a8c34aed0a71d4674178d116c7a8ec99186377b2
hiram
  Tue Aug 18 08:51:45 2020 -0700
lastz chainNet to canFam5 complete refs #25917

diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt
index efef10d..f2ab9d1 100644
--- src/hg/makeDb/doc/hg38/lastzRuns.txt
+++ src/hg/makeDb/doc/hg38/lastzRuns.txt
@@ -12729,59 +12729,57 @@
 
     time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
         -chainMinScore=3000 -chainLinearGap=medium \
           -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
             -syntenicNet) > do.log 2>&1
     # real    1038m20.721s
 
     cat fb.hg38.chainCanFam5Link.txt
     # 1545648756 bases of 3110768607 (49.687%) in intersection
 
     cat fb.hg38.chainSynCanFam5Link.txt
     # 1484758745 bases of 3110768607 (47.730%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
 	hg38 canFam5) > rbest.log 2>&1 &
-XXX - running - Mon Aug 17 12:41:45 PDT 2020
-    # real    310m32.196s
+    # real    283m55.399s
 
     cat fb.hg38.chainRBest.CanFam5.txt
-    # 1425406620 bases of 3110768607 (45.822%) in intersection
+    # 1422619513 bases of 3110768607 (45.732%) in intersection
 
     # and for the swap:
     mkdir /hive/data/genomes/canFam5/bed/blastz.hg38.swap
     cd /hive/data/genomes/canFam5/bed/blastz.hg38.swap
 
     time (doBlastzChainNet.pl -verbose=2 \
       /hive/data/genomes/hg38/bed/lastzCanFam5.2020-07-29/DEF \
         -swap -chainMinScore=3000 -chainLinearGap=medium \
           -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
             -syntenicNet) > swap.log 2>&1
-XXX - running - Mon Aug 17 12:42:53 PDT 2020
-    #  real    99m10.990s
+    #  real    78m37.078s
 
     cat fb.canFam5.chainHg38Link.txt
-    # 1493209286 bases of 2481941580 (60.163%) in intersection
+    # 1460025525 bases of 2337131234 (62.471%) in intersection
     cat fb.canFam5.chainSynHg38Link.txt
-    # 1448164376 bases of 2481941580 (58.348%) in intersection
+    # 1423305734 bases of 2337131234 (60.900%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
 	canFam5 hg38) > rbest.log 2>&1 &
-    # real    257m59.713s
+    # real    255m9.076s
 
     cat fb.canFam5.chainRBest.Hg38.txt
-    # 1425296830 bases of 2481941580 (57.427%) in intersection
+    # 1422612399 bases of 2337131234 (60.870%) in intersection
 
 ############################################################################
 # LASTZ MOUSE Mm39 (DONE - 2020-08-17 - Hiram)
     # can no longer use the lineage specific repeats with the new lastz
     # use a screen to manage this longish job:
     screen -S hg38Mm39
 
     mkdir /hive/data/genomes/hg38/bed/lastzMm39.2020-08-17
     cd /hive/data/genomes/hg38/bed/lastzMm39.2020-08-17
 
     # best to always specify an exact path to lastz so we know which one is used
     # lastz default parameters are human-mouse parameters
 
     printf '# human vs mouse
 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz