src/hg/makeDb/doc/monDom5.txt 1.23
1.23 2010/04/20 17:34:31 chinhli
Finished lastz with Sheep oviAri1
Index: src/hg/makeDb/doc/monDom5.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/monDom5.txt,v
retrieving revision 1.22
retrieving revision 1.23
diff -b -B -U 4 -r1.22 -r1.23
--- src/hg/makeDb/doc/monDom5.txt 12 Apr 2010 21:32:38 -0000 1.22
+++ src/hg/makeDb/doc/monDom5.txt 20 Apr 2010 17:34:31 -0000 1.23
@@ -1687,12 +1687,12 @@
cat fb.susScr2.chainMonDom5Link.txt
# 182834643 bases of 2231298548 (8.194%) in intersection
##############################################################################
-# oviAri1 Sheep BLASTZ/CHAIN/NET (working - 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/monDom5/bed/lastzOviAri1.2010-04-09
- cd /hive/data/genomes/monDom5/bed/lastzOviAri1.2010-04-09
+ mkdir /hive/data/genomes/monDom5/bed/lastzOviAri1.2010-04-16
+ cd /hive/data/genomes/monDom5/bed/lastzOviAri1.2010-04-16
cat << '_EOF_' > DEF
# Sheep vs. Opossum
BLASTZ_M=50
@@ -1708,30 +1708,30 @@
SEQ2_LEN=/scratch/data/oviAri1/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
-BASE=/hive/data/genomes/monDom5/bed/lastzOviAri1.2010-04-09
+BASE=/hive/data/genomes/monDom5/bed/lastzOviAri1.2010-04-16
TMPDIR=/scratch/tmp
'_EOF_'
# << this line keeps emacs coloring happy
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF \
-noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
-chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 &
- # Elapsed time: 529m47s
+ # real 756m34.317s
cat fb.monDom5.chainOviAri1Link.txt
# 133534458 bases of 3501660299 (3.813%) in intersection
-
# and the swap
+
mkdir /hive/data/genomes/oviAri1/bed/blastz.monDom5.swap
cd /hive/data/genomes/oviAri1/bed/blastz.monDom5.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
- /hive/data/genomes/monDom5/bed/lastzOviAri1.2010-04-09/DEF \
+ /hive/data/genomes/monDom5/bed/lastzOviAri1.2010-04-16/DEF \
-swap -noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=memn -bigClusterHub=pk \
-chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
- # real 41m46.506s
+ # real 39m13.430s
cat fb.oviAri1.chainMonDom5Link.txt
# 117493519 bases of 1201271277 (9.781%) in intersection