src/hg/makeDb/doc/hg19.txt 1.102
1.102 2010/04/20 17:34:31 chinhli
Finished lastz with Sheep oviAri1
Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.101
retrieving revision 1.102
diff -b -B -U 4 -r1.101 -r1.102
--- src/hg/makeDb/doc/hg19.txt 16 Apr 2010 17:47:00 -0000 1.101
+++ src/hg/makeDb/doc/hg19.txt 20 Apr 2010 17:34:31 -0000 1.102
@@ -9001,12 +9001,12 @@
featureBits hg19 vegaPseudoGene
# 8494715 bases of 2897316137 (0.293%) 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/hg19/bed/lastzOviAri1.2010-04-09
- cd /hive/data/genomes/hg19/bed/lastzOviAri1.2010-04-09
+ mkdir /hive/data/genomes/hg19/bed/lastzOviAri1.2010-04-16
+ cd /hive/data/genomes/hg19/bed/lastzOviAri1.2010-04-16
cat << '_EOF_' > DEF
# Sheep vs. Human
BLASTZ_M=50
@@ -9022,9 +9022,9 @@
SEQ2_LEN=/scratch/data/oviAri1/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
-BASE=/hive/data/genomes/hg19/bed/lastzOviAri1.2010-04-09
+BASE=/hive/data/genomes/hg19/bed/lastzOviAri1.2010-04-16
TMPDIR=/scratch/tmp
'_EOF_'
# << this line keeps emacs coloring happy
@@ -9032,21 +9032,21 @@
`pwd`/DEF \
-noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
- # Elapsed time: 391m53s
+ # real 578m58.918s
cat fb.hg19.chainOviAri1Link.txt
# 878545517 bases of 2897316137 (30.323%) in intersection
# and the swap
mkdir /hive/data/genomes/oviAri1/bed/blastz.hg19.swap
cd /hive/data/genomes/oviAri1/bed/blastz.hg19.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
- /hive/data/genomes/hg19/bed/lastzOviAri1.2010-04-09/DEF \
+ /hive/data/genomes/hg19/bed/lastzOviAri1.2010-04-16/DEF \
-swap -noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
- # real 71m37.020s
+ # real 72m47.780s
cat fb.oviAri1.chainHg19Link.txt
# 824310420 bases of 1201271277 (68.620%) in intersection