# for emacs: -*- mode: sh; -*-

# Caenorhabditis elegans
# Washington University School of Medicine GSC and Sanger Institute WS200

#  $Id: ce7.txt,v 1.4 2009/09/24 20:54:50 hiram Exp $

#########################################################################
# DOWNLOAD SEQUENCE (DONE - 2009-07-21 - Hiram)
    mkdir /hive/data/genomes/ce7
    cd /hive/data/genomes/ce7
    mkdir ws200
    cd ws200
TOP=/hive/data/genomes/ce7/ws200
export TOP
for D in annotation genome_feature_tables/GFF2 \
        genome_feature_tables/SUPPLEMENTARY_GFF sequences/dna \
        sequences/protein sequences/rna
do
    mkdir -p ${D}
    cd ${D}
    wget --timestamping \
ftp://ftp.sanger.ac.uk/pub2/wormbase/WS200/genomes/c_elegans/${D}/*.*
    cd ${TOP}
done
    #	that took a long time, many many hours.  The transfer speed from
    #	sanger was very slow

#########################################################################
# NORMALIZE SEQUENCE NAMES TO BEGIN WITH chr (DONE - 2009-07-22 - Hiram)
    mkdir /hive/data/genomes/ce7/sanger
    cd /hive/data/genomes/ce7/sanger
    # Fix fasta names:
    cat ../ws200/sequences/dna/CHR*.dna \
    | sed -e '/^$/ d;  s/^>CHROMOSOME_MtDNA/>chrM/;  s/^>CHROMOSOME_/>chr/;' \
    | gzip -c > UCSC.fa.gz
    faSize -detailed UCSC.fa.gz
# chrI    15072421
# chrII   15279324
# chrIII  13783682
# chrIV   17493784
# chrM    13794
# chrV    20924143
# chrX    17718854

    # Make sure we get the same sizes from this command:
    cat ../ws200/sequences/dna/CHR*.dna | sed -e '/^$/ d;' \
	| faSize -detailed stdin

    faCount UCSC.fa.gz
#seq    len     A       C       G       T       N       cpg
# chrI    15072421        4835939 2695879 2692150 4848453 0       503521
# chrII   15279324        4878196 2769216 2762198 4869714 0       492149
# chrIII  13783682        4444652 2449139 2466321 4423570 0       459669
# chrIV   17493784        5711040 3034767 3017008 5730969 0       522372
# chrM    13794   4335    1225    2055    6179    0       110
# chrV    20924143        6750393 3712058 3701397 6760295 0       638983
# chrX    17718854        5747199 3119702 3117868 5734085 0       514715
# total   100286002       32371754  17781986  17758997  323732650  3131519

    # Fix AGP names:
    sed -e 's/^/chr/' ../ws200/sequences/dna/CHR*.agp > UCSC.agp
    # And add a fake mitochondrial AGP entry for the sake of downstream
    # tools (make sure the GenBank sequence is identical to given):
    echo -e "chrM\t1\t13794\t1\tF\tNC_001328.1\t1\t13794\t+" >> UCSC.agp

#########################################################################
# run the makeGenomeDb procedure to create the db and unmasked sequence
#	(DONE - 2009-07-22 - Hiram)
    cd /hive/data/genomes/ce7
    cat << '_EOF_' > ce7.config.ra
# Config parameters for makeGenomeDb.pl:
db ce7
clade worm
genomeCladePriority 10
scientificName Caenorhabditis elegans
commonName C. elegans
assemblyDate Feb 2009
assemblyLabel Washington University School of Medicine GSC and Sanger Institute WS200
orderKey 825
mitoAcc none
fastaFiles /hive/data/genomes/ce7/sanger/UCSC.fa.gz
agpFiles   /hive/data/genomes/ce7/sanger/UCSC.agp
# qualFiles /dev/null
dbDbSpeciesDir worm
taxId 6239
'_EOF_'
    # << emacs

    mkdir jkStuff
    #	run just to AGP to make sure things are sane first
    nice -n +19 makeGenomeDb.pl ce7.config.ra -stop agp \
      > jkStuff/makeGenomeDb.agp.log 2>&1
    #	now, continuing to make the Db and all
    time nice -n +19 makeGenomeDb.pl ce7.config.ra -continue db \
      > jkStuff/makeGenomeDb.db.log 2>&1
    #	real    1m26.382s
    #	take the trackDb business there and check it into the source tree
    #	fixup the description, gap and gold html page descriptions

