src/hg/makeDb/doc/equCab2.txt 1.30

Index: src/hg/makeDb/doc/equCab2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/equCab2.txt,v
retrieving revision 1.29
retrieving revision 1.30
diff -b -B -U 4 -r1.29 -r1.30
--- src/hg/makeDb/doc/equCab2.txt	5 Feb 2010 00:06:41 -0000	1.29
+++ src/hg/makeDb/doc/equCab2.txt	12 Apr 2010 21:32:38 -0000	1.30
@@ -2370,5 +2370,56 @@
 # xenoRefGene - (2010-02-04 markd)
 
    # enable xeno RefSeq track per user request: add to etc/genbank.conf:
 equCab2.refseq.mrna.xeno.load = yes
+
+#####################################################################
+# oviAri1 Sheep BLASTZ/CHAIN/NET (DONE - 2010-04-09 - Chin)
+    screen # use a screen to manage this multi-day job
+    mkdir /hive/data/genomes/equCab2/bed/lastzOviAri1.2010-04-09
+    cd /hive/data/genomes/equCab2/bed/lastzOviAri1.2010-04-09
+
+    cat << '_EOF_' > DEF
+# Sheep vs. Mouse
+BLASTZ_M=50
+
+# TARGET: Horse EquCab2
+SEQ1_DIR=/scratch/data/equCab2/equCab2.2bit
+SEQ1_LEN=/scratch/data/equCab2/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Sheep OviAri1
+SEQ2_DIR=/scratch/data/oviAri1/oviAri1.2bit
+SEQ2_LEN=/scratch/data/oviAri1/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/equCab2/bed/lastzOviAri1.2010-04-09
+TMPDIR=/scratch/tmp
+'_EOF_'
+    # << this line keeps emacs coloring happy
+
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+        `pwd`/DEF \
+        -noLoadChainSplit -syntenicNet \
+        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+        -chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+    #   Elapsed time: 433m14s
+    cat fb.equCab2.chainOviAri1Link.txt
+    #   1012763540 bases of 2428790173 (41.698%) in intersection 
+
+    mkdir /hive/data/genomes/oviAri1/bed/blastz.equCab2.swap
+    cd /hive/data/genomes/oviAri1/bed/blastz.equCab2.swap
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+        /hive/data/genomes/equCab2/bed/lastzOviAri1.2010-04-09/DEF \
+        -swap -noLoadChainSplit -syntenicNet \
+        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
+        -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+    #    real    100m49.583s
+
+
+    cat fb.oviAri1.chainEquCab2Link.txt
+    #   940763026 bases of 1201271277 (78.314%) in intersection
+
+
 ############################################################################