5ea80cd83327f973e24ee93695b321a77fd8bbd9
hiram
  Mon Aug 17 12:49:16 2020 -0700
starting lastz chainNet to canFam5 refs #25917

diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt
new file mode 100644
index 0000000..d64412e
--- /dev/null
+++ src/hg/makeDb/doc/mm39/lastzRuns.txt
@@ -0,0 +1,69 @@
+##############################################################################
+# LASTZ Great Dane canFam5 (DONE - 2020-08-17 - Hiram)
+    #	establish a screen to control this job
+    mkdir /hive/data/genomes/mm39/bed/lastzCanFam5.2020-08-17
+    cd /hive/data/genomes/mm39/bed/lastzCanFam5.2020-08-17
+
+    printf '# German shepard canFam5 vs mouse
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+BLASTZ_M=254
+
+# TARGET: Mouse Mm10
+SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
+SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: German shepard canFam5
+SEQ2_DIR=/hive/data/genomes/canFam5/canFam5.2bit
+SEQ2_LEN=/hive/data/genomes/canFam5/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LIMIT=20
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/mm39/bed/lastzCanFam5.2020-08-17
+TMPDIR=/dev/shm
+' > DEF
+
+    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
+	-syntenicNet \
+	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+	-chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 &
+XXX - running - Mon Aug 17 12:48:39 PDT 2020
+    #	real    1052m41.484s
+
+    cat fb.mm39.chainCanFam5Link.txt
+    #	776486006 bases of 2652783500 (29.271%) in intersection
+    cat fb.mm39.chainSynCanFam5Link.txt
+    #   735561772 bases of 2652783500 (27.728%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev mm39 canFam5 \
+      -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
+    #	real    219m16.168s
+
+    cat fb.mm39.chainRBest.CanFam5.txt
+    # 741307883 bases of 2652783500 (27.945%) in intersection
+
+    mkdir /hive/data/genomes/canFam5/bed/blastz.mm39.swap
+    cd /hive/data/genomes/canFam5/bed/blastz.mm39.swap
+    time (doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/mm39/bed/lastzCanFam5.2020-08-17/DEF \
+	-swap -syntenicNet \
+	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 &
+    #	real    50m20.639s
+
+    cat fb.canFam5.chainMm10Link.txt
+    #	772902855 bases of 2481941580 (31.141%) in intersection
+    cat fb.canFam5.chainSynMm10Link.txt
+    #   737924732 bases of 2481941580 (29.732%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev canFam5 mm39 \
+      -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
+    # real    173m38.016s
+
+    cat fb.canFam5.chainRBest.Mm10.txt
+    # 740357755 bases of 2481941580 (29.830%) in intersection
+
+##############################################################################