src/hg/makeDb/doc/felCatV17e.txt 1.5

Index: src/hg/makeDb/doc/felCatV17e.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/felCatV17e.txt,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 4 -r1.4 -r1.5
--- src/hg/makeDb/doc/felCatV17e.txt	30 Mar 2010 21:23:39 -0000	1.4
+++ src/hg/makeDb/doc/felCatV17e.txt	30 Mar 2010 22:54:33 -0000	1.5
@@ -467,12 +467,45 @@
 
     #   cleanup
     rm -fr hardMaskedFa
 
-
-#####################################################################
-# LASTZ Dog Swap (DONE - 2010-03-22 - Chin)
+#######################################################################
+# felCatV17e Cat BLASTZ/CHAIN/NET (DONE  - 2010-03-22 - Chin)
+    screen # use a screen to manage this multi-day job
+    mkdir /hive/data/genomes/canFam2/bed/lastzFelCatV17e.2010-03-22
     cd /hive/data/genomes/canFam2/bed/lastzFelCatV17e.2010-03-22
+
+    cat << '_EOF_' > DEF
+# dog vs. cat
+# maximum M allowed with lastz is only 254
+BLASTZ_M=254
+
+# TARGET: Dog canFan2
+SEQ1_DIR=/scratch/data/canFam2/canFam2.2bit
+SEQ1_LEN=/scratch/data/canFam2/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=5
+
+# QUERY: Cat (felCatV17e)
+SEQ2_DIR=/scratch/data/felCatV17e/felCatV17e.2bit
+SEQ2_LEN=/scratch/data/felCatV17e/chrom.sizes
+SEQ2_LIMIT=50
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/canFam2/bed/lastzFelCatV17e.2010-03-22
+TMPDIR=/scratch/tmp
+'_EOF_'
+    # << this line keeps emacs coloring happy
+
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+        `pwd`/DEF \
+        -syntenicNet -noDbNameCheck \
+        -chainMinScore=3000 -chainLinearGap=medium \
+        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+        > do.log 2>&1 &
+    #   real    287m24.258s
     cat fb.canFam2.chainFelCatV17eLink.txt
     #  1481040604 bases of 2384996543 (62.098%) in intersection
 
     mkdir /hive/data/genomes/felCatV17e/bed/blastz.canFam2.swap