src/hg/makeDb/doc/hg19.txt 1.13
1.13 2009/05/14 04:56:59 hiram
Had some of the SEQ2_LAP mixed up with SEQ1_LAP
Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.12
retrieving revision 1.13
diff -b -B -U 4 -r1.12 -r1.13
--- src/hg/makeDb/doc/hg19.txt 13 May 2009 20:51:33 -0000 1.12
+++ src/hg/makeDb/doc/hg19.txt 14 May 2009 04:56:59 -0000 1.13
@@ -2100,11 +2100,11 @@
hgsql hg19 \
-e 'LOAD DATA LOCAL INFILE "ensemblLift.tab" INTO TABLE ensemblLift'
##############################################################################
-# BLASTZ MOUSE Mm9 (DONE - 2009-05-11 - Hiram)
- mkdir /hive/data/genomes/hg19/bed/lastzMm9.2009-05-11
- cd /hive/data/genomes/hg19/bed/lastzMm9.2009-05-11
+# BLASTZ MOUSE Mm9 (DONE - 2009-05-13 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzMm9.2009-05-13
+ cd /hive/data/genomes/hg19/bed/lastzMm9.2009-05-13
cat << '_EOF_' > DEF
# human vs mouse
BLASTZ_ABRIDGE_REPEATS=1
@@ -2113,29 +2113,31 @@
SEQ1_DIR=/scratch/data/hg19/nib
SEQ1_SMSK=/scratch/data/hg19/linSpecRep/lineageSpecificRepeats
SEQ1_LEN=/scratch/data/hg19/chrom.sizes
SEQ1_CHUNK=10000000
-SEQ1_LAP=0
+SEQ1_LAP=10000
# QUERY: Mouse Mm9
SEQ2_DIR=/scratch/data/mm9/nib
SEQ2_SMSK=/scratch/data/mm9/notInOthers
SEQ2_LEN=/scratch/data/mm9/chrom.sizes
SEQ2_CHUNK=10000000
-SEQ2_LAP=10000
+SEQ2_LAP=0
-BASE=/hive/data/genomes/hg19/bed/lastzMm9.2009-05-11
+BASE=/hive/data/genomes/hg19/bed/lastzMm9.2009-05-13
TMPDIR=/scratch/tmp
'_EOF_'
# << happy emacs
# establish a screen to control this job
screen
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF \
- -noLoadChainSplit \
+ -noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+XXX - running Wed May 13 16:51:48 PDT 2009
+
# fixed up some bugs in the doBlastzChainNet.pl script, finished
# the lastz run manually, then continuing:
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF \
@@ -2151,11 +2153,11 @@
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > synNet.log 2>&1 &
#########################################################################
-# BLASTZ Dog CanFam2 (DONE - 2009-05-11 - Hiram)
- mkdir /hive/data/genomes/hg19/bed/lastzCanFam2.2009-05-11
- cd /hive/data/genomes/hg19/bed/lastzCanFam2.2009-05-11
+# BLASTZ Dog CanFam2 (DONE - 2009-05-13 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzCanFam2.2009-05-13
+ cd /hive/data/genomes/hg19/bed/lastzCanFam2.2009-05-13
cat << '_EOF_' > DEF
# human vs dog
BLASTZ_ABRIDGE_REPEATS=1
@@ -2164,30 +2166,32 @@
SEQ1_DIR=/scratch/data/hg19/nib
SEQ1_SMSK=/scratch/data/hg19/linSpecRep/lineageSpecificRepeats
SEQ1_LEN=/scratch/data/hg19/chrom.sizes
SEQ1_CHUNK=10000000
-SEQ1_LAP=0
+SEQ1_LAP=10000
# QUERY: Dog CanFam2
SEQ2_DIR=/scratch/data/canFam2/nib
SEQ2_LEN=/scratch/data/canFam2/chrom.sizes
SEQ2_SMSK=/scratch/scratch/data/canFam2/linSpecRep.notInHuman
SEQ2_IN_CONTIGS=0
SEQ2_CHUNK=20000000
-SEQ2_LAP=10000
+SEQ2_LAP=0
-BASE=/hive/data/genomes/hg19/bed/lastzCanFam2.2009-05-11
+BASE=/hive/data/genomes/hg19/bed/lastzCanFam2.2009-05-13
TMPDIR=/scratch/tmp
'_EOF_'
# << happy emacs
# establish a screen to control this job
screen
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF \
- -noLoadChainSplit \
+ -noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+XXX - running Wed May 13 16:48:16 PDT 2009
+
# fixed up some bugs in the doBlastzChainNet.pl script, finished
# the lastz run manually, then continuing:
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF \
@@ -2278,16 +2282,16 @@
# TARGET: Human Hg19
SEQ1_DIR=/scratch/data/hg19/hg19.2bit
SEQ1_LEN=/scratch/data/hg19/chrom.sizes
SEQ1_CHUNK=10000000
-SEQ1_LAP=0
+SEQ1_LAP=10000
SEQ1_IN_CONTIGS=0
# QUERY: Macaca Mulatta RheMac2
SEQ2_DIR=/scratch/data/rheMac2/rheMac2.2bit
SEQ2_LEN=/scratch/data/rheMac2/chrom.sizes
SEQ2_CHUNK=20000000
-SEQ2_LAP=10000
+SEQ2_LAP=0
SEQ2_IN_CONTIGS=0
BASE=/hive/data/genomes/hg19/bed/lastzRheMac2.2009-05-13
TMPDIR=/scratch/tmp
@@ -2315,16 +2319,16 @@
SEQ1_DIR=/scratch/data/hg19/nib
SEQ1_SMSK=/scratch/data/hg19/lineageSpecificRepeats
SEQ1_LEN=/scratch/data/hg19/chrom.sizes
SEQ1_CHUNK=10000000
-SEQ1_LAP=0
+SEQ1_LAP=10000
# QUERY: Rat Rn4
SEQ2_DIR=/scratch/data/rn4/nib
SEQ2_SMSK=/scratch/data/rn4/linSpecRep.notInHuman
SEQ2_LEN=/scratch/data/rn4/chrom.sizes
SEQ2_CHUNK=10000000
-SEQ2_LAP=10000
+SEQ2_LAP=0
BASE=/hive/data/genomes/hg19/bed/lastzRn4.2009-05-13
TMPDIR=/scratch/tmp
'_EOF_'
@@ -2336,8 +2340,10 @@
`pwd`/DEF \
-syntenicNet -noLoadChainSplit \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+XXX - running Wed May 13 16:48:04 PDT 2009
+ # real 314m18.227s
##############################################################################
# BLASTZ Rat Rn4 (WORKING - 2009-05-13 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzRn4.2009-05-13
@@ -2360,16 +2366,16 @@
# TARGET: Human Hg19
SEQ1_DIR=/scratch/data/hg19/hg19.2bit
SEQ1_LEN=/scratch/data/hg19/chrom.sizes
SEQ1_CHUNK=10000000
-SEQ1_LAP=0
+SEQ1_LAP=10000
SEQ1_IN_CONTIGS=0
# QUERY: Orangutan PonAbe1
SEQ2_DIR=/scratch/data/ponAbe2/ponAbe2.2bit
SEQ2_LEN=/scratch/data/ponAbe2/chrom.sizes
SEQ2_CHUNK=20000000
-SEQ2_LAP=10000
+SEQ2_LAP=0
SEQ2_IN_CONTIGS=0
BASE=/hive/data/genomes/hg19/bed/lastzPonAbe2.2009-05-13
TMPDIR=/scratch/tmp