src/hg/makeDb/doc/hg19.txt 1.97
1.97 2010/04/09 15:24:24 chinhli
Rerun blastz with felCatV17e
Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.96
retrieving revision 1.97
diff -b -B -U 4 -r1.96 -r1.97
--- src/hg/makeDb/doc/hg19.txt 7 Apr 2010 17:42:44 -0000 1.96
+++ src/hg/makeDb/doc/hg19.txt 9 Apr 2010 15:24:24 -0000 1.97
@@ -8823,8 +8823,9 @@
#######################################################################
# felCatV17e Cat BLASTZ/CHAIN/NET (DONE - 2010-03-22 - Chin)
+# Rerun the complete doBlastzChainNet.pl (2010-04-07 -Chin)
screen # use a screen to manage this multi-day job
mkdir /hive/data/genomes/hg19/bed/lastzFelCatV17e.2010-03-22
cd /hive/data/genomes/hg19/bed/lastzFelCatV17e.2010-03-22
@@ -8864,9 +8865,9 @@
# then continue
# with:
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
- `pw`/DEF \
+ `pwd`/DEF \
-continue=download -syntenicNet -noDbNameCheck \
-chainMinScore=3000 -chainLinearGap=medium \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
> download.log 2>&1 &
@@ -8876,19 +8877,32 @@
# make it time independent and indicate that it is really done
cd /hive/data/genomes/hg19/bed
ln -s lastzFelCatV17e.2010-03-22 lastz.felCatV17e
+# 04/07 re-reun the doBlastzChinNet.pl steps with screen
+ cd /hive/data/genomes/hg19/bed/lastzFelCatV17e.2010-03-22
+
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -syntenicNet -noDbNameCheck \
+ -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=pk -bigClusterHub=swarm \
+ > do.log 2>&1 &
+ # real 423m7.683s
+
+
# Swap
mkdir /hive/data/genomes/felCatV17e/bed/blastz.hg19.swap
cd /hive/data/genomes/felCatV17e/bed/blastz.hg19.swap
+
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
/hive/data/genomes/hg19/bed/lastzFelCatV17e.2010-03-22/DEF \
-swap -syntenicNet -noDbNameCheck \
- -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
+ -workhorse=hgwdev -smallClusterHub=pk -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
- # real 120m42.991s
+ # real 200m43.245s
cat fb.felCatV17e.chainHg19Link.txt
- # 2030475813 bases of 2752505800 (73.768%) in intersection
+ # 1211702270 bases of 1990635005 (60.870%) in intersection
#####################################################################
# susScr2 Pig BLASTZ/CHAIN/NET (DONE - 2010-03-26,27 - Hiram)
screen # use a screen to manage this multi-day job