src/hg/makeDb/doc/rn4.txt 1.40
1.40 2010/04/01 17:34:25 hiram
done with Panda ailMel1 lastz
Index: src/hg/makeDb/doc/rn4.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/rn4.txt,v
retrieving revision 1.39
retrieving revision 1.40
diff -b -B -U 4 -r1.39 -r1.40
--- src/hg/makeDb/doc/rn4.txt 12 Mar 2010 17:12:24 -0000 1.39
+++ src/hg/makeDb/doc/rn4.txt 1 Apr 2010 17:34:25 -0000 1.40
@@ -5018,11 +5018,11 @@
cat fb.bosTau4.chainRn4Link.txt
# 664253901 bases of 2731830700 (24.315%) in intersection
#########################################################################
-# ailMel1 Panda alignment (DONE - 2010-01-21 - Hiram)
- mkdir /hive/data/genomes/rn4/bed/lastzAilMel1.2010-01-21
- cd /hive/data/genomes/rn4/bed/lastzAilMel1.2010-01-21
+# ailMel1 Panda alignment (DONE - 2010-02-04 - Hiram)
+ mkdir /hive/data/genomes/rn4/bed/lastzAilMel1.2010-02-04
+ cd /hive/data/genomes/rn4/bed/lastzAilMel1.2010-02-04
cat << '_EOF_' > DEF
# Rat vs. Panda
# parameters from the Panda paper supplemental where they describe
@@ -5049,32 +5049,32 @@
SEQ2_CHUNK=10000000
SEQ2_LIMIT=50
SEQ2_LAP=0
-BASE=/hive/data/genomes/rn4/bed/lastzAilMel1.2010-01-21
+BASE=/hive/data/genomes/rn4/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=pk \
-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
- # real 129m23.300s
+ # real 501m27.760s
cat fb.rn4.chainAilMel1Link.txt
- # 707335282 bases of 2571531505 (27.506%) in intersection
+ # 708197812 bases of 2571531505 (27.540%) in intersection
mkdir /hive/data/genomes/ailMel1/bed/blastz.rn4.swap
cd /hive/data/genomes/ailMel1/bed/blastz.rn4.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
- /hive/data/genomes/rn4/bed/lastzAilMel1.2010-01-21/DEF \
- -swap -noLoadChainSplit -syntenicNet \
+ /hive/data/genomes/rn4/bed/lastzAilMel1.2010-02-04/DEF \
+ -swap -syntenicNet \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
- # real 65m7.728s
+ # real 73m37.751s
cat fb.ailMel1.chainRn4Link.txt
- # 693099721 bases of 2225124764 (31.149%) in intersection
+ # 695366144 bases of 2245312831 (30.970%) in intersection
############################################################################
# tRNAs track (2010-03-12, Fan RE-BUILT)
#