src/hg/makeDb/doc/monDom5.txt 1.19
1.19 2010/02/16 04:47:42 hiram
completed calJac3 lastz alignment
Index: src/hg/makeDb/doc/monDom5.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/monDom5.txt,v
retrieving revision 1.18
retrieving revision 1.19
diff -b -B -U 4 -r1.18 -r1.19
--- src/hg/makeDb/doc/monDom5.txt 6 Feb 2010 00:17:33 -0000 1.18
+++ src/hg/makeDb/doc/monDom5.txt 16 Feb 2010 04:47:42 -0000 1.19
@@ -1533,5 +1533,52 @@
# real 69m35.464s
cat fb.ailMel1.chainMonDom5Link.txt
# 211209682 bases of 2245312831 (9.407%) in intersection
-#########################################################################
+##############################################################################
+# calJac3 Marmoset LASTZ/CHAIN/NET (DONE - 2010-02-12 - Hiram)
+ screen # use a screen to manage this multi-day job
+ mkdir /hive/data/genomes/monDom5/bed/lastzCalJac3.2010-02-12
+ cd /hive/data/genomes/monDom5/bed/lastzCalJac3.2010-02-12
+
+ cat << '_EOF_' > DEF
+# Marmoset 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: Marmoset CalJac3
+SEQ2_DIR=/scratch/data/calJac3/calJac3.2bit
+SEQ2_LEN=/scratch/data/calJac3/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/monDom5/bed/lastzCalJac3.2010-02-12
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << this line keeps emacs coloring happy
+
+ time nice -n +19 $HOME/kent/src/hg/utils/automation/doBlastzChainNet.pl \
+ -verbose=2 `pwd`/DEF \
+ -syntenicNet -workhorse=hgwdev -smallClusterHub=memk \
+ -bigClusterHub=swarm -chainMinScore=5000 -chainLinearGap=loose \
+ > do.log 2>&1 &
+ # real 2772m44.886s
+ cat fb.monDom5.chainCalJac3Link.txt
+ # 216197506 bases of 3501660299 (6.174%) in intersection
+
+ mkdir /hive/data/genomes/calJac3/bed/blastz.monDom5.swap
+ cd /hive/data/genomes/calJac3/bed/blastz.monDom5.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/monDom5/bed/lastzCalJac3.2010-02-12/DEF \
+ -swap -noLoadChainSplit -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ -chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
+ # real 110m13.435s
+ cat fb.calJac3.chainMonDom5Link.txt
+ # 217614612 bases of 2752505800 (7.906%) in intersection
+
+##############################################################################