src/hg/makeDb/doc/mm9.txt 1.125
1.125 2010/02/16 04:47:43 hiram
completed calJac3 lastz alignment
Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.124
retrieving revision 1.125
diff -b -B -U 4 -r1.124 -r1.125
--- src/hg/makeDb/doc/mm9.txt 9 Feb 2010 23:16:41 -0000 1.124
+++ src/hg/makeDb/doc/mm9.txt 16 Feb 2010 04:47:43 -0000 1.125
@@ -10031,9 +10031,8 @@
-swap -noLoadChainSplit -bigClusterHub=swarm -smallClusterHub=memk \
-workhorse=hgwdev \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
# real 54m57.140s
- # real 48m59.568s
cat fb.ailMel1.chainMm9Link.txt
# 739076250 bases of 2245312831 (32.916%) in intersection
############################################################################
@@ -10163,6 +10162,53 @@
mkdir /hive/data/gbdb/mm9/RNA-img
cp -p * /hive/data/gbdb/mm9/RNA-img
#####################################################################
+# LASTZ/CHAIN/NET Marmoset calJac3 (DONE - 2010-02-12 - Hiram)
+ # use a screen to control this job
+ screen
+ mkdir /hive/data/genomes/mm9/bed/lastzCalJac3.2010-02-12
+ cd /hive/data/genomes/mm9/bed/lastzCalJac3.2010-02-12
+ cat << '_EOF_' > DEF
+# mouse vs marmoset
+BLASTZ_M=50
+
+# TARGET: Mouse Mm9
+SEQ1_DIR=/scratch/data/mm9/nib
+SEQ1_LEN=/scratch/data/mm9/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_LIMIT=75
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/mm9/bed/lastzCalJac3.2010-02-12
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time nice -n +19 $HOME/kent/src/hg/utils/automation/doBlastzChainNet.pl \
+ -verbose=2 `pwd`/DEF \
+ -syntenicNet -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ > do.log 2>&1 &
+ # real 445m42.381s
+ cat fb.mm9.chainCalJac3Link.txt
+ # 859869647 bases of 2620346127 (32.815%) in intersection
+
+ mkdir /hive/data/genomes/calJac3/bed/blastz.mm9.swap
+ cd /hive/data/genomes/calJac3/bed/blastz.mm9.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/mm9/bed/lastzCalJac3.2010-02-12/DEF \
+ -swap -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 90m38.739s
+ cat fb.calJac3.chainHg19Link.txt
+ # 861811978 bases of 2752505800 (31.310%) in intersection
+
+#####################################################################