src/hg/makeDb/doc/hg19.txt 1.16
1.16 2009/05/14 23:44:55 hiram
Additional lastz runs started
Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.15
retrieving revision 1.16
diff -b -B -U 4 -r1.15 -r1.16
--- src/hg/makeDb/doc/hg19.txt 14 May 2009 19:00:51 -0000 1.15
+++ src/hg/makeDb/doc/hg19.txt 14 May 2009 23:44:55 -0000 1.16
@@ -1902,9 +1902,10 @@
# jang at ncbi.nlm.nih.gov - I have asked for clarification where
# such a file can be fetched without resorting to email.
# Get current clone/accession information
- wget --timestamping http://www.ncbi.nlm.nih.gov/genome/clone/DATA/clac.out
+ wget --timestamping ftp://ftp.ncbi.nih.gov/repository/clone/reports/clac.out
+http://www.ncbi.nlm.nih.gov/genome/clone/DATA/clac.out
# Create initial Fish Clones bed file
ssh kkstore02
mkdir /hive/data/genomes/hg19/bed/fishClones
@@ -2147,8 +2148,11 @@
/hive/data/genomes/hg19/bed/lastzMm9.2009-05-13/DEF \
-swap -noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 131m58.763s
+ cat fb.mm9.chainHg19Link.txt
+ # 1013880568 bases of 2620346127 (38.693%) in intersection
#########################################################################
# LASTZ Dog CanFam2 (DONE - 2009-05-13 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzCanFam2.2009-05-13
@@ -2459,9 +2463,9 @@
> do.log 2>&1 &
XXX - running Thu May 14 10:18:26 PDT 2009
##############################################################################
-# LASTZ Tetraodon TetNig1 (WORKING - 2009-05-14 - Hiram)
+# LASTZ Tetraodon TetNig1 (DONE - 2009-05-14 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzTetNig1.2009-05-14
cd /hive/data/genomes/hg19/bed/lastzTetNig1.2009-05-14
cat << '_EOF_' > DEF
@@ -2497,12 +2501,14 @@
`pwd`/DEF \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
> do.log 2>&1 &
-XXX - running Thu May 14 10:18:26 PDT 2009
+ # real 166m19.745s
+ cat fb.hg19.chainTetNig1Link.txt
+ # 58038079 bases of 2897316137 (2.003%) in intersection
##############################################################################
-# LASTZ Stickleback GasAcu1 (WORKING - 2009-05-14 - Hiram)
+# LASTZ Stickleback GasAcu1 (DONE - 2009-05-14 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzGasAcu1.2009-05-14
cd /hive/data/genomes/hg19/bed/lastzGasAcu1.2009-05-14
cat << '_EOF_' > DEF
@@ -2538,12 +2544,14 @@
`pwd`/DEF \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
> do.log 2>&1 &
-XXX - running Thu May 14 10:18:26 PDT 2009
+ # real 174m40.659s
+ cat fb.hg19.chainGasAcu1Link.txt
+ # 55509003 bases of 2897316137 (1.916%) in intersection
##############################################################################
-# LASTZ Macaca Mulatta RheMac2 (DONE - 2009-05-13 - Hiram)
+# LASTZ Marmoset CalJac1 (DONE - 2009-05-14 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzCalJac1.2009-05-14
cd /hive/data/genomes/hg19/bed/lastzCalJac1.2009-05-14
cat << '_EOF_' > DEF
@@ -2584,10 +2592,115 @@
-syntenicNet \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=medium \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
> do.log 2>&1 &
-XXX - running Thu May 14 12:00:31 PDT 2009
- # real 760m22.810s
- cat fb.hg19.chainRheMac2Link.txt
- # 2397361211 bases of 2897316137 (82.744%) in intersection
+ # real 214m16.294s
+ cat fb.hg19.chainCalJac1Link.txt
+ # 2053025318 bases of 2897316137 (70.860%) in intersection
+
+#########################################################################
+# LASTZ Tarsier TarSyr1 (WORKING - 2009-05-14 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzTarSyr1.2009-05-14
+ cd /hive/data/genomes/hg19/bed/lastzTarSyr1.2009-05-14
+
+ cat << '_EOF_' > DEF
+# Human vs. Tarsier
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/hg19.2bit
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=200000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=5
+
+# QUERY: Tarsier
+SEQ2_DIR=/scratch/data/tarSyr1/tarSyr1.2bit
+SEQ2_LEN=/scratch/data/tarSyr1/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=50
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzTarSyr1.2009-05-14
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time nice -n +19 $HOME/kent/src/hg/utils/automation/doBlastzChainNet.pl \
+ -verbose=2 \
+ `pwd`/DEF \
+ -noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ > do.log 2>&1 &
+XXX - running
+Thu May 14 16:30:50 PDT 2009
+
+#########################################################################
+# LASTZ Bushbaby OtoGar1 (WORKING - 2009-05-14 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzOtoGar1.2009-05-14
+ cd /hive/data/genomes/hg19/bed/lastzOtoGar1.2009-05-14
+
+ cat << '_EOF_' > DEF
+# Human vs. Bushbaby
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/hg19.2bit
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=200000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=5
+
+# QUERY: Bushbaby otoGar1 - single chunk big enough to run largest scaffold
+SEQ2_DIR=/scratch/data/otoGar1/otoGar1.rmsk.2bit
+SEQ2_LEN=/hive/data/genomes/otoGar1/chrom.sizes
+SEQ2_LIMIT=200
+SEQ2_CHUNK=30000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzOtoGar1.2009-05-14
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time nice -n +19 $HOME/kent/src/hg/utils/automation/doBlastzChainNet.pl \
+ -verbose=2 \
+ `pwd`/DEF \
+ -noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ > do.log 2>&1 &
+XXX - running Thu May 14 16:36:50 PDT 2009
+
+#########################################################################
+# LASTZ Mouse lemur MicMur1 (WORKING - 2009-05-14 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzMicMur1.2009-05-14
+ cd /hive/data/genomes/hg19/bed/lastzMicMur1.2009-05-14
+
+ cat << '_EOF_' > DEF
+# Human vs. Mouse lemur
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/hg19.2bit
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=200000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=5
+
+# QUERY: Mouse lemur
+SEQ2_DIR=/hive/data/genomes/micMur1/bed/repeatMasker/micMur1.rmsk.2bit
+SEQ2_LEN=/hive/data/genomes/micMur1/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=100
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzMicMur1.2009-05-14
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time nice -n +19 $HOME/kent/src/hg/utils/automation/doBlastzChainNet.pl \
+ -verbose=2 \
+ `pwd`/DEF \
+ -noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ > do.log 2>&1 &
+XXX - running Thu May 14 16:36:50 PDT 2009
#########################################################################