src/hg/makeDb/doc/hg19.txt 1.21
1.21 2009/05/30 03:22:22 hiram
lastz run updates, now running the last two, and many are finished
Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.20
retrieving revision 1.21
diff -b -B -U 4 -r1.20 -r1.21
--- src/hg/makeDb/doc/hg19.txt 27 May 2009 23:14:37 -0000 1.20
+++ src/hg/makeDb/doc/hg19.txt 30 May 2009 03:22:22 -0000 1.21
@@ -3137,12 +3137,33 @@
`pwd`/DEF \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
> do.log 2>&1 &
-XXX - running Sat May 23 15:11:31 PDT 2009
+ # One job took a long time to complete, had to run it manually on
+ # swarm:
+# /cluster/bin/scripts/blastz-run-ucsc -outFormat psl \
+# /scratch/data/hg19/hg19.2bit:chr19:50000000-59128983 \
+# /scratch/data/monDom5/monDom5.2bit:chr4:390000000-420000000 \
+# ../DEF \
+# ../psl/hg19.2bit:chr19:50000000-59128983/hg19.2bit:chr19:50000000-59128983_monDom5.2bit:chr4:390000000-420000000.psl
+ # took about 48 hours, continuing:
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ -continue=cat > cat.log 2>&1 &
+ # real 1508m18.471s == about 25h08m
+ cat fb.hg19.chainMonDom5Link.txt
+ # 415997117 bases of 2897316137 (14.358%) in intersection
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ -continue=syntenicNet -syntenicNet > syntenicNet.log 2>&1 &
+XXX - running Fri May 29 20:14:45 PDT 2009
##############################################################################
-# LASTZ Armadillo DasNov2 (WORKING - 2009-05-23 - Hiram)
+# LASTZ Armadillo DasNov2 (DONE - 2009-05-23,28 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzDasNov2.2009-05-23
cd /hive/data/genomes/hg19/bed/lastzDasNov2.2009-05-23
cat << '_EOF_' > DEF
@@ -3181,9 +3202,14 @@
`pwd`/DEF \
-noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
-continue=cat > cat.log 2>&1 &
-XXX - running Wed May 27 10:59:18 PDT 2009
+ # real 458m11.304s
+ cat fb.hg19.chainDasNov2Link.txt
+ # 971847303 bases of 2897316137 (33.543%) in intersection
+ time nice -n +19 doRecipBest.pl -buildDir=`pwd` hg19 dasNov2 \
+ > rbest.log 2>&1
+ # time about 6h30m
##############################################################################
# LASTZ Rock Hyrax ProCap1 (WORKING - 2009-05-23 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzProCap1.2009-05-23
@@ -3338,9 +3364,9 @@
-continue=chainRun -qRepeats=windowmaskerSdust > chainRun.log 2>&1 &
# real 16m31.552s
##############################################################################
-# LASTZ X. tropicalis XenTro2 (WORKING - 2009-05-26 - Hiram)
+# LASTZ X. tropicalis XenTro2 (DONE - 2009-05-26 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzXenTro2.2009-05-26
cd /hive/data/genomes/hg19/bed/lastzXenTro2.2009-05-26
cat << '_EOF_' > DEF
@@ -3382,9 +3408,11 @@
`pwd`/DEF \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
-continue=cat > cat.log 2>&1 &
-XXX - running Wed May 27 10:42:27 PDT 2009
+ # time about 1h30m
+ cat fb.hg19.chainXenTro2Link.txt
+ # 92015242 bases of 2897316137 (3.176%) in intersection
##############################################################################
# LASTZ Zebrafish DanRer5 (WORKING - 2009-05-26 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzDanRer5.2009-05-26
@@ -3427,9 +3455,9 @@
cat fb.hg19.chainDanRer5Link.txt
# 74229561 bases of 2897316137 (2.562%) in intersection
##############################################################################
-# LASTZ Platypus OrnAna1 (WORKING - 2009-05-26 - Hiram)
+# LASTZ Platypus OrnAna1 (DONE - 2009-05-26 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzOrnAna1.2009-05-26
cd /hive/data/genomes/hg19/bed/lastzOrnAna1.2009-05-26
cat << '_EOF_' > DEF
@@ -3468,9 +3496,9 @@
