src/hg/makeDb/doc/hg19.txt 1.82
1.82 2010/02/12 23:43:45 hiram
rerun the Panda lastz, and the calJac3
Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.81
retrieving revision 1.82
diff -b -B -U 4 -r1.81 -r1.82
--- src/hg/makeDb/doc/hg19.txt 9 Feb 2010 23:15:08 -0000 1.81
+++ src/hg/makeDb/doc/hg19.txt 12 Feb 2010 23:43:45 -0000 1.82
@@ -8316,11 +8316,11 @@
-tab -sqlTable=$HOME/kent/src/hg/lib/gwasCatalog.sql -notItemRgb -allowStartEqualEnd
########################################################################
-# ailMel1 Panda alignment (DONE - 2010-01-21 - Hiram)
- mkdir /hive/data/genomes/hg19/bed/lastzAilMel1.2010-01-21
- cd /hive/data/genomes/hg19/bed/lastzAilMel1.2010-01-21
+# ailMel1 Panda alignment (DONE - 2010-02-04 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzAilMel1.2010-02-04
+ cd /hive/data/genomes/hg19/bed/lastzAilMel1.2010-02-04
cat << '_EOF_' > DEF
# Human vs. Panda
# parameters from the Panda paper supplemental where they describe
@@ -8347,32 +8347,32 @@
SEQ2_CHUNK=10000000
SEQ2_LIMIT=50
SEQ2_LAP=0
-BASE=/hive/data/genomes/hg19/bed/lastzAilMel1.2010-01-21
+BASE=/hive/data/genomes/hg19/bed/lastzAilMel1.2010-02-04
TMPDIR=/scratch/tmp
'_EOF_'
# << happy emacs
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF \
-noLoadChainSplit -syntenicNet \
- -workhorse=hgwdev -smallClusterHub=pk -bigClusterHub=swarm \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
- # real 150m41.538s
+ # real 434m21.792s
cat fb.hg19.chainAilMel1Link.txt
- # 1449290504 bases of 2897316137 (50.022%) in intersection
+ # 1453400264 bases of 2897316137 (50.164%) in intersection
mkdir /hive/data/genomes/ailMel1/bed/blastz.hg19.swap
cd /hive/data/genomes/ailMel1/bed/blastz.hg19.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
- /hive/data/genomes/hg19/bed/lastzAilMel1.2010-01-21/DEF \
+ /hive/data/genomes/hg19/bed/lastzAilMel1.2010-02-04/DEF \
-swap -noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
- # real 104m38.416s
+ real 124m14.393s
cat fb.ailMel1.chainHg19Link.txt
- # 1403163838 bases of 2225124764 (63.060%) in intersection
+ # 1411953704 bases of 2245312831 (62.884%) in intersection
#########################################################################
# susScr1 Pig BLASTZ/CHAIN/NET (DONE - 2010-01-21 - Hiram)
screen # use a screen to manage this multi-day job
@@ -8531,6 +8531,64 @@
mkdir /hive/data/gbdb/hg19/RNA-img
cp -p * /hive/data/gbdb/hg19/RNA-img
#####################################################################
+# calJac3 Marmoset BLASTZ/CHAIN/NET (DONE - 2010-01-21 - Hiram)
+ screen # use a screen to manage this multi-day job
+ mkdir /hive/data/genomes/hg19/bed/lastzCalJac3.2010-02-11
+ cd /hive/data/genomes/hg19/bed/lastzCalJac3.2010-02-11
+
+ cat << '_EOF_' > DEF
+# human 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: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/hg19.2bit
+SEQ1_LEN=/scratch/data/hg19/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/hg19/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 287m24.258s
+ cat fb.hg19.chainCalJac3Link.txt
+ # 2047068864 bases of 2897316137 (70.654%) in intersection
+ mkdir /hive/data/genomes/calJac3/bed/blastz.hg19.swap
+ cd /hive/data/genomes/calJac3/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzCalJac3.2010-02-11/DEF \
+ -swap -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ -chainMinScore=5000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 120m42.991s
+ cat fb.calJac3.chainHg19Link.txt
+ # 2030475813 bases of 2752505800 (73.768%) in intersection
+#####################################################################