src/hg/makeDb/doc/hg19.txt 1.22
1.22 2009/06/02 18:35:57 hiram
Begin running the swaps
Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.21
retrieving revision 1.22
diff -b -B -U 4 -r1.21 -r1.22
--- src/hg/makeDb/doc/hg19.txt 30 May 2009 03:22:22 -0000 1.21
+++ src/hg/makeDb/doc/hg19.txt 2 Jun 2009 18:35:57 -0000 1.22
@@ -659,9 +659,9 @@
# chrY 10000 2649520
# chrY 59034049 59363566
############################################################################
-# Gorilla Lastz run (WORKING - 2009-03-21 - Hiram)
+# Gorilla Lastz run (DONE - 2009-03-21,05-13 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzGorGor1.2009-03-21
cd /hive/data/genomes/hg19/bed/lastzGorGor1.2009-03-21
cat << '_EOF_'
# human vs gorilla
@@ -991,9 +991,9 @@
# Advisory lock has been released
# All done
##############################################################################
-# BACEND SEQUENCE ALIGNMENTS (WORKING - 2009-04-28 - Hiram)
+# BACEND SEQUENCE ALIGNMENTS (DONE - 2009-04-28,05-20 - Hiram)
mkdir -p /hive/data/genomes/hg19/bed/bacends/run.blat
cd /hive/data/genomes/hg19/bed/bacends/run.blat
# going to run separate runs for the golden path sequence vs. the
# randoms, haplotypes, chrUn and chrM
@@ -1099,9 +1099,9 @@
bacEndPairsBad.bed | headRest 2 stdin | sort -k14,14 -k16,16n \
> bacEndPairs.load.psl
############################################################################
-# BACEND Randoms SEQUENCE ALIGNMENTS (WORKING - 2009-04-28 - Hiram)
+# BACEND Randoms SEQUENCE ALIGNMENTS (DONE - 2009-04-28,05-20 - Hiram)
mkdir -p /hive/data/genomes/hg19/bed/bacends/run.randoms
cd /hive/data/genomes/hg19/bed/bacends/run.randoms
# this separate run for the randoms, haplotypes, chrUn and chrM
partitionSequence.pl 5000000 20000 /scratch/data/hg19/hg19.2bit \
@@ -1897,8 +1897,9 @@
# some other things we have here.
$HOME/kent/src/hg/fishClones/fixup.hbrc.pl hbrc.txt \
/hive/data/genomes/hg19/bed/fishClones/seq_clone.pmd > fixed.hbrc.txt \
2> dbg
+XXX - need to get this seq_clone.pmd from NCBI, maybe Paul Kitts
# the seq_clone.pmd file was obtained via email from Wonhee Jang
# jang at ncbi.nlm.nih.gov - I have asked for clarification where
# such a file can be fetched without resorting to email.
@@ -2191,8 +2192,20 @@
-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
cat fb.hg19.chainCanFam2Link.txt
# 1532073507 bases of 2897316137 (52.879%) in intersection
+ # running the swap
+ mkdir /hive/data/genomes/canFam2/bed/blastz.hg19.swap
+ cd /hive/data/genomes/canFam2/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzCanFam2.2009-05-13/DEF \
+ -noLoadChainSplit -swap \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:19:50 PDT 2009
+ # real 723m41.377s
+ cat fb.canFam2.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
#########################################################################
# LASTZ Chicken GalGal3 (DONE - 2009-05-13 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzGalGal3.2009-05-13
cd /hive/data/genomes/hg19/bed/lastzGalGal3.2009-05-13
@@ -2234,8 +2247,21 @@
-chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1
cat fb.hg19.chainGalGal3Link.txt
# 104053179 bases of 2897316137 (3.591%) in intersection
+ # running the swap
+ mkdir /hive/data/genomes/galGal3/bed/blastz.hg19.swap
+ cd /hive/data/genomes/galGal3/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzGalGal3.2009-05-13/DEF \
+ -swap \
+ -noLoadChainSplit \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ -chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1
+XXX - running Tue Jun 2 11:24:11 PDT 2009
+ # real 723m41.377s
+ cat fb.galGal3.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
#########################################################################
# LASTZ Macaca Mulatta RheMac2 (DONE - 2009-05-13 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzRheMac2.2009-05-13
cd /hive/data/genomes/hg19/bed/lastzRheMac2.2009-05-13
@@ -2282,8 +2308,21 @@
# real 760m22.810s
cat fb.hg19.chainRheMac2Link.txt
# 2397361211 bases of 2897316137 (82.744%) in intersection
+ # running the swap
+ mkdir /hive/data/genomes/rheMac2/bed/blastz.hg19.swap
+ cd /hive/data/genomes/rheMac2/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzRheMac2.2009-05-13/DEF \
+ -swap \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:16:25 PDT 2009
+ # real 723m41.377s
+ cat fb.rheMac2.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
