92caabd2ff459cd75f8b5451f9d0f7fa5043d3b9
hiram
  Fri Feb 25 10:58:18 2022 -0800
finished lastz to bosTau9 no redmine

diff --git src/hg/makeDb/doc/rn7/lastzRuns.txt src/hg/makeDb/doc/rn7/lastzRuns.txt
index dd93900..68f4cd6 100644
--- src/hg/makeDb/doc/rn7/lastzRuns.txt
+++ src/hg/makeDb/doc/rn7/lastzRuns.txt
@@ -1,73 +1,74 @@
 #############################################################################
 # LASTZ rat/rn7 vs. cow bosTau9 (WORKING - 2021-04-28 - Hiram)
 
     mkdir /hive/data/genomes/rn7/bed/lastzBosTau9.2021-04-28
     cd /hive/data/genomes/rn7/bed/lastzBosTau9.2021-04-28
 
     printf '# Rat vs. cow bosTau9
 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
 BLASTZ_M=254
 BLASTZ_Y=3400
 BLASTZ_L=6000
 BLASTZ_K=2200
 BLASTZ_Q=/hive/data/staging/data/blastz/HoxD55.q
 
 # TARGET: Rat Rn7
 SEQ1_DIR=/hive/data/genomes/rn7/rn7.2bit
 SEQ1_LEN=/hive/data/genomes/rn7/chrom.sizes
 SEQ1_CHUNK=20000000
 SEQ1_LAP=10000
 SEQ1_LIMIT=5
 
 # QUERY: cow bosTau9
 SEQ2_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit
 SEQ2_LEN=/hive/data/genomes/bosTau9/chrom.sizes
 SEQ2_CHUNK=20000000
 SEQ2_LAP=0
 SEQ2_LIMIT=20
 
 BASE=/hive/data/genomes/rn7/bed/lastzBosTau9.2021-04-28
 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    798m53.424s
+    # real    304m14.733s
 
-    cat fb.rn7.chainBosTau9.txt
-    # 1717059254 bases of 2729860805 (62.899%) in intersection
-    cat fb.rn7.chainSynBosTau9.txt
-    # 1453767990 bases of 2729860805 (53.254%) in intersection
+    sed -e 's/^/    # /;' fb.rn7.chainBosTau9Link.txt
+    # 872723875 bases of 2626580772 (33.227%) in intersection
+    sed -e 's/^/    # /;' fb.rn7.chainSynBosTau9Link.txt
+    # 775681551 bases of 2626580772 (29.532%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
 	rn7 bosTau9) > rbest.log 2>&1 &
-    # real    1789m7.359s
+    # real    648m32.765s
 
-    cat fb.rn7.chainRBest.BosTau9.txt
-    # 1436075393 bases of 2729860805 (52.606%) in intersection
+    sed -e 's/^/    # /;' fb.rn7.chainRBest.BosTau9.txt
+    # 796235597 bases of 2626580772 (30.315%) in intersection
 
     # and for the swap:
     mkdir /hive/data/genomes/bosTau9/bed/blastz.rn7.swap
     cd /hive/data/genomes/bosTau9/bed/blastz.rn7.swap
 
     time (doBlastzChainNet.pl -verbose=2 \
       /hive/data/genomes/rn7/bed/lastzBosTau9.2021-04-28/DEF \
         -swap -chainMinScore=3000 -chainLinearGap=medium \
           -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
-            -noDbNameCheck -syntenicNet) > swap.log 2>&1
-    #  real    79m18.904s
+            -syntenicNet) > swap.log 2>&1
+    #  real    93m58.566s
 
-    cat fb.bosTau9.chainRn7Link.txt
-    # 1694175880 bases of 2266312740 (74.755%) in intersection
-    cat fb.bosTau9.chainSynRn7Link.txt
-    # 1402196536 bases of 2266312740 (61.871%) in intersection
+    sed -e 's/^/    # /;' fb.bosTau9.chainRn7Link.txt
+    # 857332479 bases of 2715853792 (31.568%) in intersection
+
+    sed -e 's/^/    # /;' fb.bosTau9.chainSynRn7Link.txt
+    # 779374329 bases of 2715853792 (28.697%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
 	bosTau9 rn7) > rbest.log 2>&1 &
-    # real    1687m33.035s
+    # real    533m51.949s
 
     cat fb.bosTau9.chainRBest.Rn7.txt
-    # 1435220608 bases of 2266312740 (63.328%) in intersection
+    # 794580345 bases of 2715853792 (29.257%) in intersection
 
 ##############################################################################