src/hg/makeDb/doc/mm9.txt 1.107

Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.106
retrieving revision 1.107
diff -b -B -U 4 -r1.106 -r1.107
--- src/hg/makeDb/doc/mm9.txt	23 Aug 2009 04:14:30 -0000	1.106
+++ src/hg/makeDb/doc/mm9.txt	27 Aug 2009 18:05:07 -0000	1.107
@@ -9578,4 +9578,59 @@
    # Loaded succesfully
    # Added code to hgc.c to use printEnsemblOrVegaCustomUrl() in 
    # doVegaGene() to add the links to Vega reports on the details pages.
 ############################################################################
+# Blastz Elephant loxAfr3 (DONE - 2009-08-12 - Hiram)
+    mkdir /hive/data/genomes/mm9/bed/lastzLoxAfr3.2009-08-12
+    cd /hive/data/genomes/mm9/bed/lastzLoxAfr3.2009-08-12
+
+    cat << '_EOF_' > DEF
+# Mouse vs. Elephant
+BLASTZ_M=50
+
+# TARGET: Mouse Mm9
+SEQ1_DIR=/scratch/data/mm9/nib
+SEQ1_LEN=/scratch/data/mm9/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Elephant loxAfr3
+SEQ2_DIR=/scratch/data/loxAfr3/loxAfr3.2bit
+SEQ2_LEN=/scratch/data/loxAfr3/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=50
+SEQ2_LAP=0
+
+BASE=/cluster/data/mm9/bed/lastzLoxAfr3.2009-08-12
+TMPDIR=/scratch/tmp
+'_EOF_'
+    # << happy emacs
+
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+	`pwd`/DEF \
+	-noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
+	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+	> do.log 2>&1 &
+    #	real 498m44.261s
+    cat fb.mm9.chainLoxAfr3Link.txt
+    #	684326090 bases of 2620346127 (26.116%) in intersection
+
+    #	trying syntenic nets
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+	`pwd`/DEF \
+	-noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
+	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+	-continue=syntenicNet -syntenicNet > syntenicNet.log 2>&1 &
+    #	about 20 minutes
+
+    mkdir /hive/data/genomes/loxAfr3/bed/blastz.mm9.swap
+    cd /hive/data/genomes/loxAfr3/bed/blastz.mm9.swap
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/mm9/bed/lastzLoxAfr3.2009-08-12/DEF \
+	-swap -noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
+	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+	-syntenicNet > swap.log 2>&1 &
+    #	real    123m9.342s
+    cat fb.loxAfr3.chainMm9Link.txt 
+    #	673856452 bases of 3118565340 (21.608%) in intersection
+
+#########################################################################