       \
+        bosTau9 bosTau5) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	74m31.401s
+
+    sed -e 's/^/    # /;' fb.bosTau9.chainRBest.BosTau5.txt
+    # 2540513150 bases of 2715853792 (93.544%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/bosTau5/bed/blastz.bosTau9.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -swap -verbose=2 \
+    /hive/data/genomes/bosTau9/bed/lastzBosTau5.2022-02-18/DEF -swapDir=`pwd` \
+  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
+
+    grep -w real swap.log | sed -e 's/^/    # /;'
+    # real	601m9.542s
+
+    sed -e 's/^/    # /;' fb.bosTau5.chainBosTau9Link.txt
+    # 2706702737 bases of 2732505379 (99.056%) in intersection
+    sed -e 's/^/    # /;' fb.bosTau5.chainSynBosTau9Link.txt
+    # 2673116410 bases of 2732505379 (97.827%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
+    \
+    \
+   bosTau5 bosTau9) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	74m16.598s
+
+    sed -e 's/^/    # /;' fb.bosTau5.chainRBest.BosTau9.txt
+    # 2543778039 bases of 2732505379 (93.093%) in intersection
+
+##############################################################################
+
+real	675m26.699s
+user	0m0.945s
+sys	0m1.486s