#########################################################################
# LASTZ Rat Rn4 (DONE - 2009-05-13 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzRn4.2009-05-13
cd /hive/data/genomes/hg19/bed/lastzRn4.2009-05-13
@@ -2321,8 +2360,20 @@
# real 314m18.227s
cat fb.hg19.chainRn4Link.txt
# 952605822 bases of 2897316137 (32.879%) in intersection
+ # running the swap
+ mkdir /hive/data/genomes/rn4/bed/blastz.hg19.swap
+ cd /hive/data/genomes/rn4/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzRn4.2009-05-13/DEF \
+ -swap -noLoadChainSplit \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:21:44 PDT 2009
+ # real 723m41.377s
+ cat fb.rn4.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
##############################################################################
# LASTZ Orangutan PonAbe2 (DONE - 2009-05-13 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzPonAbe2.2009-05-13
cd /hive/data/genomes/hg19/bed/lastzPonAbe2.2009-05-13
@@ -2370,8 +2421,21 @@
> do.log 2>&1 &
cat fb.hg19.chainPonAbe2Link.txt
# 2646687531 bases of 2897316137 (91.350%) in intersection
+ # running the swap
+ mkdir /hive/data/genomes/ponAbe2/bed/blastz.hg19.swap
+ cd /hive/data/genomes/ponAbe2/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzPonAbe2.2009-05-13/DEF \
+ -swap \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:08:17 PDT 2009
+ # real 723m41.377s
+ cat fb.ponAbe2.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
##############################################################################
# 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
@@ -2414,8 +2478,21 @@
# real 113m20.116s
cat fb.hg19.chainPetMar1Link.txt
# 31347143 bases of 2897316137 (1.082%) in intersection
+ # running the swap
+ mkdir /hive/data/genomes/petMar1/bed/blastz.hg19.swap
+ cd /hive/data/genomes/petMar1/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzPetMar1.2009-05-14/DEF \
+ -qRepeats=windowmaskerSdust \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
+ -swap > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:35:37 PDT 2009
+ # real 723m41.377s
+ cat fb.petMar1.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
##############################################################################
# LASTZ Fugu Fr2 (DONE - 2009-05-14 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzFr2.2009-05-14
cd /hive/data/genomes/hg19/bed/lastzFr2.2009-05-14
@@ -2471,8 +2548,21 @@
> cat.log 2>&1 &
cat fb.hg19.chainFr2Link.txt
# 49309456 bases of 2897316137 (1.702%) in intersection
+ # running the swap
+ mkdir /hive/data/genomes/fr2/bed/blastz.hg19.swap
+ cd /hive/data/genomes/fr2/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzFr2.2009-05-14/DEF \
+ -qRepeats=windowmaskerSdust \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=encodek \
+ -swap > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:30:44 PDT 2009
+ # real 723m41.377s
+ cat fb.fr2.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
##############################################################################
# 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
@@ -2514,8 +2604,20 @@
# real 166m19.745s
cat fb.hg19.chainTetNig1Link.txt
# 58038079 bases of 2897316137 (2.003%) in intersection
+ # running the swap
+ mkdir /hive/data/genomes/tetNig1/bed/blastz.hg19.swap
+ cd /hive/data/genomes/tetNig1/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzTetNig1.2009-05-14/DEF \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ -swap > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:33:01 PDT 2009
+ # real 723m41.377s
+ cat fb.tetNig1.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
##############################################################################
# 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
@@ -2557,8 +2659,20 @@
# real 174m40.659s
cat fb.hg19.chainGasAcu1Link.txt
# 55509003 bases of 2897316137 (1.916%) in intersection
+ # running the swap
+ mkdir /hive/data/genomes/gasAcu1/bed/blastz.hg19.swap
+ cd /hive/data/genomes/gasAcu1/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzGasAcu1.2009-05-14/DEF \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ -swap > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:08:17 PDT 2009
+ # real 723m41.377s
+ cat fb.gasAcu1.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
##############################################################################
