cdff74ba43136ebbc37d590fe95d2eaf43c8fcb6
hiram
  Fri Jun 5 09:37:29 2020 -0700
liftOver and chainNet to canFam4 refs #25279

diff --git src/hg/makeDb/doc/canFam3.txt src/hg/makeDb/doc/canFam3.txt
index 93deb3c..93db850 100644
--- src/hg/makeDb/doc/canFam3.txt
+++ src/hg/makeDb/doc/canFam3.txt
@@ -1021,21 +1021,89 @@
     # real    131m41.477s
 
 ##############################################################################
 # LIFTOVER TO canFam4 (DONE - 2020-04-02 - Hiram)
     ssh hgwdev
     mkdir /hive/data/genomes/canFam3/bed/blat.canFam4.2020-04-02
     cd /hive/data/genomes/canFam3/bed/blat.canFam4.2020-04-02
     doSameSpeciesLiftOver.pl -verbose=2 \
         -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/canFam3/jkStuff/canFam3.11.ooc \
          canFam3 canFam4
     time (doSameSpeciesLiftOver.pl -verbose=2 \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/canFam3/jkStuff/canFam3.11.ooc \
          canFam3 canFam4) > doLiftOverToCanFam4.log 2>&1
-XXX - running - Thu Apr  2 10:22:07 PDT 2020
     # real    1264m58.309s
 
     # see if the liftOver menus function in the browser from canFam3 to canFam4
 
 ##############################################################################
+# LASTZ German shepard canFam4 (DONE - 2020-05-11 - Hiram)
+    # establish a screen to control this job with a name to indicate what it is
+    screen -S canFam3CanFam4
+    mkdir /hive/data/genomes/canFam3/bed/lastzCanFam4.2020-05-11
+    cd /hive/data/genomes/canFam3/bed/lastzCanFam4.2020-05-11
+
+    printf '# boxer vs german shepard
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+BLASTZ_M=254
+
+# TARGET: boxer Tasha/canFam3
+SEQ1_DIR=/hive/data/genomes/canFam3/canFam3.2bit
+SEQ1_LEN=/hive/data/genomes/canFam3/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=30
+
+# QUERY: German shepard Mischka/canFam4
+SEQ2_DIR=/hive/data/genomes/canFam4/canFam4.2bit
+SEQ2_LEN=/hive/data/genomes/canFam4/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LIMIT=30
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/canFam3/bed/lastzCanFam4.2020-05-11
+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
+
+    cat fb.canFam3.chainCanFam4Link.txt
+    #	2362925930 bases of 2392715236 (98.755%) in intersection
+
+    cat fb.canFam3.chainSynCanFam4Link.txt
+    #   2353029988 bases of 2392715236 (98.341%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+	canFam3 canFam4) > rbest.log 2>&1 &
+    # 2318530060 bases of 2392715236 (96.900%) in intersection
+    # real    42m53.973s
+
+    # and the swap
+
+    mkdir /hive/data/genomes/canFam4/bed/blastz.canFam3.swap
+    cd /hive/data/genomes/canFam4/bed/blastz.canFam3.swap
+    time (doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/canFam3/bed/lastzCanFam4.2020-05-11/DEF \
+	-swap -syntenicNet \
+	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
+    # real    237m57.356s
+
+    cat fb.canFam4.chainCanFam3Link.txt
+    #	2441363671 bases of 2481941580 (98.365%) in intersection
+
+    cat fb.canFam4.chainSynCanFam3Link.txt
+    #   2422035026 bases of 2481941580 (97.586%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+	canFam4 canFam3) > rbest.log 2>&1
+    # real    46m50.771s
+
+    cat fb.canFam4.chainRBest.CanFam3.txt
+    # 2326711360 bases of 2481941580 (93.746%) in intersection
+
+##############################################################################