src/hg/makeDb/doc/hg19.txt 1.20
1.20 2009/05/27 23:14:37 hiram
Running Elephant and Tenrec lastz
Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.19
retrieving revision 1.20
diff -b -B -U 4 -r1.19 -r1.20
--- src/hg/makeDb/doc/hg19.txt 26 May 2009 23:28:38 -0000 1.19
+++ src/hg/makeDb/doc/hg19.txt 27 May 2009 23:14:37 -0000 1.20
@@ -3175,14 +3175,15 @@
-noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
> do.log 2>&1 &
# finished the lastz run manually after hive maintenance outages
-XXX - running Sat May 23 15:18:48 PDT 2009
+ # then, continuing:
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`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
##############################################################################
# LASTZ Rock Hyrax ProCap1 (WORKING - 2009-05-23 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzProCap1.2009-05-23
@@ -3234,9 +3235,9 @@
cat fb.hg19.chainProCap1Link.txt
# 894221652 bases of 2897316137 (30.864%) in intersection
time nice -n +19 doRecipBest.pl -buildDir=`pwd` hg19 proCap1 \
> rbest.log 2>&1
-XXX - running Tue May 26 16:04:55 PDT 2009
+ # real 251m59.549s
##############################################################################
# LASTZ Zebra Finch TaeGut1 (DONE - 2009-05-26 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzTaeGut1.2009-05-26
@@ -3327,9 +3328,16 @@
`pwd`/DEF \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
-qRepeats=windowmaskerSdust > do.log 2>&1 &
-XXX - running Tue May 26 11:27:47 PDT 2009
+ # real 369m5.335s
+ # problem on memk during cat step, finish than, then continuing:
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ -continue=chainRun -qRepeats=windowmaskerSdust > chainRun.log 2>&1 &
+ # real 16m31.552s
##############################################################################
# LASTZ X. tropicalis XenTro2 (WORKING - 2009-05-26 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzXenTro2.2009-05-26
@@ -3367,9 +3375,16 @@
`pwd`/DEF \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
> do.log 2>&1 &
-XXX - running Tue May 26 15:02:27 PDT 2009
+ # real 1129m11.568s
+ # finished the lastz run manually after hive difficulties, continuing:
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `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
##############################################################################
# LASTZ Zebrafish DanRer5 (WORKING - 2009-05-26 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzDanRer5.2009-05-26
@@ -3407,9 +3422,11 @@
`pwd`/DEF \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
> do.log 2>&1 &
-XXX - running Tue May 26 15:02:27 PDT 2009
+ # real 311m39.817s
+ cat fb.hg19.chainDanRer5Link.txt
+ # 74229561 bases of 2897316137 (2.562%) in intersection
##############################################################################
# LASTZ Platypus OrnAna1 (WORKING - 2009-05-26 - Hiram)
mkdir /hive/data/genomes/hg19/bed/lastzOrnAna1.2009-05-26
@@ -3447,7 +3464,87 @@
`pwd`/DEF \
-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
> do.log 2>&1 &
-XXX - running Tue May 26 16:28:05 PDT 2009
+ # 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
+
+##############################################################################
+# LASTZ Elephant LoxAfr2 (WORKING - 2009-05-27 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzLoxAfr2.2009-05-27
+ cd /hive/data/genomes/hg19/bed/lastzLoxAfr2.2009-05-27
+
+ cat << '_EOF_' > DEF
+# Human vs. Elephant
+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: Elephant
+SEQ2_DIR=/scratch/data/loxAfr2/loxAfr2.2bit
+SEQ2_LEN=/scratch/data/loxAfr2/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=300
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzLoxAfr2.2009-05-27
+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=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
+
+##############################################################################
+# LASTZ Tenrec EchTel1 (WORKING - 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
+# Human vs. Tenrec
+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: Tenrec
+SEQ2_DIR=/scratch/data/echTel1/echTel1.2bit
+SEQ2_LEN=/scratch/data/echTel1/chrom.sizes
+SEQ2_CHUNK=30000000
+SEQ2_LIMIT=400
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzEchTel1.2009-05-27
+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=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
##############################################################################