# LASTZ Marmoset CalJac1 (DONE - 2009-05-14,22 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzCalJac1.2009-05-14
cd /hive/data/genomes/hg19/bed/lastzCalJac1.2009-05-14
@@ -2607,10 +2721,24 @@
# 2053025318 bases of 2897316137 (70.860%) in intersection
time doRecipBest.pl -buildDir=`pwd` hg19 calJac1 > rbest.log 2>&1 &
# real 97m17.207s
+ # running the swap
+ mkdir /hive/data/genomes/calJac1/bed/blastz.hg19.swap
+ cd /hive/data/genomes/calJac1/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzCalJac1.2009-05-14/DEF \
+ -swap \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:17:56 PDT 2009
+ # real 723m41.377s
+ cat fb.calJac1.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
+
#########################################################################
-# LASTZ Tarsier TarSyr1 (WORKING - 2009-05-14 - Hiram)
+# LASTZ Tarsier TarSyr1 (DONE - 2009-05-14,30 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzTarSyr1.2009-05-14
cd /hive/data/genomes/hg19/bed/lastzTarSyr1.2009-05-14
cat << '_EOF_' > DEF
@@ -2713,11 +2841,13 @@
-noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
> download.log 2>&1 &
# real 48m6.573s
+ # ran the script on swarm to recover after hive outages
time doRecipBest.pl -buildDir=`pwd` hg19 tarSyr1 > rbest.log 2>&1 &
- # real 150m27.228s
-XXX failed
+ # real 404m0.201s
+ time doRecipBest.pl -continue=download -buildDir=`pwd` \
+ hg19 tarSyr1 > rbest.download.log 2>&1 &
#########################################################################
# LASTZ Bushbaby OtoGar1 (DONE - 2009-05-14,22 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzOtoGar1.2009-05-14
@@ -3098,10 +3228,23 @@
# real 124m5.298s
cat fb.hg19.chainOryLat2Link.txt
# 53571737 bases of 2897316137 (1.849%) in intersection
+ # running the swap
+ mkdir /hive/data/genomes/oryLat2/bed/blastz.hg19.swap
+ cd /hive/data/genomes/oryLat2/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzOryLat2.2009-05-22/DEF \
+ -qRepeats=windowmaskerSdust \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ -swap > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:08:17 PDT 2009
+ # real 723m41.377s
+ cat fb.oryLat2.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
##############################################################################
-# LASTZ Opossum MonDom5 (WORKING - 2009-05-23 - Hiram)
+# LASTZ Opossum MonDom5 (DONE - 2009-05-23,29 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzMonDom5.2009-05-23
cd /hive/data/genomes/hg19/bed/lastzMonDom5.2009-05-23
cat << '_EOF_' > DEF
@@ -3158,9 +3301,9 @@
`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
+ # real 20m29.049s
##############################################################################
# LASTZ Armadillo DasNov2 (DONE - 2009-05-23,28 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzDasNov2.2009-05-23
@@ -3210,9 +3353,9 @@
> rbest.log 2>&1
# time about 6h30m
##############################################################################
-# LASTZ Rock Hyrax ProCap1 (WORKING - 2009-05-23 - Hiram)
+# LASTZ Rock Hyrax ProCap1 (DONE - 2009-05-23,26 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzProCap1.2009-05-23
cd /hive/data/genomes/hg19/bed/lastzProCap1.2009-05-23
cat << '_EOF_' > DEF
@@ -3316,12 +3459,26 @@
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-continue=syntenicNet -qRepeats=windowmaskerSdust > synNet.log 2>&1 &
# real 4m10.261s
+ # running the swap
+ mkdir /hive/data/genomes/taeGut1/bed/blastz.hg19.swap
+ cd /hive/data/genomes/taeGut1/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzTaeGut1.2009-05-26/DEF \
+ -swap -noLoadChainSplit -chainMinScore=5000 \
+ -chainLinearGap=loose \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ -qRepeats=windowmaskerSdust > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:25:44 PDT 2009
+ # real 723m41.377s
+ cat fb.taeGut1.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
+
##############################################################################
-# LASTZ Lizard AnoCar1 (WORKING - 2009-05-26 - Hiram)
- mkdir /hive/data/genomes/hg19/bed/lastzAnoCar1.2009-05-26
- cd /hive/data/genomes/hg19/bed/lastzAnoCar1.2009-05-26
+# LASTZ Lizard AnoCar1 (DONE - 2009-05-30,31 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzAnoCar1.2009-05-30
+ cd /hive/data/genomes/hg19/bed/lastzAnoCar1.2009-05-30
cat << '_EOF_' > DEF
# human vs lizard
BLASTZ_H=2000
@@ -3337,14 +3494,14 @@
SEQ1_LAP=10000
# QUERY: Lizard anoCar1
SEQ2_DIR=/scratch/data/anoCar1/anoCar1.2bit
