44a2961414996cf4348b33a8c7daceacd3a3456e
hiram
  Tue Apr 27 14:50:55 2021 -0700
completed lastz/chain/net to mm10 mm39 hg38 for rn7 release refs #26682

diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt
index ab2ff25..8a945bc 100644
--- src/hg/makeDb/doc/mm39/lastzRuns.txt
+++ src/hg/makeDb/doc/mm39/lastzRuns.txt
@@ -1979,61 +1979,63 @@
 sed -e 's/^/    # /;' fb.$targetDb.chain.${asmId}Link.txt
     # 67418947 bases of 2728222451 (2.471%) in intersection
 sed -e 's/^/    # /;' fb.$targetDb.chainSyn.${asmId}Link.txt
     # 12681011 bases of 2728222451 (0.465%) in intersection
 
 time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
 -query2Bit="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.2bit" \
 -querySizes="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.chrom.sizes.txt" \
 $targetDb ${asmId}) >> rbest.log 2>&1
 grep -w real rbest.log | sed -e 's/^/    # /;'
     # real    323m14.591s
 
 sed -e 's/^/    # /;' fb.$targetDb.chainRBest.$asmId.txt
     # 52282223 bases of 2728222451 (1.916%) in intersection
 
-### XXX haven't done this yet
 export target="mm39"
 export Target="Mm39"
 export query="GCF_009829145.1"
 export asmId="GCF_009829145.1_bChiLan1.pri"
 export gcPath="GCF/009/829/145"
 
 mkdir /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap
 cd /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap
 
 time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 -swapDir=`pwd` \
     /hive/data/genomes/${target}/bed/lastz.${query}/DEF -syntenicNet \
   -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
     -swap -chainMinScore=3000 -chainLinearGap=medium) >> swap.log 2>&1
 grep -w real swap.log | sed -e 's/^/    # /;'
-    # real      70m57.610s
+    # real      5m33.993s
 
 sed -e 's/^/    # /;' fb.${query}.chain.${Target}Link.txt
-    # 1021869459 bases of 2518306565 (40.578%) in intersection
+    # 56730326 bases of 1089631598 (5.206%) in intersection
 sed -e 's/^/    # /;' fb.${query}.chainSyn.${Target}Link.txt
-    # 879061651 bases of 2518306565 (34.907%) in intersection
+    # 12678262 bases of 1089631598 (1.164%) in intersection
 
 time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
 -target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \
 $query $target) >> rbest.log 2>&1
 grep -w real rbest.log | sed -e 's/^/    # /;'
-    # real      294m45.010s
+    # real      288m55.058s
 
 sed -e 's/^/    # /;' fb.${query}.chainRBest.${Target}.txt
-    # 913513030 bases of 2518306565 (36.275%) in intersection
+    # 51851922 bases of 1089631598 (4.759%) in intersection
+
+    # overall time for all swap
+    # real    294m29.066s
 
 ##############################################################################
 # LASTZ  Chinese hamster CHO GCF_003668045.3 (DONE - 2020-12-08 - Hiram)
     mkdir /hive/data/genomes/mm39/bed/lastzGCF_003668045.3.2020-12-08
     cd /hive/data/genomes/mm39/bed/lastzGCF_003668045.3.2020-12-08
 
     printf '# GCF_003668045.3 vs mm39
 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
 # TARGET: Mouse Mm39
 SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
 SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
 SEQ1_CHUNK=20000000
 SEQ1_LAP=10000
 
 # QUERY: Chinese hamster GCF_003668045.3