src/hg/makeDb/doc/hg19.txt 1.23
1.23 2009/06/02 21:43:00 hiram
the swap lastz are done for those genomes that are public on the RR
Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.22
retrieving revision 1.23
diff -b -B -U 4 -r1.22 -r1.23
--- src/hg/makeDb/doc/hg19.txt 2 Jun 2009 18:35:57 -0000 1.22
+++ src/hg/makeDb/doc/hg19.txt 2 Jun 2009 21:43:00 -0000 1.23
@@ -608,9 +608,9 @@
# real 47m17.871s
cat fb.hg19.chainPanTro2Link.txt
# 2747983350 bases of 2897316137 (94.846%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-05-24
ssh swarm
mkdir /hive/data/genomes/panTro2/bed/blastz.hg19.swap
cd /hive/data/genomes/panTro2/bed/blastz.hg19.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
@@ -2192,20 +2192,19 @@
-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
cat fb.hg19.chainCanFam2Link.txt
# 1532073507 bases of 2897316137 (52.879%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real 200m17.158s
cat fb.canFam2.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 1480018167 bases of 2384996543 (62.055%) 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
@@ -2247,21 +2246,21 @@
-chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1
cat fb.hg19.chainGalGal3Link.txt
# 104053179 bases of 2897316137 (3.591%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real 16m45.090s
cat fb.galGal3.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 91605899 bases of 1042591351 (8.786%) 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
@@ -2308,21 +2307,20 @@
# real 760m22.810s
cat fb.hg19.chainRheMac2Link.txt
# 2397361211 bases of 2897316137 (82.744%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real 83m51.483s
cat fb.rheMac2.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 2313806886 bases of 2646704109 (87.422%) 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
@@ -2360,20 +2358,19 @@
# real 314m18.227s
cat fb.hg19.chainRn4Link.txt
# 952605822 bases of 2897316137 (32.879%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real 188m0.163s
cat fb.rn4.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 947862300 bases of 2571531505 (36.860%) 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
@@ -2421,21 +2418,20 @@
> do.log 2>&1 &
cat fb.hg19.chainPonAbe2Link.txt
# 2646687531 bases of 2897316137 (91.350%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real 124m3.610s
cat fb.ponAbe2.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 2772351468 bases of 3093572278 (89.617%) 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
@@ -2478,21 +2474,20 @@
# real 113m20.116s
cat fb.hg19.chainPetMar1Link.txt
# 31347143 bases of 2897316137 (1.082%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real 59m14.813s
cat fb.petMar1.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 26615001 bases of 831696438 (3.200%) 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
@@ -2548,21 +2543,21 @@
> cat.log 2>&1 &
cat fb.hg19.chainFr2Link.txt
# 49309456 bases of 2897316137 (1.702%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real 25m8.491s
cat fb.fr2.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 42984130 bases of 393312790 (10.929%) 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
@@ -2604,20 +2599,19 @@
# real 166m19.745s
cat fb.hg19.chainTetNig1Link.txt
# 58038079 bases of 2897316137 (2.003%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real 29m20.968s
cat fb.tetNig1.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 49453375 bases of 342403326 (14.443%) 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
@@ -2659,20 +2653,19 @@
# real 174m40.659s
cat fb.hg19.chainGasAcu1Link.txt
# 55509003 bases of 2897316137 (1.916%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real 29m41.433s
cat fb.gasAcu1.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 49909819 bases of 446627861 (11.175%) 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
@@ -2721,21 +2714,20 @@
# 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
+ # running the swap - DONE - 2009-06-02
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
+ # real 162m52.189s
cat fb.calJac1.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 2105959656 bases of 2929139385 (71.897%) in intersection
#########################################################################
# LASTZ Tarsier TarSyr1 (DONE - 2009-05-14,30 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzTarSyr1.2009-05-14
@@ -3228,21 +3220,20 @@
# real 124m5.298s
cat fb.hg19.chainOryLat2Link.txt
# 53571737 bases of 2897316137 (1.849%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real 28m35.174s
cat fb.oryLat2.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 46961818 bases of 700386597 (6.705%) in intersection
##############################################################################
# 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
@@ -3459,21 +3450,20 @@
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-continue=syntenicNet -qRepeats=windowmaskerSdust > synNet.log 2>&1 &
# real 4m10.261s
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real real 16m45.080s
cat fb.taeGut1.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 95320369 bases of 1222864691 (7.795%) in intersection
##############################################################################
# LASTZ Lizard AnoCar1 (DONE - 2009-05-30,31 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzAnoCar1.2009-05-30
@@ -3517,20 +3507,19 @@
# 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
+ # running the swap - DONE - 2009-06-02
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 \
/hive/data/genomes/hg19/bed/lastzAnoCar1.2009-05-30/DEF \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
-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
+ # real 34m55.857s
cat fb.anoCar1.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 89608316 bases of 1741478929 (5.146%) 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
@@ -3578,20 +3567,19 @@
# time about 1h30m
cat fb.hg19.chainXenTro2Link.txt
# 92015242 bases of 2897316137 (3.176%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real 130m53.860s
cat fb.xenTro2.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 92070065 bases of 1359412157 (6.773%) in intersection
##############################################################################
# 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
@@ -3632,20 +3620,19 @@
# real 311m39.817s
cat fb.hg19.chainDanRer5Link.txt
# 74229561 bases of 2897316137 (2.562%) in intersection
- # running the swap
+ # running the swap - DONE - 2009-06-02
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
+ # real 26m54.605s
cat fb.danRer5.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 73852780 bases of 1435609608 (5.144%) 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
@@ -3688,20 +3675,19 @@
# 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
+ # running the swap - DONE - 2009-06-02
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
+ # real 146m52.638s
cat fb.ornAna1.chainHg19Link.txt
- # 2761343871 bases of 2909485072 (94.908%) in intersection
+ # 207415519 bases of 1842236818 (11.259%) in intersection
##############################################################################
# LASTZ Elephant LoxAfr2 (DONE - 2009-05-27,29 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzLoxAfr2.2009-05-27
@@ -3783,9 +3769,9 @@
time doRecipBest.pl -buildDir=`pwd` hg19 echTel1 > rbest.log 2>&1
# time about 7h13m
##############################################################################
-# LASTZ Tree Shrew TupBel1 (WORKING - 2009-05-27 - Hiram)
+# LASTZ Tree Shrew TupBel1 (DONE - 2009-05-27,06-02 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzTupBel1.2009-05-27
cd /hive/data/genomes/hg19/bed/lastzTupBel1.2009-05-27
cat << '_EOF_' > DEF
@@ -3852,9 +3838,9 @@
-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
+ # time about 4h22m
##############################################################################
# LASTZ Shrew SorAra1 (DONE - 2009-05-28,30 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzSorAra1.2009-05-28