src/hg/makeDb/doc/mm9.txt 1.135
1.135 2010/04/20 17:34:31 chinhli
Finished lastz with Sheep oviAri1
Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.134
retrieving revision 1.135
diff -b -B -U 4 -r1.134 -r1.135
--- src/hg/makeDb/doc/mm9.txt 12 Apr 2010 21:32:37 -0000 1.134
+++ src/hg/makeDb/doc/mm9.txt 20 Apr 2010 17:34:31 -0000 1.135
@@ -10366,12 +10366,12 @@
featureBits mm9 vegaPseudoGene
# 3060300 bases of 2620346127 (0.117%) in intersection
#####################################################################
-# oviAri1 Sheep BLASTZ/CHAIN/NET (DONE - 2010-04-09 - Chin)
+# oviAri1 Sheep BLASTZ/CHAIN/NET (DONE - 2010-04-16 - Chin)
screen # use a screen to manage this multi-day job
- mkdir /hive/data/genomes/mm9/bed/lastzOviAri1.2010-04-09
- cd /hive/data/genomes/mm9/bed/lastzOviAri1.2010-04-09
+ mkdir /hive/data/genomes/mm9/bed/lastzOviAri1.2010-04-16
+ cd /hive/data/genomes/mm9/bed/lastzOviAri1.2010-04-16
cat << '_EOF_' > DEF
# Sheep vs. Mouse
BLASTZ_M=50
@@ -10387,9 +10387,9 @@
SEQ2_LEN=/scratch/data/oviAri1/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
-BASE=/hive/data/genomes/mm9/bed/lastzOviAri1.2010-04-09
+BASE=/hive/data/genomes/mm9/bed/lastzOviAri1.2010-04-16
TMPDIR=/scratch/tmp
'_EOF_'
# << this line keeps emacs coloring happy
@@ -10397,21 +10397,22 @@
`pwd`/DEF \
-noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
- # real 370m21.462s
+ # real 269m58.488s
cat fb.mm9.chainOviAri1Link.txt
# 406407377 bases of 2620346127 (15.510%) in intersection
# and the swap
mkdir /hive/data/genomes/oviAri1/bed/blastz.mm9.swap
cd /hive/data/genomes/oviAri1/bed/blastz.mm9.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
- /hive/data/genomes/mm9/bed/lastzOviAri1.2010-04-09/DEF \
+ /hive/data/genomes/mm9/bed/lastzOviAri1.2010-04-16/DEF \
-swap -noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
- # real 37m25.345s
+ # real 35m25.217s
+
cat fb.oviAri1.chainMm9Link.txt
# 383753361 bases of 1201271277 (31.946%) in intersection