src/hg/makeDb/doc/hg19.txt 1.15
1.15 2009/05/14 19:00:51 hiram
lastz runs updated
Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.14
retrieving revision 1.15
diff -b -B -U 4 -r1.14 -r1.15
--- src/hg/makeDb/doc/hg19.txt 14 May 2009 17:37:13 -0000 1.14
+++ src/hg/makeDb/doc/hg19.txt 14 May 2009 19:00:51 -0000 1.15
@@ -2367,9 +2367,9 @@
cat fb.hg19.chainPonAbe2Link.txt
# 2646687531 bases of 2897316137 (91.350%) in intersection
##############################################################################
-# LASTZ Lamprey PetMar1 (WORKING - 2009-05-14 - Hiram)
+# LASTZ Lamprey PetMar1 (DONE - 2009-05-14 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzPetMar1.2009-05-14
cd /hive/data/genomes/hg19/bed/lastzPetMar1.2009-05-14
cat << '_EOF_' > DEF
@@ -2406,9 +2406,11 @@
-qRepeats=windowmaskerSdust \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
> do.log 2>&1 &
-XXX - running Thu May 14 10:18:36 PDT 2009
+ # real 113m20.116s
+ cat fb.hg19.chainPetMar1Link.txt
+ # 31347143 bases of 2897316137 (1.082%) in intersection
##############################################################################
# LASTZ Fugu Fr2 (WORKING - 2009-05-14 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzFr2.2009-05-14
@@ -2457,4 +2459,135 @@
> do.log 2>&1 &
XXX - running Thu May 14 10:18:26 PDT 2009
##############################################################################
+# LASTZ Tetraodon TetNig1 (WORKING - 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
+# human vs tetraodon
+BLASTZ_Y=3400
+BLASTZ_L=6000
+BLASTZ_K=2200
+BLASTZ_M=50
+BLASTZ_Q=/scratch/data/blastz/HoxD55.q
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/hg19.2bit
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=5
+
+# QUERY: Tetraodon TetNig1 - single chunk big enough to run entire genome
+SEQ2_DIR=/scratch/data/tetNig1/tetNig1.2bit
+SEQ2_LEN=/hive/data/genomes/tetNig1/chrom.sizes
+SEQ2_CHUNK=410000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzTetNig1.2009-05-14
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ # establish a screen to control this job
+ screen
+ time nice -n +19 $HOME/kent/src/hg/utils/automation/doBlastzChainNet.pl \
+ -verbose=2 \
+ `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
+
+##############################################################################
+# LASTZ Stickleback GasAcu1 (WORKING - 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
+# Human vs. Stickleback
+BLASTZ_Y=3400
+BLASTZ_L=6000
+BLASTZ_K=2200
+BLASTZ_M=50
+BLASTZ_Q=/scratch/data/blastz/HoxD55.q
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/hg19.2bit
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=5
+
+# TARGET: Stickleback gasAcu1
+SEQ2_DIR=/scratch/data/gasAcu1/gasAcu1.2bit
+SEQ2_LEN=/hive/data/genomes/gasAcu1/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzGasAcu1.2009-05-14
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ # establish a screen to control this job
+ screen
+ time nice -n +19 $HOME/kent/src/hg/utils/automation/doBlastzChainNet.pl \
+ -verbose=2 \
+ `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
+
+##############################################################################
+# LASTZ Macaca Mulatta RheMac2 (DONE - 2009-05-13 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzCalJac1.2009-05-14
+ cd /hive/data/genomes/hg19/bed/lastzCalJac1.2009-05-14
+
+ cat << '_EOF_' > DEF
+# human vs. marmoset
+BLASTZ=lastz
+# maximum M allowed with lastz is only 254
+BLASTZ_M=254
+BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
+# and place those items here
+BLASTZ_O=600
+BLASTZ_E=150
+# other parameters from panTro2 vs hg18 lastz on advice from Webb
+BLASTZ_K=4500
+BLASTZ_Y=15000
+BLASTZ_T=2
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/hg19.2bit
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=5
+
+# QUERY: Marmoset (calJac1)
+SEQ2_DIR=/scratch/data/calJac1/calJac1.2bit
+SEQ2_LEN=/scratch/data/calJac1/chrom.sizes
+SEQ2_LIMIT=200
+SEQ2_CHUNK=30000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzCalJac1.2009-05-14
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -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
+
+#########################################################################