#########################################################################
# REPEATMASKER (DONE - 2009-07-22 - Hiram)
    screen 	#	use screen to control the job
    mkdir /hive/data/genomes/ce7/bed/repeatMasker
    cd /hive/data/genomes/ce7/bed/repeatMasker
    time nice -n +19 doRepeatMasker.pl -bigClusterHub=swarm \
	-buildDir=`pwd` ce7 > do.log 2>&1 &
    #	real    35m46.794s
    cat faSize.rmsk.txt
# 100286002 bases (0 N's 100286002 real 87035663 upper 13250339 lower)
#	in 7 sequences in 1 files
# %13.21 masked total, %13.21 masked real

    #	from the do.log:
    #   June 4 2009 (open-3-2-8) version of RepeatMasker
    #	CC   RELEASE 20090604;   

#########################################################################
# SIMPLE REPEATS (DONE - 2009-07-22 - Hiram)
    ssh kkstore06
    screen 	#	use screen to control the job
    mkdir /hive/data/genomes/ce7/bed/simpleRepeat
    cd /hive/data/genomes/ce7/bed/simpleRepeat
    time nice -n +19 doSimpleRepeat.pl -smallClusterHub=encodek \
	-buildDir=`pwd` ce7 > do.log 2>&1 &
    #	about 18 minutes

#########################################################################
# MASK SEQUENCE WITH RM+TRF (DONE - 2009-07-22 - Hiram)
    # Since both doRepeatMasker.pl and doSimpleRepeats.pl have completed,
    # now it's time to combine the masking into the final ce7.2bit,
    # following the instructions at the end of doSimpleRepeat's output.
    cd /hive/data/genomes/ce7
    twoBitMask ce7.rmsk.2bit -add bed/simpleRepeat/trfMask.bed ce7.2bit
    # You can safely ignore the warning about extra BED columns
    twoBitToFa ce7.2bit stdout | faSize stdin
# 100286002 bases (0 N's 100286002 real 86863809 upper 13422193 lower)
#	in 7 sequences in 1 files
# %13.38 masked total, %13.38 masked real

    #	set the symlink on hgwdev to /gbdb/ce7
    rm -f /gbdb/ce7/ce7.2bit
    ln -s /hive/data/genomes/ce7/ce7.2bit /gbdb/ce7/ce7.2bit

#########################################################################
# MAKE 11.OOC FILE FOR BLAT (DONE - 2009-07-22 - Hiram)
    # Use -repMatch=100 (based on size -- for human we use 1024, and 
    # worm size is ~3.4% of human judging by gapless ce4 vs. hg18 genome 
    # size from featureBits. So we would use 34, but that yields a very
    # high number of tiles to ignore, especially for a small more compact 
    # genome.  Bump that up a bit to be more conservative.
    cd /hive/data/genomes/ce7
    blat ce7.2bit /dev/null /dev/null -tileSize=11 \
      -makeOoc=jkStuff/ce7.11.ooc -repMatch=100
    #	Wrote 8502 overused 11-mers to jkStuff/ce7.11.ooc
    #	copy all of this stuff to the klusters:
    mkdir /hive/data/staging/data/ce7
    cp -p jkStuff/ce7.11.ooc chrom.sizes ce7.2bit /hive/data/staging/data/ce7

#########################################################################
## BLASTZ caePb2 (DONE - 2009-07-23 - Hiram)
    screen 	#	use screen to control the job
    mkdir /hive/data/genomes/ce7/bed/lastzCaePb2.2009-07-23
    cd /hive/data/genomes/ce7/bed/lastzCaePb2.2009-07-23

    cat << '_EOF_' > DEF
# ce7 vs caePb2
BLASTZ_H=2000
BLASTZ_M=50

# TARGET: elegans Ce7
SEQ1_DIR=/scratch/data/ce7/ce7.2bit
SEQ1_LEN=/scratch/data/ce7/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: C. PB2801 caePb2
SEQ2_DIR=/scratch/data/caePb2/caePb2.2bit
SEQ2_LEN=/scratch/data/caePb2/chrom.sizes
SEQ2_CTGDIR=/scratch/data/caePb2/caePb2.supercontigs.2bit
SEQ2_CTGLEN=/scratch/data/caePb2/caePb2.supercontigs.sizes
SEQ2_LIFT=/scratch/data/caePb2/caePb2.supercontigs.lift
SEQ2_CHUNK=1000000
SEQ2_LAP=0
SEQ2_LIMIT=50

