src/hg/makeDb/doc/equCab2.txt 1.31
1.31 2010/04/20 17:34:31 chinhli
Finished lastz with Sheep oviAri1
Index: src/hg/makeDb/doc/equCab2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/equCab2.txt,v
retrieving revision 1.30
retrieving revision 1.31
diff -b -B -U 4 -r1.30 -r1.31
--- src/hg/makeDb/doc/equCab2.txt 12 Apr 2010 21:32:38 -0000 1.30
+++ src/hg/makeDb/doc/equCab2.txt 20 Apr 2010 17:34:31 -0000 1.31
@@ -2372,12 +2372,12 @@
# enable xeno RefSeq track per user request: add to etc/genbank.conf:
equCab2.refseq.mrna.xeno.load = yes
#####################################################################
-# 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/equCab2/bed/lastzOviAri1.2010-04-09
- cd /hive/data/genomes/equCab2/bed/lastzOviAri1.2010-04-09
+ mkdir /hive/data/genomes/equCab2/bed/lastzOviAri1.2010-04-16
+ cd /hive/data/genomes/equCab2/bed/lastzOviAri1.2010-04-16
cat << '_EOF_' > DEF
# Sheep vs. Mouse
BLASTZ_M=50
@@ -2393,9 +2393,9 @@
SEQ2_LEN=/scratch/data/oviAri1/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
-BASE=/hive/data/genomes/equCab2/bed/lastzOviAri1.2010-04-09
+BASE=/hive/data/genomes/equCab2/bed/lastzOviAri1.2010-04-16
TMPDIR=/scratch/tmp
'_EOF_'
# << this line keeps emacs coloring happy
@@ -2403,21 +2403,20 @@
`pwd`/DEF \
-noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
- # Elapsed time: 433m14s
+ # real 397m26.503s
cat fb.equCab2.chainOviAri1Link.txt
# 1012763540 bases of 2428790173 (41.698%) in intersection
mkdir /hive/data/genomes/oviAri1/bed/blastz.equCab2.swap
cd /hive/data/genomes/oviAri1/bed/blastz.equCab2.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
- /hive/data/genomes/equCab2/bed/lastzOviAri1.2010-04-09/DEF \
+ /hive/data/genomes/equCab2/bed/lastzOviAri1.2010-04-16/DEF \
-swap -noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
- # real 100m49.583s
-
+ # real 103m0.724s
cat fb.oviAri1.chainEquCab2Link.txt
# 940763026 bases of 1201271277 (78.314%) in intersection