52797440fc9be789b26f8f64fc70f9d40c9ca2c0
jcasper
  Fri Apr 24 15:41:54 2020 -0700
Belated doc commit for hg38 lastz run against enhLutNer1, refs #21152

diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt
index 20b43a6..e1e180c 100644
--- src/hg/makeDb/doc/hg38/lastzRuns.txt
+++ src/hg/makeDb/doc/hg38/lastzRuns.txt
@@ -12456,30 +12456,103 @@
     #  real    79m18.904s
 
     cat fb.regenCho1.chainHg38Link.txt
     # 956720146 bases of 2266312740 (42.215%) in intersection
     cat fb.regenCho1.chainSynHg38Link.txt
     # 895755077 bases of 2266312740 (39.525%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
 	regenCho1 hg38) > rbest.log 2>&1 &
     # real    289m24.440s
 
     cat fb.regenCho1.chainRBest.Hg38.txt
     # 902782523 bases of 2266312740 (39.835%) in intersection
 
 #############################################################################
+# LASTZ human/hg38 vs. Southern Sea Otter/enhLutNer1
+#	(DONE - 2019-12-22 - Jonathan)
+
+    mkdir /hive/data/genomes/hg38/bed/lastzEnhLutNer1.2019-12-20
+    cd /hive/data/genomes/hg38/bed/lastzEnhLutNer1.2019-12-20
+
+    printf '# human vs Southern sea otter
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/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: Southern sea otter enhLutNer1
+SEQ2_DIR=/hive/data/genomes/enhLutNer1/enhLutNer1.2bit
+SEQ2_LEN=/hive/data/genomes/enhLutNer1/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=20
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg38/bed/lastzEnhLutNer1.2019-12-20
+TMPDIR=/dev/shm
+' > DEF
+
+    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
+        -chainMinScore=3000 -chainLinearGap=medium \
+          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+            -noDbNameCheck -syntenicNet) > do.log 2>&1
+    # real    336m47.917s
+
+    cat fb.hg38.chainEnhLutNer1Link.txt
+    # 1537745313 bases of 3095998939 (49.669%) in intersection
+    cat fb.hg38.chainSynEnhLutNer1Link.txt
+    # 1454400074 bases of 3095998939 (46.977%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+	hg38 enhLutNer1) > rbest.log 2>&1 &
+    # real    336m47.917s
+
+    cat fb.hg38.chainRBest.EnhLutNer1.txt
+    # 1413203552 bases of 3095998939 (45.646%) in intersection
+
+    # and for the swap:
+    mkdir /hive/data/genomes/enhLutNer1/bed/blastz.hg38.swap
+    cd /hive/data/genomes/enhLutNer1/bed/blastz.hg38.swap
+
+    time (doBlastzChainNet.pl -verbose=2 \
+      /hive/data/genomes/hg38/bed/lastzEnhLutNer1.2019-12-20/DEF \
+        -swap -chainMinScore=3000 -chainLinearGap=medium \
+          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+            -noDbNameCheck -syntenicNet) > swap.log 2>&1
+    #  real    88m38.087s
+
+    cat fb.enhLutNer1.chainHg38Link.txt
+    # 1526639908 bases of 2413653822 (63.250%) in intersection
+    cat fb.enhLutNer1.chainSynHg38Link.txt
+    # 1403546142 bases of 2413653822 (58.150%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+	enhLutNer1 hg38) > rbest.log 2>&1 &
+    # real    319m54.030s
+
+    cat fb.enhLutNer1.chainRBest.Hg38.txt
+    # 1414347523 bases of 2413653822 (58.598%) in intersection
+
+#########################################################################
 # LASTZ human/hg38 vs. German shepard/canFam4
 #	(DONE - 2020-04-02 - Hiram)
 
     mkdir /hive/data/genomes/hg38/bed/lastzCanFam4.2020-04-02
     cd /hive/data/genomes/hg38/bed/lastzCanFam4.2020-04-02
 
     printf '# human vs. German shepard
 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