-SEQ2_LEN=/hive/data/genomes/anoCar1/chrom.sizes
+SEQ2_LEN=/scratch/data/anoCar1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=50
-BASE=/hive/data/genomes/hg19/bed/lastzAnoCar1.2009-05-26
+BASE=/hive/data/genomes/hg19/bed/lastzAnoCar1.2009-05-30
TMPDIR=/scratch/tmp
'_EOF_'
# << happy emacs
@@ -3352,19 +3509,28 @@
screen
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
- -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
-qRepeats=windowmaskerSdust > do.log 2>&1 &
- # real 369m5.335s
- # problem on memk during cat step, finish than, then continuing:
+ # real 168m32.016s
+ cat fb.hg19.chainAnoCar1Link.txt
+ # 104045950 bases of 2897316137 (3.591%) in intersection
+ time doRecipBest.pl -buildDir=`pwd` hg19 anoCar1 > rbest.log 2>&1
+ # real 45m58.001s
+
+ # running the swap
+ mkdir /hive/data/genomes/anoCar1/bed/blastz.hg19.swap
+ cd /hive/data/genomes/anoCar1/bed/blastz.hg19.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
- `pwd`/DEF \
+ /hive/data/genomes/hg19/bed/lastzAnoCar1.2009-05-30/DEF \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
- -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
- -continue=chainRun -qRepeats=windowmaskerSdust > chainRun.log 2>&1 &
- # real 16m31.552s
-
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ -swap -qRepeats=windowmaskerSdust > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:26:55 PDT 2009
+ # real 723m41.377s
+ cat fb.anoCar1.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
##############################################################################
# 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
@@ -3412,10 +3578,22 @@
# time about 1h30m
cat fb.hg19.chainXenTro2Link.txt
# 92015242 bases of 2897316137 (3.176%) in intersection
+ # running the swap
+ mkdir /hive/data/genomes/xenTro2/bed/blastz.hg19.swap
+ cd /hive/data/genomes/xenTro2/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzXenTro2.2009-05-26/DEF \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ -swap > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:28:06 PDT 2009
+ # real 723m41.377s
+ cat fb.xenTro2.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
##############################################################################
-# LASTZ Zebrafish DanRer5 (WORKING - 2009-05-26 - Hiram)
+# LASTZ Zebrafish DanRer5 (DONE - 2009-05-26 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzDanRer5.2009-05-26
cd /hive/data/genomes/hg19/bed/lastzDanRer5.2009-05-26
cat << '_EOF_' > DEF
@@ -3454,8 +3632,20 @@
# real 311m39.817s
cat fb.hg19.chainDanRer5Link.txt
# 74229561 bases of 2897316137 (2.562%) in intersection
+ # running the swap
+ mkdir /hive/data/genomes/danRer5/bed/blastz.hg19.swap
+ cd /hive/data/genomes/danRer5/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzDanRer5.2009-05-26/DEF \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ -swap > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:31:49 PDT 2009
+ # real 723m41.377s
+ cat fb.danRer5.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
##############################################################################
# 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
@@ -3498,10 +3688,23 @@
# 220977689 bases of 2897316137 (7.627%) in intersection
time doRecipBest.pl -buildDir=`pwd` hg19 ornAna1 > rbest.log 2>&1
# time about 1h32m
+ # running the swap
+ mkdir /hive/data/genomes/ornAna1/bed/blastz.hg19.swap
+ cd /hive/data/genomes/ornAna1/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzOrnAna1.2009-05-26/DEF \
+ -swap -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ > swap.log 2>&1 &
+XXX - running Tue Jun 2 11:23:00 PDT 2009
+ # real 723m41.377s
+ cat fb.ornAna1.chainHg19Link.txt
+ # 2761343871 bases of 2909485072 (94.908%) in intersection
+
##############################################################################
-# LASTZ Elephant LoxAfr2 (WORKING - 2009-05-27 - Hiram)
+# LASTZ Elephant LoxAfr2 (DONE - 2009-05-27,29 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzLoxAfr2.2009-05-27
cd /hive/data/genomes/hg19/bed/lastzLoxAfr2.2009-05-27
cat << '_EOF_' > DEF
@@ -3538,9 +3741,8 @@
# 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 (DONE - 2009-05-27 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzEchTel1.2009-05-27
@@ -3616,14 +3818,46 @@
-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
+ # XXX there is one job that is taking forever ...
