b4ce6229cd32c26b3c1c7c7fb5d443db348ce75b
jcasper
  Fri Apr 17 16:31:19 2020 -0700
Adding mm10 vs enhLutNer1 alignment, refs #21152

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index 1a1a7be..9d9538d 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -18510,15 +18510,82 @@
     # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include
     make DBS=mm10
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM25.joiner
     # verify with:
     pushd /hive/data/genomes/mm10/bed/gencodeVM25Pre
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm10 alpha
     # if pushing public: add ticket and MARK QA READY
 
 ##############################################################################
+# LASTZ Southern sea otter enhLutNer1 (DONE - 2020-04-16 - Jonathan)
+    #	establish a screen to control this job
+    mkdir /hive/data/genomes/mm10/bed/lastzEnhLutNer1.2020-04-15
+    cd /hive/data/genomes/mm10/bed/lastzEnhLutNer1.2020-04-15
+
+    printf '# Southern sea otter vs mouse
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
+
+# TARGET: Mouse Mm10
+SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit
+SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: Southern sea otter enhLutNer1
+SEQ2_DIR=/hive/data/genomes/enhLutNer1/enhLutNer1.2bit
+SEQ2_LEN=/hive/data/genomes/enhLutNer1/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LIMIT=180
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/mm10/bed/lastzEnhLutNer1.2020-04-15
+TMPDIR=/dev/shm
+' > DEF
+
+    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
+	-noDbNameCheck -syntenicNet \
+	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+	-chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 &
+    #	real    140m43.505s
+
+    cat fb.mm10.chainEnhLutNer1Link.txt
+    #   772059271 bases of 2652783500 (29.104%) in intersection
+    cat fb.mm10.chainSynEnhLutNer1Link.txt
+    #   717097454 bases of 2652783500 (27.032%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev mm10 enhLutNer1 \
+      -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
+    #	real    174m28.167s
+
+    cat fb.mm10.chainRBest.EnhLutNer1.txt
+    # 734878489 bases of 2652783500 (27.702%) in intersection
+
+    mkdir /hive/data/genomes/enhLutNer1/bed/blastz.mm10.swap
+    cd /hive/data/genomes/enhLutNer1/bed/blastz.mm10.swap
+    time (doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/mm10/bed/lastzEnhLutNer1.2020-04-15/DEF \
+	-noDbNameCheck -swap -syntenicNet \
+	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 &
+    #	real    48m44.604s
+
+    cat fb.enhLutNer1.chainMm10Link.txt
+    #   787727864 bases of 2413653822 (32.636%) in intersection
+    cat fb.enhLutNer1.chainSynMm10Link.txt
+    #   712950571 bases of 2413653822 (29.538%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev enhLutNer1 mm10 \
+      -buildDir=`pwd`) > rbest.log 2>&1 &
+    # real    167m45.490s
+
+    cat fb.enhLutNer1.chainRBest.Mm10.txt
+    # 734620004 bases of 2413653822 (30.436%) in intersection
+
+##############################################################################
+