6a31a3cb05530a6c630b865796b58d4406f3ea0e
hiram
  Tue Jun 16 13:21:58 2020 -0700
lastz chain Net to panPan3 refs #25720

diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt
index e1e180c..2ca3a12 100644
--- src/hg/makeDb/doc/hg38/lastzRuns.txt
+++ src/hg/makeDb/doc/hg38/lastzRuns.txt
@@ -12602,15 +12602,97 @@
     #  real    99m10.990s
 
     cat fb.canFam4.chainHg38Link.txt
     # 1493209286 bases of 2481941580 (60.163%) in intersection
     cat fb.canFam4.chainSynHg38Link.txt
     # 1448164376 bases of 2481941580 (58.348%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
 	canFam4 hg38) > rbest.log 2>&1 &
     # real    257m59.713s
 
     cat fb.canFam4.chainRBest.Hg38.txt
     # 1425296830 bases of 2481941580 (57.427%) in intersection
 
 #########################################################################
+# LASTZ human/hg38 bonobo/panPan3 - (DONE - 2020-06-15 - Hiram)
+    mkdir /hive/data/genomes/hg38/bed/lastzPanPan3.2020-06-15
+    cd /hive/data/genomes/hg38/bed/lastzPanPan3.2020-06-15
+
+    printf '# human vs bonobo
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+BLASTZ_T=2
+BLASTZ_O=600
+BLASTZ_E=150
+BLASTZ_M=254
+BLASTZ_K=4500
+BLASTZ_L=4500
+BLASTZ_Y=15000
+BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
+#       A     C     G     T
+# A    90  -330  -236  -356
+# C  -330   100  -318  -236
+# G  -236  -318   100  -330
+# T  -356  -236  -330    90
+
+# 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=10
+SEQ1_LAP=10000
+
+# QUERY: bonobo panPan3
+SEQ2_DIR=/hive/data/genomes/panPan3/panPan3.2bit
+SEQ2_LEN=/hive/data/genomes/panPan3/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=50
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg38/bed/lastzPanPan3.2020-06-15
+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    117m56.403s
+
+    cat fb.hg38.chainPanPan3Link.txt
+    # 2897225010 bases of 3110768607 (93.135%) in intersection
+
+    cat fb.hg38.chainSynPanPan3Link.txt
+    # 2880116277 bases of 3110768607 (92.585%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+	hg38 panPan3) > rbest.log 2>&1 &
+    # real    68m45.187s
+    cat fb.hg38.chainRBest.PanPan3.txt
+    # 2727319248 bases of 3110768607 (87.673%) in intersection
+
+    # and for the swap:
+    mkdir /hive/data/genomes/panPan3/bed/blastz.hg38.swap
+    cd /hive/data/genomes/panPan3/bed/blastz.hg38.swap
+
+    time (doBlastzChainNet.pl -verbose=2 \
+      /hive/data/genomes/hg38/bed/lastzPanPan3.2020-06-15/DEF \
+        -swap -chainMinScore=3000 -chainLinearGap=medium \
+          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+            -syntenicNet) > swap.log 2>&1
+    #  real    73m50.456s
+
+    cat fb.panPan3.chainHg38Link.txt
+    # 2777869191 bases of 3015350297 (92.124%) in intersection
+    cat fb.panPan3.chainSynHg38Link.txt
+    # 2768018012 bases of 3015350297 (91.798%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+      panPan3 hg38) > rbest.log 2>&1 &
+    # real    66m52.340s
+    cat fb.panPan3.chainRBest.Hg38.txt
+    # 2732415393 bases of 3015350297 (90.617%) in intersection
+
+#########################################################################