+ # finished it in pieces on swarm in a few minutes, like this:
+ mkdir /hive/data/genomes/hg19/bed/lastzTupBel1.2009-05-27/run.blastz/lastJob
+ cd /hive/data/genomes/hg19/bed/lastzTupBel1.2009-05-27/run.blastz/lastJob
+#!/bin/sh
+
+S=100000000
+E=101010000
+export S E
+for I in 0 1 2 3 4 5 6 7 8 9
+do
+echo $S $E
+/usr/bin/time -p /cluster/bin/scripts/blastz-run-ucsc -outFormat psl \
+/scratch/data/hg19/nib/chr1.nib:chr1:${S}-${E} ../qParts/part019.lst \
+../../DEF psl/chr1.nib:chr1:${S}-${E}_part019.lst.psl
+nextS=`echo $S | awk '{printf "%d", $1 + 1000000}'`
+nextE=`echo $E | awk '{printf "%d", $1 + 1000000}'`
+S=$nextS
+E=$nextE
+done
- time doRecipBest.pl -buildDir=`pwd` hg19 loxAfr1 > rbest.log 2>&1
+ grep -h "^#" psl/chr* | sort -u > result.psl
+ grep -h -v "^#" psl/chr* | sort -k14,14 -k16,16n >> result.psl
+ cp -p result.psl \
+../../psl/chr1.nib:chr1:100000000-110010000/chr1.nib:chr1:100000000-110010000_part019.lst.psl
+
+ # then, continuing:
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
+ -continue=cat > cat.log 2>&1 &
+ # real 212m22.707s
+ time doRecipBest.pl -buildDir=`pwd` hg19 tupBel1 > rbest.log 2>&1
+XXX - running Tue Jun 2 10:15:24 PDT 2009
##############################################################################
-# LASTZ Shrew SorAra1 (WORKING - 2009-05-28 - Hiram)
+# LASTZ Shrew SorAra1 (DONE - 2009-05-28,30 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzSorAra1.2009-05-28
cd /hive/data/genomes/hg19/bed/lastzSorAra1.2009-05-28
cat << '_EOF_' > DEF
@@ -3659,12 +3893,12 @@
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
+ # real 251m20.055s
##############################################################################
-# LASTZ Rabbit OryCun1 (WORKING - 2009-05-28 - Hiram)
+# LASTZ Rabbit OryCun1 (DONE - 2009-05-28,30 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzOryCun1.2009-05-28
cd /hive/data/genomes/hg19/bed/lastzOryCun1.2009-05-28
cat << '_EOF_' > DEF
@@ -3700,12 +3934,12 @@
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
+ # real 318m1.142s
##############################################################################
-# LASTZ Rabbit EriEur1 (WORKING - 2009-05-28 - Hiram)
+# LASTZ Hedgehog EriEur1 (DONE - 2009-05-28,30 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzEriEur1.2009-05-28
cd /hive/data/genomes/hg19/bed/lastzEriEur1.2009-05-28
cat << '_EOF_' > DEF
@@ -3736,14 +3970,16 @@
`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
+ # real 2043m33.198s
+ cat fb.hg19.chainEriEur1Link.txt
+ # 560965051 bases of 2897316137 (19.362%) in intersection
+ time doRecipBest.pl -buildDir=`pwd` hg19 eriEur1 > rbest.log 2>&1
+ # real 350m17.737s
##############################################################################
-# LASTZ Pika OchPri2 (WORKING - 2009-05-29 - Hiram)
+# LASTZ Pika OchPri2 (DONE - 2009-05-29,30 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzOchPri2.2009-05-29
cd /hive/data/genomes/hg19/bed/lastzOchPri2.2009-05-29
cat << '_EOF_' > DEF
@@ -3774,14 +4010,16 @@
`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
+ # real 393m42.569s
+ cat fb.hg19.chainOchPri2Link.txt
+ # 804516397 bases of 2897316137 (27.768%) in intersection
+ time doRecipBest.pl -buildDir=`pwd` hg19 ochPri2 > rbest.log 2>&1
+ # real 224m47.979s
##############################################################################
-# LASTZ Kangaroo Rat DipOrd1 (WORKING - 2009-05-29 - Hiram)
+# LASTZ Kangaroo Rat DipOrd1 (DONE - 2009-05-29,30 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzDipOrd1.2009-05-29
cd /hive/data/genomes/hg19/bed/lastzDipOrd1.2009-05-29
cat << '_EOF_' > DEF
@@ -3812,9 +4050,9 @@
`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
+ # real 688m47.595s
+ time doRecipBest.pl -buildDir=`pwd` hg19 dipOrd1 > rbest.log 2>&1
+ # real 140m42.014s
##############################################################################