src/hg/makeDb/doc/rheMac2.txt 1.20
1.20 2010/02/12 23:51:36 hiram
last runs to Marmoset calJac3
Index: src/hg/makeDb/doc/rheMac2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/rheMac2.txt,v
retrieving revision 1.19
retrieving revision 1.20
diff -b -B -U 4 -r1.19 -r1.20
--- src/hg/makeDb/doc/rheMac2.txt 25 Nov 2009 21:48:42 -0000 1.19
+++ src/hg/makeDb/doc/rheMac2.txt 12 Feb 2010 23:51:36 -0000 1.20
@@ -1609,5 +1609,66 @@
by a single Makefile. This is available from:
svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2009-09-13
see doc/builds.txt for specific details.
+
############################################################################
+# calJac3 Marmoset BLASTZ/CHAIN/NET (DONE - 2010-02-11 - Hiram)
+ screen # use a screen to manage this multi-day job
+ mkdir /hive/data/genomes/rheMac2/bed/lastzCalJac3.2010-02-11
+ cd /hive/data/genomes/rheMac2/bed/lastzCalJac3.2010-02-11
+
+ # same kind of parameters as used in human<->marmoset
+ cat << '_EOF_' > DEF
+# Rhesus vs. marmoset
+BLASTZ=lastz
+# maximum M allowed with lastz is only 254
+BLASTZ_M=254
+BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
+# and place those items here
+BLASTZ_O=600
+BLASTZ_E=150
+BLASTZ_K=4500
+BLASTZ_Y=15000
+BLASTZ_T=2
+
+# TARGET: Rhesus RheMac2
+SEQ1_DIR=/scratch/data/rheMac2/rheMac2.2bit
+SEQ1_LEN=/scratch/data/rheMac2/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=5
+
+# QUERY: Marmoset (calJac3)
+SEQ2_DIR=/scratch/data/calJac3/calJac3.2bit
+SEQ2_LEN=/scratch/data/calJac3/chrom.sizes
+SEQ2_LIMIT=50
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/rheMac2/bed/lastzCalJac3.2010-02-11
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << this line keeps emacs coloring happy
+
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -syntenicNet \
+ -chainMinScore=5000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ > do.log 2>&1 &
+ # real 248m5.651s
+ cat fb.rheMac2.chainCalJac3Link.txt
+ # 1871513554 bases of 2646704109 (70.711%) in intersection
+
+ mkdir /hive/data/genomes/calJac3/bed/blastz.rheMac2.swap
+ cd /hive/data/genomes/calJac3/bed/blastz.rheMac2.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/rheMac2/bed/lastzCalJac3.2010-02-11/DEF \
+ -swap -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ -chainMinScore=5000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 142m34.894s
+ cat fb.calJac3.chainHg19Link.txt
+ # 1916431926 bases of 2752505800 (69.625%) in intersection
+############################################################################
+