# real 572m18.808s
cat fb.hg19.chainOrnAna1Link.txt
# 220977689 bases of 2897316137 (7.627%) in intersection
time doRecipBest.pl -buildDir=`pwd` hg19 ornAna1 > rbest.log 2>&1
-XXX - running Wed May 27 10:48:56 PDT 2009
+ # time about 1h32m
##############################################################################
# LASTZ Elephant LoxAfr2 (WORKING - 2009-05-27 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzLoxAfr2.2009-05-27
@@ -3504,14 +3532,18 @@
`pwd`/DEF \
-noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
> do.log 2>&1 &
-XXX - running Wed May 27 11:18:13 PDT 2009
-
- time doRecipBest.pl -buildDir=`pwd` hg19 loxAfr1 > rbest.log 2>&1
+ # time about 3h23m
+ cat fb.hg19.chainLoxAfr2Link.txt
+ # 1018502258 bases of 2897316137 (35.153%) in intersection
+
+ time doRecipBest.pl -buildDir=`pwd` hg19 loxAfr2 > rbest.log 2>&1
+ # real 322m37.502s
+XXX - running Thu May 28 22:40:56 PDT 2009
##############################################################################
-# LASTZ Tenrec EchTel1 (WORKING - 2009-05-27 - Hiram)
+# LASTZ Tenrec EchTel1 (DONE - 2009-05-27 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzEchTel1.2009-05-27
cd /hive/data/genomes/hg19/bed/lastzEchTel1.2009-05-27
cat << '_EOF_' > DEF
@@ -3542,9 +3574,247 @@
`pwd`/DEF \
-noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
> do.log 2>&1 &
-XXX - running Wed May 27 11:18:13 PDT 2009
+ # real 1153m34.595s
+ cat fb.hg19.chainEchTel1Link.txt
+ # 669856841 bases of 2897316137 (23.120%) in intersection
+ time doRecipBest.pl -buildDir=`pwd` hg19 echTel1 > rbest.log 2>&1
+ # time about 7h13m
+
+##############################################################################
+# LASTZ Tree Shrew TupBel1 (WORKING - 2009-05-27 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzTupBel1.2009-05-27
+ cd /hive/data/genomes/hg19/bed/lastzTupBel1.2009-05-27
+
+ cat << '_EOF_' > DEF
+# Human vs. Tree Shrew
+BLASTZ_M=50
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/nib
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Tree Shrew
+SEQ2_DIR=/scratch/data/tupBel1/tupBel1.2bit
+SEQ2_LEN=/scratch/data/tupBel1/chrom.sizes
+SEQ2_CHUNK=30000000
+SEQ2_LIMIT=400
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzTupBel1.2009-05-27
+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 -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
+ > do.log 2>&1 &
+ # real 811m54.095s
+ # having trouble with pk, finished manually
+XXX - running Thu May 28 10:38:42 PDT 2009
+
+ time doRecipBest.pl -buildDir=`pwd` hg19 loxAfr1 > rbest.log 2>&1
+
+##############################################################################
+# LASTZ Shrew SorAra1 (WORKING - 2009-05-28 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzSorAra1.2009-05-28
+ cd /hive/data/genomes/hg19/bed/lastzSorAra1.2009-05-28
+
+ cat << '_EOF_' > DEF
+# Human vs. Shrew
+BLASTZ_M=50
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/nib
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Shrew
+SEQ2_DIR=/scratch/data/sorAra1/sorAra1.2bit
+SEQ2_LEN=/scratch/data/sorAra1/chrom.sizes
+SEQ2_CHUNK=30000000
+SEQ2_LIMIT=400
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzSorAra1.2009-05-28
+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 -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ > do.log 2>&1 &
+ # time about 23h26m
+ cat fb.hg19.chainSorAra1Link.txt
+ # 572519288 bases of 2897316137 (19.760%) in intersection
+
+ time doRecipBest.pl -buildDir=`pwd` hg19 sorAra1 > rbest.log 2>&1
+XXX - running Fri May 29 20:17:16 PDT 2009
+
+##############################################################################
