src/hg/makeDb/doc/panTro2.txt 1.18
1.18 2010/02/12 23:51:36 hiram
last runs to Marmoset calJac3
Index: src/hg/makeDb/doc/panTro2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/panTro2.txt,v
retrieving revision 1.17
retrieving revision 1.18
diff -b -B -U 4 -r1.17 -r1.18
--- src/hg/makeDb/doc/panTro2.txt 20 Sep 2009 17:16:46 -0000 1.17
+++ src/hg/makeDb/doc/panTro2.txt 12 Feb 2010 23:51:36 -0000 1.18
@@ -3256,5 +3256,68 @@
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/panTro2/bed/lastzCalJac3.2010-02-11
+ cd /hive/data/genomes/panTro2/bed/lastzCalJac3.2010-02-11
+
+ # same kind of parameters as used in human<->marmoset
+ cat << '_EOF_' > DEF
+# chimp 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
+# other parameters from panTro2 vs hg18 lastz on advice from Webb
+BLASTZ_K=4500
+BLASTZ_Y=15000
+BLASTZ_T=2
+
+# TARGET: Chimp PanTro2
+SEQ1_DIR=/scratch/data/panTro2/panTro2.2bit
+SEQ1_LEN=/scratch/data/panTro2/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/panTro2/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 \
+ -stop=partition -syntenicNet \
+ -chainMinScore=5000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ > do.log 2>&1 &
+ # real 311m31.090s
+ cat fb.panTro2.chainCalJac3Link.txt
+ # 2016331285 bases of 2909485072 (69.302%) in intersection
+
+ mkdir /hive/data/genomes/calJac3/bed/blastz.panTro2.swap
+ cd /hive/data/genomes/calJac3/bed/blastz.panTro2.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/panTro2/bed/lastzCalJac3.2010-02-11/DEF \
+ -swap -noLoadChainSplit -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ -chainMinScore=5000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 118m42.203s
+ cat fb.calJac3.chainHg19Link.txt
+ # 1990168262 bases of 2752505800 (72.304%) in intersection
+
+############################################################################
+