3da24c002ed1f1bba8eab282fccaf194ac80b1fe
hiram
  Tue Jul 9 09:28:39 2019 -0700
lastz chainNet to regenRn0 and rheMac10 refs #21579 #23771

diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt
index a756d58..72cae22 100644
--- src/hg/makeDb/doc/hg38/lastzRuns.txt
+++ src/hg/makeDb/doc/hg38/lastzRuns.txt
@@ -12085,15 +12085,161 @@
     #  real    60m31.849s
 
     cat fb.GRCm38B.chainHg38Link.txt
     # 941205213 bases of 2655285420 (35.446%) in intersection
     cat fb.GRCm38B.chainSynHg38Link.txt
     # 891450770 bases of 2655285420 (33.573%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` GRCm38B hg38) \
      > rbest.log 2>&1 &
     # real    331m35.578s
 
     cat fb.GRCm38B.chainRBest.Hg38.txt
     # 893587236 bases of 2655285420 (33.653%) in intersection
 
 #########################################################################
+# LASTZ human/hg38 vs. rat/regenRn0 - (DONE - 2019-07-01 - Hiram)
+    mkdir /hive/data/genomes/hg38/bed/lastzRegenRn0.2019-07-01
+    cd /hive/data/genomes/hg38/bed/lastzRegenRn0.2019-07-01
+
+    printf '# human vs rat
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
+
+# 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=30
+SEQ1_LAP=10000
+
+# QUERY: rat regenRn0
+SEQ2_DIR=/hive/data/genomes/regenRn0/regenRn0.2bit
+SEQ2_LEN=/hive/data/genomes/regenRn0/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=30
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg38/bed/lastzRegenRn0.2019-07-01
+TMPDIR=/dev/shm
+' > DEF
+
+    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
+        -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \
+          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+            -syntenicNet) > do.log 2>&1 &
+    # real    256m8.479s
+
+    cat fb.hg38.chainRegenRn0Link.txt
+    # 930788096 bases of 3095998939 (30.064%) in intersection
+    cat fb.hg38.chainSynRegenRn0Link.txt
+    # 870556908 bases of 3095998939 (28.119%) in intersection
+
+    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` hg38 regenRn0) > rbest.log 2>&1 &
+    # real    328m4.069s
+
+    cat fb.hg38.chainRBest.RegenRn0.txt
+    # 857127621 bases of 3095998939 (27.685%) in intersection
+
+    # and for the swap:
+    mkdir /hive/data/genomes/regenRn0/bed/blastz.hg38.swap
+    cd /hive/data/genomes/regenRn0/bed/blastz.hg38.swap
+
+    time (doBlastzChainNet.pl -verbose=2 \
+      /hive/data/genomes/hg38/bed/lastzRegenRn0.2019-07-01/DEF \
+        -swap -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \
+          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+            -syntenicNet) > swap.log 2>&1
+    #  real    64m34.515s
+
+    cat fb.regenRn0.chainHg38Link.txt
+    # 906790361 bases of 2534810853 (35.773%) in intersection
+    cat fb.regenRn0.chainSynHg38Link.txt
+    # 849997639 bases of 2534810853 (33.533%) in intersection
+
+    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` regenRn0 hg38) > rbest.log 2>&1
+    # real    300m30.411s
+
+    cat fb.regenRn0.chainRBest.Hg38.txt
+    # 858923025 bases of 2534810853 (33.885%) in intersection
+
+#########################################################################
+# LASTZ human/hg38 Tree chimp/rheMac10 - (DONE - 2019-07-03 - Hiram)
+    mkdir /hive/data/genomes/hg38/bed/lastzRheMac10.2019-07-03
+    cd /hive/data/genomes/hg38/bed/lastzRheMac10.2019-07-03
+
+    printf '# human vs macaca mulatta
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
+# maximum M allowed with lastz is only 254
+BLASTZ_M=254
+BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
+BLASTZ_O=600
+BLASTZ_E=150
+# other parameters from panTro2 vs hg18 lastz on advice from Webb
+BLASTZ_K=4500
+BLASTZ_Y=15000
+BLASTZ_T=2
+
+# 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=20000000
+SEQ1_LAP=10000
+
+# QUERY: Macaca Mulatta RheMac10
+SEQ2_DIR=/hive/data/genomes/rheMac10/rheMac10.2bit
+SEQ2_LEN=/hive/data/genomes/rheMac10/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=600
+SEQ2_LAP=0
+SEQ2_IN_CONTIGS=0
+
+BASE=/hive/data/genomes/hg38/bed/lastzRheMac10.2019-07-03
+TMPDIR=/dev/shm
+' > DEF
+    # << happy emacs
+
+    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
+        -syntenicNet -fileServer=hgwdev \
+        -chainMinScore=5000 -chainLinearGap=medium \
+        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > do.log 2>&1
+    # real    97m36.383s
+
+    cat fb.hg38.chainRheMac10Link.txt
+    # 2596157811 bases of 3095998939 (83.855%) in intersection
+    cat fb.hg38.chainSynRheMac10Link.txt
+    # 2564291936 bases of 3095998939 (82.826%) in intersection
+
+    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` hg38 rheMac10) > rbest.log 2>&1 &
+    # real    120m8.526s
+
+    cat fb.hg38.chainRBest.RheMac10.txt
+    # 2422981614 bases of 3095998939 (78.262%) in intersection
+
+    # and for the swap:
+    mkdir /hive/data/genomes/rheMac10/bed/blastz.hg38.swap
+    cd /hive/data/genomes/rheMac10/bed/blastz.hg38.swap
+
+    time (doBlastzChainNet.pl -verbose=2 \
+      /hive/data/genomes/hg38/bed/lastzRheMac10.2019-07-03/DEF \
+        -swap -chainMinScore=5000 -chainLinearGap=medium \
+          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+            -syntenicNet) > swap.log 2>&1
+    #  real    61m39.505s
+
+    cat fb.rheMac10.chainHg38Link.txt
+    # 2485840115 bases of 2936892733 (84.642%) in intersection
+    cat fb.rheMac10.chainSynHg38Link.txt
+    # 2465210442 bases of 2936892733 (83.939%) in intersection
+
+    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` rheMac10 hg38) > rbest.log 2>&1
+    # real    126m29.919s
+
+    cat fb.rheMac10.chainRBest.Hg38.txt
+    # 2424028492 bases of 2936892733 (82.537%) in intersection
+
+#########################################################################