86543de97fd1c1f6d8c3c34e23109ffc3703cf82
hiram
  Mon Jun 15 10:39:41 2020 -0700
starting lastz chain net to panPan3 refs #25720

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index 4dee6ba..56315a2 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -17660,31 +17660,30 @@
 BASE=/hive/data/genomes/mm10/bed/lastzCanFam4.2020-04-02
 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 &
     #	real    483m10.607s
 
     cat fb.mm10.chainCanFam4Link.txt
     #	777883731 bases of 2652783500 (29.323%) in intersection
     cat fb.mm10.chainSynCanFam4Link.txt
     #   736602602 bases of 2652783500 (27.767%) in intersection
 
-
     time (doRecipBest.pl -load -workhorse=hgwdev mm10 canFam4 \
       -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
     #	real    219m16.168s
 
     cat fb.mm10.chainRBest.CanFam4.txt
     # 741307883 bases of 2652783500 (27.945%) in intersection
 
     mkdir /hive/data/genomes/canFam4/bed/blastz.mm10.swap
     cd /hive/data/genomes/canFam4/bed/blastz.mm10.swap
     time (doBlastzChainNet.pl -verbose=2 \
 	/hive/data/genomes/mm10/bed/lastzCanFam4.2020-04-02/DEF \
 	-swap -syntenicNet \
 	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
 	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 &
     #	real    50m20.639s
@@ -17820,16 +17819,81 @@
 # score using zscore,  min(zscore*100),1000), and reformat
 awk '{OFS="\t"; print $1, $2, $3, $4, ($13>10)? 1000 : int($13 * 100), $6, $7, $8, $9, $10, $13}' \
         ccres.prescored.bed | bedSort stdin ccres.scored.bed
 set f = encodeCcreCombined
 
 # Reformat to add fields for filtering and mouseover, etc.
 set bin = ~/kent/src/hg/makeDb/outside/encode3/ccre
 perl $bin/makeCcreCombined.pl < ccres.scored.bed > $f.bed
 set lib = ~/kent/src/hg/lib
 bedToBigBed -tab -type=bed9+6 -as=$lib/$f.as $f.bed /hive/data/genomes/mm10/chrom.sizes $f.bb
 mkdir -p /gbdb/mm10/encode3/ccre
 ln -s `pwd`/$f.bb /gbdb/mm10/encode3/ccre
 
 
 ##############################################################################
+# LASTZ mouse/mm10 bonobo/panPan3 - (DONE - 2020-06-15 - Hiram)
+    mkdir /hive/data/genomes/mm10/bed/lastzPanPan3.2020-06-15
+    cd /hive/data/genomes/mm10/bed/lastzPanPan3.2020-06-15
 
+    printf '# mouse vs bonobo
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+BLASTZ_M=254
+
+# 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
+# the default matrix is:
+#       A     C     G     T
+# A    91  -114   -31  -123
+# C  -114   100  -125   -31
+# G   -31  -125   100  -114
+# T  -123   -31  -114    91
+
+# QUERY: bonobo panPan3
+SEQ2_DIR=/hive/data/genomes/panPan3/panPan3.2bit
+SEQ2_LEN=/hive/data/genomes/panPan3/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=30
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/mm10/bed/lastzPanPan3.2020-06-15
+TMPDIR=/dev/shm
+' > DEF
+
+    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
+        -chainMinScore=3000 -chainLinearGap=medium \
+          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+            -syntenicNet) > do.log 2>&1
+XXX - running - Mon Jun 15 10:19:12 PDT 2020
+    # real    360m9.534s
+
+    cat fb.mm10.chainPanPan3Link.txt
+    # 928638440 bases of 2652783500 (35.006%) in intersection
+    cat fb.mm10.chainSynPanPan3Link.txt
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` mm10 panPan3) \
+      > rbest.log 2>&1 &
+    # real    765m26.648s
+    cat fb.mm10.chainRBest.PanPan3.txt
+
+    # and for the swap:
+    mkdir /hive/data/genomes/panPan3/bed/blastz.mm10.swap
+    cd /hive/data/genomes/panPan3/bed/blastz.mm10.swap
+
+    time (doBlastzChainNet.pl -verbose=2 \
+      /hive/data/genomes/mm10/bed/lastzPanPan3.2020-06-15/DEF \
+        -swap -chainMinScore=3000 -chainLinearGap=medium \
+          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+            -syntenicNet) > swap.log 2>&1
+    #  real    106m54.032s
+
+    cat fb.panPan3.chainMm10Link.txt
+    # 911279510 bases of 2725937399 (33.430%) in intersection
+
+    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` panPan3 mm10) \
+       > rbest.log 2>&1
+    # real    620m0.039s
+
+##############################################################################