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

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index 56315a2..396679f 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -17852,48 +17852,54 @@
 # 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 \
+          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
             -syntenicNet) > do.log 2>&1
-XXX - running - Mon Jun 15 10:19:12 PDT 2020
-    # real    360m9.534s
+    # real    385m29.712s
 
     cat fb.mm10.chainPanPan3Link.txt
-    # 928638440 bases of 2652783500 (35.006%) in intersection
+    # 935579510 bases of 2652783500 (35.268%) in intersection
     cat fb.mm10.chainSynPanPan3Link.txt
+    # 888900388 bases of 2652783500 (33.508%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` mm10 panPan3) \
       > rbest.log 2>&1 &
-    # real    765m26.648s
+    # real    329m28.051s
     cat fb.mm10.chainRBest.PanPan3.txt
+    # 890894306 bases of 2652783500 (33.583%) in intersection
 
     # 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 \
+          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
             -syntenicNet) > swap.log 2>&1
-    #  real    106m54.032s
+    #  real    55m23.982s
 
     cat fb.panPan3.chainMm10Link.txt
-    # 911279510 bases of 2725937399 (33.430%) in intersection
+    # 954214151 bases of 3015350297 (31.645%) in intersection
+    cat fb.panPan3.chainSynMm10Link.txt
+    # 887980807 bases of 3015350297 (29.449%) in intersection
 
-    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` panPan3 mm10) \
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` panPan3 mm10) \
        > rbest.log 2>&1
+XXX - running - Tue Jun 16 12:57:31 PDT 2020
     # real    620m0.039s
 
+    cat fb.panPan3.chainRBest.Mm01.txt
+
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