6091558bab452de0ba020f3e08a9d20ef9aa3d81
hiram
  Wed Mar 18 19:09:58 2020 -0700
lastz runs for 12-way alignment on danRer10 per research request no redmine

diff --git src/hg/makeDb/doc/xenTro9/lastzRuns.txt src/hg/makeDb/doc/xenTro9/lastzRuns.txt
index 2985ac2..d83b3c9 100644
--- src/hg/makeDb/doc/xenTro9/lastzRuns.txt
+++ src/hg/makeDb/doc/xenTro9/lastzRuns.txt
@@ -410,16 +410,82 @@
     cd /hive/data/genomes/xenTro9/bed/blastz.monDom5.swap
     time (doBlastzChainNet.pl -verbose=2 \
         /hive/data/genomes/monDom5/bed/lastzXenTro9.2017-04-05/DEF \
         -swap -syntenicNet \
         -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
         -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1
     #	real    63m13.594s
 
     cat fb.xenTro9.chainMonDom5Link.txt
     #	74164292 bases of 1369865365 (5.414%) in intersection
 
     time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` xenTro9 monDom5) \
            > rbest.log 2>&1 &
     #	real    798m41.569s
 
-############################################################################
+##############################################################################
+# zebrafish/danRer10 Lastz run  (DONE - 2020-02-25 - Hiram)
+    mkdir /hive/data/genomes/xenTro9/bed/lastzDanRer10.2020-02-25
+    cd /hive/data/genomes/xenTro9/bed/lastzDanRer10.2020-02-25
+
+    printf '# X. tropicalis vs. zebrafish
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
+BLASTZ_Y=3400
+BLASTZ_L=6000
+BLASTZ_K=2200
+BLASTZ_Q=/cluster/data/blastz/HoxD55.q
+
+# TARGET: X. tropicalis xenTro9
+SEQ1_DIR=/hive/data/genomes/xenTro9/xenTro9.2bit
+SEQ1_LEN=/hive/data/genomes/xenTro9/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=50
+
+# QUERY: zebrafish danRer10
+SEQ2_DIR=/hive/data/genomes/danRer10/danRer10.2bit
+SEQ2_LEN=/hive/data/genomes/danRer10/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+SEQ2_LIMIT=400
+
+BASE=/hive/data/genomes/xenTro9/bed/lastzDanRer10.2020-02-25
+TMPDIR=/dev/shm
+' > DEF
+
+    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
+        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+        -syntenicNet -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 &
+    #	real    352m56.937s
+
+    cat fb.xenTro9.chainDanRer10Link.txt
+    #	96287465 bases of 1369865365 (7.029%) in intersection
+
+    cat fb.xenTro9.chainSynDanRer10Link.txt
+    #   14698582 bases of 1369865365 (1.073%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+        xenTro9 danRer10) > rbest.log 2>&1 &
+    # real    199m53.878s
+
+    #	and for the swap
+    mkdir /hive/data/genomes/danRer10/bed/blastz.xenTro9.swap
+    cd /hive/data/genomes/danRer10/bed/blastz.xenTro9.swap
+    time (doBlastzChainNet.pl -verbose=2 -syntenicNet \
+	/hive/data/genomes/xenTro9/bed/lastzDanRer10.2020-02-25/DEF \
+        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+        -swap -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 &
+    #	real    23m32.189s
+
+    cat  fb.danRer10.chainXenTro9Link.txt
+    #	92191324 bases of 1369683683 (6.731%) in intersection
+    cat fb.danRer10.chainSynXenTro9Link.txt
+    #	15810671 bases of 1369683683 (1.154%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+          danRer10 xenTro9) > rbest.log 2>&1 &
+    #  real    221m8.515s
+
+    cat fb.danRer10.chainRBest.XenTro9.txt
+    #   54642559 bases of 1369683683 (3.989%) in intersection
+
+##############################################################################