BASE=/hive/data/genomes/ce7/bed/lastzCaePb2.2009-07-23
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	`pwd`/DEF -verbose=2 -bigClusterHub=pk -workhorse=hgwdev \
	-qRepeats=windowmaskerSdust -noLoadChainSplit -smallClusterHub=memk \
	> do.log 2>&1 &
    #	real   62m19.458s
    #	forgot the -qRepeats=windowmaskerSdust
    rm axtChain/ce7.caePb2.net
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	`pwd`/DEF -verbose=2 -bigClusterHub=pk -workhorse=hgwdev \
	-qRepeats=windowmaskerSdust -noLoadChainSplit -smallClusterHub=memk \
	-continue=load > load.log 2>&1 &
    cat fb.ce7.chainCaePb2Link.txt 
    #	40793071 bases of 100286002 (40.677%) in intersection

    #	swap, this is also in caePb2.txt
    mkdir /hive/data/genomes/caePb2/bed/blastz.ce7.swap
    cd /hive/data/genomes/caePb2/bed/blastz.ce7.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	-workhorse=hgwdev -qRepeats=windowmaskerSdust \
	/hive/data/genomes/ce7/bed/lastzCaePb2.2009-07-23/DEF \
	-bigClusterHub=pk -smallClusterHub=memk -swap > swap.log 2>&1 &
    #	real    3m22.808s
    cat fb.caePb2.chainCe7Link.txt
    #	55084634 bases of 170473138 (32.313%) in intersection

#########################################################################
## BLASTZ caeJap2 (DONE - 2009-07-24 - Hiram)
    screen 	#	use screen to control the job
    mkdir /hive/data/genomes/ce7/bed/lastzCaeJap2.2009-07-24
    cd /hive/data/genomes/ce7/bed/lastzCaeJap2.2009-07-24

    cat << '_EOF_' > DEF
# ce7 vs caeJap2
BLASTZ_H=2000
BLASTZ_M=50

# TARGET: elegans Ce7
SEQ1_DIR=/scratch/data/ce7/ce7.2bit
SEQ1_LEN=/scratch/data/ce7/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: C. japonica caeJap2
SEQ2_DIR=/scratch/data/caeJap2/caeJap2.2bit
SEQ2_LEN=/scratch/data/caeJap2/chrom.sizes
SEQ2_CTGDIR=/scratch/data/caeJap2/caeJap2.supers.2bit
SEQ2_CTGLEN=/scratch/data/caeJap2/caeJap2.supers.sizes
SEQ2_LIFT=/scratch/data/caeJap2/caeJap2.chrUn.lift
SEQ2_CHUNK=1000000
SEQ2_LAP=0
SEQ2_LIMIT=50

BASE=/hive/data/genomes/ce7/bed/lastzCaeJap2.2009-07-24
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	`pwd`/DEF \
	-bigClusterHub=pk -noLoadChainSplit -qRepeats=windowmaskerSdust \
	-workhorse=hgwdev -smallClusterHub=memk > do.log 2>&1 &
    #	real    87m1.988s
    cat fb.ce7.chainCaeJap2Link.txt 
    #	27270064 bases of 100286002 (27.192%) in intersection

    #	swap, this is also in caeJap2.txt
    mkdir /hive/data/genomes/caeJap2/bed/blastz.ce7.swap
    cd /hive/data/genomes/caeJap2/bed/blastz.ce7.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	-qRepeats=windowmaskerSdust -bigClusterHub=pk -noLoadChainSplit \
	/hive/data/genomes/ce7/bed/lastzCaeJap2.2009-07-24/DEF \
	-smallClusterHub=memk -swap > swap.log 2>&1 &
    #	real    4m23.124s
    cat fb.caeJap2.chainCe7Link.txt 
    #	26441005 bases of 129295754 (20.450%) in intersection

############################################################################
## BLASTZ cb3 (DONE - 2009-07-24 - Hiram)
    screen 	#	use screen to control the job
    mkdir /hive/data/genomes/ce7/bed/lastzCb3.2009-07-24
    cd /hive/data/genomes/ce7/bed/lastzCb3.2009-07-24

    cat << '_EOF_' > DEF
# ce7 vs cb3
BLASTZ_H=2000
BLASTZ_M=50

# TARGET: elegans Ce7
SEQ1_DIR=/scratch/data/ce7/ce7.2bit
SEQ1_LEN=/scratch/data/ce7/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: C. briggsae cb3
SEQ2_DIR=/hive/data/genomes/cb3/cb3.rmskTrf.2bit
SEQ2_LEN=/hive/data/genomes/cb3/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LAP=0

