src/hg/makeDb/doc/mm9.txt 1.122
1.122 2010/02/06 00:17:33 hiram
re-run the Panda chain net
Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.121
retrieving revision 1.122
diff -b -B -U 4 -r1.121 -r1.122
--- src/hg/makeDb/doc/mm9.txt 25 Jan 2010 19:16:12 -0000 1.121
+++ src/hg/makeDb/doc/mm9.txt 6 Feb 2010 00:17:33 -0000 1.122
@@ -9978,11 +9978,11 @@
cat fb.oryCun2.chainMm9Link.txt
# 669602734 bases of 2604023284 (25.714%) in intersection
#########################################################################
-# ailMel1 Panda alignment (DONE - 2010-01-21 - Hiram)
- mkdir /hive/data/genomes/mm9/bed/lastzAilMel1.2010-01-21
- cd /hive/data/genomes/mm9/bed/lastzAilMel1.2010-01-21
+# ailMel1 Panda alignment (DONE - 2010-02-04 - Hiram)
+ mkdir /hive/data/genomes/mm9/bed/lastzAilMel1.2010-02-04
+ cd /hive/data/genomes/mm9/bed/lastzAilMel1.2010-02-04
cat << '_EOF_' > DEF
# Mouse vs. Panda
# parameters from the Panda paper supplemental where they describe
@@ -10009,38 +10009,33 @@
SEQ2_CHUNK=10000000
SEQ2_LIMIT=50
SEQ2_LAP=0
-BASE=/hive/data/genomes/mm9/bed/lastzAilMel1.2010-01-21
+BASE=/hive/data/genomes/mm9/bed/lastzAilMel1.2010-02-04
TMPDIR=/scratch/tmp
'_EOF_'
# << happy emacs
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF \
-noLoadChainSplit -syntenicNet \
- -workhorse=hgwdev -smallClusterHub=pk -bigClusterHub=swarm \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
- # real 49m23.409s
- # something failed during the cat operation, continuing:
- time nice -n +19 doBlastzChainNet.pl -verbose=2 \
- -continue=cat `pwd`/DEF \
- -noLoadChainSplit -syntenicNet \
- -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
- -chainMinScore=3000 -chainLinearGap=medium > cat.log 2>&1 &
- # real 79m11.840s
+ # real 501m27.760s
cat fb.mm9.chainAilMel1Link.txt
- # 748670674 bases of 2620346127 (28.571%) in intersection
+ # 749595031 bases of 2620346127 (28.607%) in intersection
mkdir /hive/data/genomes/ailMel1/bed/blastz.mm9.swap
cd /hive/data/genomes/ailMel1/bed/blastz.mm9.swap
time doBlastzChainNet.pl -verbose=2 \
- /hive/data/genomes/mm9/bed/lastzAilMel1.2010-01-21/DEF \
+ /hive/data/genomes/mm9/bed/lastzAilMel1.2010-02-04/DEF \
-swap -noLoadChainSplit -bigClusterHub=swarm -smallClusterHub=memk \
+ -workhorse=hgwdev \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 54m57.140s
# real 48m59.568s
cat fb.ailMel1.chainMm9Link.txt
- # 736638976 bases of 2225124764 (33.106%) in intersection
+ # 739076250 bases of 2245312831 (32.916%) in intersection
############################################################################
# susScr1 Pig BLASTZ/CHAIN/NET (WORKING - 2010-01-21 - Hiram)
screen # use a screen to manage this multi-day job