+# LASTZ Rabbit OryCun1 (WORKING - 2009-05-28 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzOryCun1.2009-05-28
+ cd /hive/data/genomes/hg19/bed/lastzOryCun1.2009-05-28
+
+ cat << '_EOF_' > DEF
+# Human vs. Rabbit
+BLASTZ_M=50
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/nib
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Rabbit
+SEQ2_DIR=/scratch/data/oryCun1/oryCun1.2bit
+SEQ2_LEN=/scratch/data/oryCun1/chrom.sizes
+SEQ2_CHUNK=30000000
+SEQ2_LIMIT=400
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzOryCun1.2009-05-28
+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 -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ > do.log 2>&1 &
+ # time about 23h09m
+ cat fb.hg19.chainOryCun1Link.txt
+ # 975693323 bases of 2897316137 (33.676%) in intersection
+
+ time doRecipBest.pl -buildDir=`pwd` hg19 oryCun1 > rbest.log 2>&1
+XXX - running Fri May 29 20:18:53 PDT 2009
+
+##############################################################################
+# LASTZ Rabbit EriEur1 (WORKING - 2009-05-28 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzEriEur1.2009-05-28
+ cd /hive/data/genomes/hg19/bed/lastzEriEur1.2009-05-28
+
+ cat << '_EOF_' > DEF
+# Human vs. Hedgehog
+BLASTZ_M=50
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/nib
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Hedgehog
+SEQ2_DIR=/scratch/data/eriEur1/eriEur1.2bit
+SEQ2_LEN=/scratch/data/eriEur1/chrom.sizes
+SEQ2_CHUNK=40000000
+SEQ2_LIMIT=500
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzEriEur1.2009-05-28
+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 -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ > do.log 2>&1 &
+XXX - running Thu May 28 11:29:22 PDT 2009
+
+ time doRecipBest.pl -buildDir=`pwd` hg19 loxAfr1 > rbest.log 2>&1
+
+##############################################################################
+# LASTZ Pika OchPri2 (WORKING - 2009-05-29 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzOchPri2.2009-05-29
+ cd /hive/data/genomes/hg19/bed/lastzOchPri2.2009-05-29
+
+ cat << '_EOF_' > DEF
+# Human vs. Pika
+BLASTZ_M=50
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/nib
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Pika
+SEQ2_DIR=/scratch/data/ochPri2/ochPri2.2bit
+SEQ2_LEN=/scratch/data/ochPri2/chrom.sizes
+SEQ2_CHUNK=40000000
+SEQ2_LIMIT=400
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzOchPri2.2009-05-29
+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 -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ > do.log 2>&1 &
+XXX - running Fri May 29 20:21:44 PDT 2009
+
+ time doRecipBest.pl -buildDir=`pwd` hg19 loxAfr1 > rbest.log 2>&1
+
+##############################################################################
+# LASTZ Kangaroo Rat DipOrd1 (WORKING - 2009-05-29 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzDipOrd1.2009-05-29
+ cd /hive/data/genomes/hg19/bed/lastzDipOrd1.2009-05-29
+
+ cat << '_EOF_' > DEF
+# Human vs. Kangaroo Rat
+BLASTZ_M=50
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/nib
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Kangaroo Rat
+SEQ2_DIR=/scratch/data/dipOrd1/dipOrd1.2bit
+SEQ2_LEN=/scratch/data/dipOrd1/chrom.sizes
+SEQ2_CHUNK=30000000
+SEQ2_LIMIT=300
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzDipOrd1.2009-05-29
+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 -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ > do.log 2>&1 &
+XXX - running Fri May 29 09:58:08 PDT 2009
time doRecipBest.pl -buildDir=`pwd` hg19 loxAfr1 > rbest.log 2>&1
##############################################################################