BASE=/hive/data/genomes/ce7/bed/lastzCb3.2009-07-24
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	`pwd`/DEF \
	-workhorse=hgwdev -bigClusterHub=pk -noLoadChainSplit \
	-smallClusterHub=memk > do.log 2>&1 &
    #	 real    50m9.701s
    cat fb.ce7.chainCb3Link.txt 
    #	42421335 bases of 100286002 (42.300%) in intersection

    #	swap, this is also in cb3.txt
    mkdir /hive/data/genomes/cb3/bed/blastz.ce7.swap
    cd /hive/data/genomes/cb3/bed/blastz.ce7.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/ce7/bed/lastzCb3.2009-07-24/DEF \
	-workhorse=hgwdev -bigClusterHub=pk -noLoadChainSplit \
	-smallClusterHub=memk -swap > swap.log 2>&1 &
    #	real    3m38.745s
    cat fb.cb3.chainCe7Link.txt 
    #	43115929 bases of 108433446 (39.763%) in intersection

############################################################################
## BLASTZ caeRem3 (DONE - 2009-07-24,09 - Hiram)
    screen 	#	use screen to control the job
    mkdir /hive/data/genomes/ce7/bed/lastzCaeRem3.2009-07-24
    cd /hive/data/genomes/ce7/bed/lastzCaeRem3.2009-07-24

    cat << '_EOF_' > DEF
# ce7 vs caeRem3
BLASTZ_H=2000
BLASTZ_M=50

# TARGET: elegans Ce7
SEQ1_DIR=/scratch/data/ce7/ce7.2bit
SEQ1_LEN=/scratch/data/ce7/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: C. remanei caeRem3
SEQ2_DIR=/scratch/data/caeRem3/caeRem3.2bit
SEQ2_LEN=/scratch/data/caeRem3/chrom.sizes
SEQ2_CTGDIR=/scratch/data/caeRem3/caeRem3.supercontigs.2bit
SEQ2_CTGLEN=/scratch/data/caeRem3/caeRem3.supercontigs.sizes
SEQ2_LIFT=/scratch/data/caeRem3/caeRem3.chrUn.lift
SEQ2_CHUNK=1000000
SEQ2_LAP=0
SEQ2_LIMIT=50

BASE=/hive/data/genomes/ce7/bed/lastzCaeRem3.2009-07-24
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	`pwd`/DEF \
	-workhorse=hgwdev -bigClusterHub=swarm -noLoadChainSplit \
	-qRepeats=windowmaskerSdust -smallClusterHub=memk > do.log 2>&1 &
    #	real    28m14.168s
    cat fb.ce7.chainCaeRem3Link.txt 
    #	41841199 bases of 100286002 (41.722%) in intersection

    #	swap, this is also in caeRem3.txt
    mkdir /hive/data/genomes/caeRem3/bed/blastz.ce7.swap
    cd /hive/data/genomes/caeRem3/bed/blastz.ce7.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	-qRepeats=windowmaskerSdust \
	-workhorse=hgwdev -noLoadChainSplit \
	/hive/data/genomes/ce7/bed/lastzCaeRem3.2009-07-24/DEF \
	-bigClusterHub=swarm -smallClusterHub=memk -swap > swap.log 2>&1 &
    #	real    2m53.936s
    cat fb.caeRem3.chainCe7Link.txt 
    #	46320678 bases of 138406388 (33.467%) in intersection

############################################################################
## 5-Way multiple alignment (DONE - 2009-07-28 - Hiram)

    mkdir /cluster/data/ce7/bed/multiz5way
    cd /cluster/data/ce7/bed/multiz5way
    #	See notes in ce6.txt for 6-way alignment.  This is the tree from
    #	there.

    cat << '_EOF_' > 5way.nh
((C._elegans_ce7:0.003000,
    (C._brenneri_caePb2:0.013000,
	(C._remanei_caeRem3:0.003000,C._briggsae_cb3:0.005000):0.004000)
		:0.002000):0.001000,
	    C._japonica_caeJap2:0.023000);
'_EOF_'
    # << happy emacs

