92f411c1e49f135fe0908dec77fbbc3e82a50157
hiram
  Thu Sep 3 15:28:59 2020 -0700
starting chainNet calJac4 to mm10 and hg38

diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt
index 5982e84..dd49110 100644
--- src/hg/makeDb/doc/hg38/lastzRuns.txt
+++ src/hg/makeDb/doc/hg38/lastzRuns.txt
@@ -12836,15 +12836,89 @@
     #   real    47m57.164s
 
     sed -e 's/^/    # /;' fb.mm39.chainHg38Link.txt
     # 939000954 bases of 2654624157 (35.372%) in intersection
     sed -e 's/^/    # /;' fb.mm39.chainSynHg38Link.txt
     # 891050480 bases of 2654624157 (33.566%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
 	mm39 hg38) > rbest.log 2>&1 &
     # real    257m59.713s
 
     sed -e 's/^/    # /;' fb.mm39.chainRBest.Hg38.txt
     # 893176796 bases of 2654624157 (33.646%) in intersection
 
 #########################################################################
+# LASTZ human/hg38 vs. marmoset/calJac4
+#	(DONE - 2020-08-03.g - Hiram)
+
+    mkdir /hive/data/genomes/hg38/bed/lastzCalJac4.2020-08-03
+    cd /hive/data/genomes/hg38/bed/lastzCalJac4.2020-08-03
+
+    printf '# human vs. marmoset
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+BLASTZ_M=254
+
+# TARGET: human hg38
+SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
+SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
+SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
+SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
+SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
+SEQ1_CHUNK=40000000
+SEQ1_LIMIT=20
+SEQ1_LAP=10000
+
+# QUERY: marmoset/calJac4
+SEQ2_DIR=/hive/data/genomes/calJac4/calJac4.2bit
+SEQ2_LEN=/hive/data/genomes/calJac4/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=20
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg38/bed/lastzCalJac4.2020-08-03
+TMPDIR=/dev/shm
+' > DEF
+
+    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
+        -chainMinScore=3000 -chainLinearGap=medium \
+          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+            -syntenicNet) > do.log 2>&1
+    # real    1038m20.721s
+
+    cat fb.hg38.chainCalJac4Link.txt
+    # 1545648756 bases of 3110768607 (49.687%) in intersection
+
+    cat fb.hg38.chainSynCalJac4Link.txt
+    # 1484758745 bases of 3110768607 (47.730%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+	hg38 calJac4) > rbest.log 2>&1 &
+    # real    283m55.399s
+
+    cat fb.hg38.chainRBest.CalJac4.txt
+    # 1422619513 bases of 3110768607 (45.732%) in intersection
+
+    # and for the swap:
+    mkdir /hive/data/genomes/calJac4/bed/blastz.hg38.swap
+    cd /hive/data/genomes/calJac4/bed/blastz.hg38.swap
+
+    time (doBlastzChainNet.pl -verbose=2 \
+      /hive/data/genomes/hg38/bed/lastzCalJac4.2020-08-03/DEF \
+        -swap -chainMinScore=3000 -chainLinearGap=medium \
+          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+            -syntenicNet) > swap.log 2>&1
+    #  real    78m37.078s
+
+    cat fb.calJac4.chainHg38Link.txt
+    # 1460025525 bases of 2337131234 (62.471%) in intersection
+    cat fb.calJac4.chainSynHg38Link.txt
+    # 1423305734 bases of 2337131234 (60.900%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+	calJac4 hg38) > rbest.log 2>&1 &
+    # real    255m9.076s
+
+    cat fb.calJac4.chainRBest.Hg38.txt
+    # 1422612399 bases of 2337131234 (60.870%) in intersection
+
+############################################################################