src/hg/makeDb/doc/canFam2.txt 1.27
1.27 2010/02/12 23:44:52 hiram
rerun the panda alignment, and starting the calJac3 marmoset
Index: src/hg/makeDb/doc/canFam2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/canFam2.txt,v
retrieving revision 1.26
retrieving revision 1.27
diff -b -B -U 4 -r1.26 -r1.27
--- src/hg/makeDb/doc/canFam2.txt 25 Jan 2010 19:16:11 -0000 1.26
+++ src/hg/makeDb/doc/canFam2.txt 12 Feb 2010 23:44:52 -0000 1.27
@@ -2981,11 +2981,11 @@
svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2009-09-13
see doc/builds.txt for specific details.
############################################################################
-# ailMel1 Panda alignment (DONE - 2010-01-19 - Hiram)
- mkdir /hive/data/genomes/canFam2/bed/lastzAilMel1.2010-01-19
- cd /hive/data/genomes/canFam2/bed/lastzAilMel1.2010-01-19
+# ailMel1 Panda alignment (DONE - 2010-02-04 - Hiram)
+ mkdir /hive/data/genomes/canFam2/bed/lastzAilMel1.2010-02-04
+ cd /hive/data/genomes/canFam2/bed/lastzAilMel1.2010-02-04
cat << '_EOF_' > DEF
# Dog vs. Panda
# parameters from the Panda paper supplemental where they describe
@@ -3012,36 +3012,70 @@
SEQ2_CHUNK=10000000
SEQ2_LIMIT=50
SEQ2_LAP=0
-BASE=/hive/data/genomes/canFam2/bed/lastzAilMel1.2010-01-19
+BASE=/hive/data/genomes/canFam2/bed/lastzAilMel1.2010-02-04
TMPDIR=/scratch/tmp
'_EOF_'
# << happy emacs
time doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF \
- -workhorse=hgwdev -noLoadChainSplit -verbose=2 -bigClusterHub=swarm \
+ -bigClusterHub=swarm -smallClusterHub=memk -workhorse=hgwdev \
+ -noLoadChainSplit \
-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
- # interrupted by storm induced power failures, finish cat step,
- # then continuing under tornado watch:
- time doBlastzChainNet.pl -verbose=2 \
- `pwd`/DEF \
- -continue=chainRun -workhorse=hgwdev -noLoadChainSplit \
- -smallClusterHub=pk -bigClusterHub=swarm \
- -chainMinScore=3000 -chainLinearGap=medium > chain.log 2>&1 &
- # real 102m27.429s
+ # real 360m31.044s
cat fb.canFam2.chainAilMel1Link.txt
- # 1785774721 bases of 2384996543 (74.875%) in intersection
+ # 1791212709 bases of 2384996543 (75.103%) in intersection
mkdir /hive/data/genomes/ailMel1/bed/blastz.canFam2.swap
cd /hive/data/genomes/ailMel1/bed/blastz.canFam2.swap
time doBlastzChainNet.pl -verbose=2 \
- /hive/data/genomes/canFam2/bed/lastzAilMel1.2010-01-19/DEF \
+ /hive/data/genomes/canFam2/bed/lastzAilMel1.2010-02-04/DEF \
-swap -noLoadChainSplit -workhorse=hgwdev -bigClusterHub=pk \
- -smallClusterHub=pk -chainMinScore=3000 -chainLinearGap=medium \
+ -smallClusterHub=memk -chainMinScore=3000 -chainLinearGap=medium \
> swap.log 2>&1 &
- # real 89m3.603s
+ # real 128m41.005s
cat fb.ailMel1.chainCanFam2Link.txt
- # 1774362211 bases of 2225124764 (79.742%) in intersection
+ # 1788107935 bases of 2245312831 (79.637%) in intersection
############################################################################
+# LASTZ/CHAIN/NET Marmoset calJac3 (DONE - 2010-02-12 - Hiram)
+ # use a screen to control this job
+ screen
+ mkdir /hive/data/genomes/canFam2/bed/lastzCalJac3.2010-02-12
+ cd /hive/data/genomes/canFam2/bed/lastzCalJac3.2010-02-12
+
+ cat << '_EOF_' > DEF
+# dog vs marmoset
+BLASTZ_M=50
+
+# TARGET: Mouse Mm9
+SEQ1_DIR=/scratch/data/canFam2/nib
+SEQ1_LEN=/scratch/data/canFam2/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Marmoset (calJac3)
+SEQ2_DIR=/scratch/data/calJac3/calJac3.2bit
+SEQ2_LEN=/scratch/data/calJac3/chrom.sizes
+SEQ2_LIMIT=75
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/canFam2/bed/lastzCalJac3.2010-02-12
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time nice -n +19 $HOME/kent/src/hg/utils/automation/doBlastzChainNet.pl \
+ -verbose=2 `pwd`/DEF \
+ -syntenicNet -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ > do.log 2>&1 &
+XXX - running Fri Feb 12 14:42:59 PST 2010
+
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
+ -stop=load -chainMinScore=3000 \
+ -chainLinearGap=medium -bigClusterHub=pk > do.log 2>&1 &
+ # real 897m58.156s
+#########################################################################