0fee4835763cc67799a462b1d0c90d66a40f2f02
hiram
  Mon Aug 17 12:45:51 2020 -0700
lastz chainNet mm10 to canFam5 in progress refs #25917

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index 9035587..682282d 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -17922,52 +17922,53 @@
 # QUERY: German shepard canFam5
 SEQ2_DIR=/hive/data/genomes/canFam5/canFam5.2bit
 SEQ2_LEN=/hive/data/genomes/canFam5/chrom.sizes
 SEQ2_CHUNK=10000000
 SEQ2_LIMIT=20
 SEQ2_LAP=0
 
 BASE=/hive/data/genomes/mm10/bed/lastzCanFam5.2020-07-29
 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 &
-XXX - running - Wed Jul 29 13:30:41 PDT 2020
-    #	real    483m10.607s
+    #	real    1052m41.484s
 
     cat fb.mm10.chainCanFam5Link.txt
-    #	777883731 bases of 2652783500 (29.323%) in intersection
+    #	776486006 bases of 2652783500 (29.271%) in intersection
     cat fb.mm10.chainSynCanFam5Link.txt
-    #   736602602 bases of 2652783500 (27.767%) in intersection
+    #   735561772 bases of 2652783500 (27.728%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev mm10 canFam5 \
       -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
+XXX - running - Mon Aug 17 12:44:00 PDT 2020
     #	real    219m16.168s
 
     cat fb.mm10.chainRBest.CanFam5.txt
     # 741307883 bases of 2652783500 (27.945%) in intersection
 
     mkdir /hive/data/genomes/canFam5/bed/blastz.mm10.swap
     cd /hive/data/genomes/canFam5/bed/blastz.mm10.swap
     time (doBlastzChainNet.pl -verbose=2 \
 	/hive/data/genomes/mm10/bed/lastzCanFam5.2020-07-29/DEF \
 	-swap -syntenicNet \
 	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
 	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 &
+XXX - running - Mon Aug 17 12:44:00 PDT 2020
     #	real    50m20.639s
 
     cat fb.canFam5.chainMm10Link.txt
     #	772902855 bases of 2481941580 (31.141%) in intersection
     cat fb.canFam5.chainSynMm10Link.txt
     #   737924732 bases of 2481941580 (29.732%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev canFam5 mm10 \
       -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
     # real    173m38.016s
 
     cat fb.canFam5.chainRBest.Mm10.txt
     # 740357755 bases of 2481941580 (29.830%) in intersection
 
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