src/hg/makeDb/doc/monDom5.txt 1.20
1.20 2010/03/29 16:01:28 hiram
done with susScr2 lastz and swap
Index: src/hg/makeDb/doc/monDom5.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/monDom5.txt,v
retrieving revision 1.19
retrieving revision 1.20
diff -b -B -U 4 -r1.19 -r1.20
--- src/hg/makeDb/doc/monDom5.txt 16 Feb 2010 04:47:42 -0000 1.19
+++ src/hg/makeDb/doc/monDom5.txt 29 Mar 2010 16:01:28 -0000 1.20
@@ -1581,4 +1581,52 @@
cat fb.calJac3.chainMonDom5Link.txt
# 217614612 bases of 2752505800 (7.906%) in intersection
##############################################################################
+# susScr2 Pig BLASTZ/CHAIN/NET (DONE - 2010-03-26,27 - Hiram)
+ screen # use a screen to manage this multi-day job
+ mkdir /hive/data/genomes/monDom5/bed/lastzSusScr2.2010-03-26
+ cd /hive/data/genomes/monDom5/bed/lastzSusScr2.2010-03-26
+
+ cat << '_EOF_' > DEF
+# Pig vs. Opossum
+BLASTZ_M=50
+
+# TARGET: Opossum MonDom5
+SEQ1_DIR=/scratch/data/monDom5/monDom5.2bit
+SEQ1_LEN=/scratch/data/monDom5/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Pig SusScr2
+SEQ2_DIR=/scratch/data/susScr2/susScr2.2bit
+SEQ2_LEN=/scratch/data/susScr2/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/monDom5/bed/lastzSusScr2.2010-03-26
+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=pk \
+ -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 &
+ # Elapsed time: 1132m5s
+ cat fb.monDom5.chainSusScr2Link.txt
+ # 179898307 bases of 3501660299 (5.138%) in intersection
+
+ mkdir /hive/data/genomes/susScr2/bed/blastz.monDom5.swap
+ cd /hive/data/genomes/susScr2/bed/blastz.monDom5.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/monDom5/bed/lastzSusScr2.2010-03-26/DEF \
+ -swap -noLoadChainSplit -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
+ -chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
+ # Elapsed time: 82m55s
+
+ cat fb.susScr2.chainMonDom5Link.txt
+ # 182834643 bases of 2231298548 (8.194%) in intersection
+
+#########################################################################