src/hg/makeDb/doc/monDom5.txt 1.18
1.18 2010/02/06 00:17:33 hiram
re-run the Panda chain net
Index: src/hg/makeDb/doc/monDom5.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/monDom5.txt,v
retrieving revision 1.17
retrieving revision 1.18
diff -b -B -U 4 -r1.17 -r1.18
--- src/hg/makeDb/doc/monDom5.txt 25 Jan 2010 19:16:13 -0000 1.17
+++ src/hg/makeDb/doc/monDom5.txt 6 Feb 2010 00:17:33 -0000 1.18
@@ -1487,12 +1487,12 @@
cat fb.susScr1.chainMonDom5Link.txt
# 182834626 bases of 2231332019 (8.194%) in intersection
#########################################################################
-# ailMel1 Panda BLASTZ/CHAIN/NET (DONE - 2010-01-22 - Hiram)
+# ailMel1 Panda BLASTZ/CHAIN/NET (DONE - 2010-02-04 - Hiram)
screen # use a screen to manage this multi-day job
- mkdir /hive/data/genomes/monDom5/bed/lastzAilMel1.2010-01-22
- cd /hive/data/genomes/monDom5/bed/lastzAilMel1.2010-01-22
+ mkdir /hive/data/genomes/monDom5/bed/lastzAilMel1.2010-02-04
+ cd /hive/data/genomes/monDom5/bed/lastzAilMel1.2010-02-04
cat << '_EOF_' > DEF
# Panda vs. Opossum
BLASTZ_M=50
@@ -1508,9 +1508,9 @@
SEQ2_LEN=/scratch/data/ailMel1/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
-BASE=/hive/data/genomes/monDom5/bed/lastzAilMel1.2010-01-22
+BASE=/hive/data/genomes/monDom5/bed/lastzAilMel1.2010-02-04
TMPDIR=/scratch/tmp
'_EOF_'
# << this line keeps emacs coloring happy
@@ -1518,20 +1518,20 @@
`pwd`/DEF \
-noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 &
- # real 293m25.573s
+ # real 492m43.088s
cat fb.monDom5.chainAilMel1Link.txt
- # 223233047 bases of 3501660299 (6.375%) in intersection
+ # 223510659 bases of 3501660299 (6.383%) in intersection
mkdir /hive/data/genomes/ailMel1/bed/blastz.monDom5.swap
cd /hive/data/genomes/ailMel1/bed/blastz.monDom5.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
- /hive/data/genomes/monDom5/bed/lastzAilMel1.2010-01-22/DEF \
+ /hive/data/genomes/monDom5/bed/lastzAilMel1.2010-02-04/DEF \
-swap -noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
- # real 65m0.711s
+ # real 69m35.464s
cat fb.ailMel1.chainMonDom5Link.txt
- # 210235815 bases of 2225124764 (9.448%) in intersection
+ # 211209682 bases of 2245312831 (9.407%) in intersection
#########################################################################