    /cluster/bin/phast/x86_64/all_dists 5way.nh > 5way.distances.txt
    grep -i ce7 5way.distances.txt | sort -k3,3n
    #	Use this output for reference, and use the calculated
    #	distances in the table below to order the organisms and check
    #	the button order on the browser.
    #	And if you can fill in the table below entirely, you have
    #	succeeded in finishing all the alignments required.
    #
#                         featureBits chainLink measures
#                                           chaince7Link   chain   linearGap
#    distance                       on Ce7      on other   minScore
#  1 0.0120  - remanei_caeRem3     (% 41.722)  (% 33.467)  1000     loose
#  2 0.0140  - briggsae_cb3        (% 42.300)  (% 39.763)  1000     loose
#  3 0.0180  - brenneri_caePb2     (% 40.677)  (% 32.313)  1000     loose
#  3 0.0270  - japonica_caeJap2    (% 27.192)  (% 20.450)  1000     loose

    cd /cluster/data/ce7/bed/multiz5way
    #	bash shell syntax here ...
    export H=/cluster/data/ce7/bed
    mkdir mafLinks
    for G in caeRem3 cb3 caePb2 caeJap2
    do
	mkdir mafLinks/$G
	if [ ! -d ${H}/lastz.${G}/mafNet ]; then
	    echo "missing directory lastz.${G}/mafNet"
	fi
	ln -s ${H}/lastz.$G/mafNet/*.maf.gz ./mafLinks/$G
    done

    #	these are x86_64 binaries
    mkdir penn
    cp -p /cluster/bin/penn/multiz.2008-11-25/multiz penn 
    cp -p /cluster/bin/penn/multiz.2008-11-25/maf_project penn 
    cp -p /cluster/bin/penn/multiz.2008-11-25/autoMZ penn 

    # the autoMultiz cluster run
    ssh memk
    cd /hive/data/genomes/ce7/bed/multiz5way/

    # create species list and stripped down tree for autoMZ
    sed -e \
's/[a-z][a-z0-9]*_//ig; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d; s/C._//g' \
	5way.nh > tmp.nh
    echo `cat tmp.nh` > tree-commas.nh
    echo `cat tree-commas.nh` | sed 's/ //g; s/,/ /g' > tree.nh
    sed 's/[()]//g; s/,/ /g' tree.nh > species.list

    mkdir maf run
    cd run

    #	NOTE: set the db and pairs directories in this script
    cat > autoMultiz.csh << '_EOF_'
#!/bin/csh -ef
set db = ce7
set c = $1
set result = $2
set run = `pwd`
set tmp = $run/tmp/$db/multiz.$c
set nway = /hive/data/genomes/ce7/bed/multiz5way
set pairs = $nway/mafLinks
/bin/rm -fr $tmp
/bin/mkdir -p $tmp
/bin/cp -p $nway/tree.nh $nway/species.list $tmp
pushd $tmp
foreach s (`sed -e "s/ $db//" species.list`)
    set in = $pairs/$s/$c.maf
    set out = $db.$s.sing.maf
    if (-e $in.gz) then
        /bin/zcat $in.gz > $out
	if (! -s $out) then
	    echo "##maf version=1 scoring=autoMZ" > $out
	endif
    else if (-e $in) then
        ln -s $in $out
    else
        echo "##maf version=1 scoring=autoMZ" > $out
    endif
end
set path = ($nway/penn $path); rehash
$nway/penn/autoMZ + T=$tmp E=$db "`cat tree.nh`" $db.*.sing.maf $c.maf
popd
/bin/rm -f $result
/bin/cp -p $tmp/$c.maf $result
/bin/rm -fr $tmp
/bin/rmdir --ignore-fail-on-non-empty $run/tmp/$db
/bin/rmdir --ignore-fail-on-non-empty $run/tmp
'_EOF_'
# << happy emacs
    chmod +x autoMultiz.csh

    cat  << '_EOF_' > template
#LOOP
./autoMultiz.csh $(root1) {check out line+ /hive/data/genomes/ce7/bed/multiz5way/maf/$(root1).maf}
#ENDLOOP
'_EOF_'
# << happy emacs

    awk '{print $1}' /cluster/data/ce7/chrom.sizes > chrom.lst
    gensub2 chrom.lst single template jobList
    para create jobList
    para -maxNode=1 push
    para check ... push ... etc ...
# Completed: 7 of 7 jobs
# CPU time in finished jobs:       1515s      25.25m     0.42h    0.02d  0.000 y
# IO & Wait Time:                   126s       2.10m     0.03h    0.00d  0.000 y
# Average job time:                 234s       3.91m     0.07h    0.00d
# Longest finished job:             334s       5.57m     0.09h    0.00d
# Submission to last job:           349s       5.82m     0.10h    0.00d

    cd /hive/data/genomes/ce7/bed/multiz5way
    time nice -n +19 catDir maf > multiz5way.maf
    # a few seconds to produce:
    #	-rw-rw-r-- 1 321148937 Jul 28 13:00 multiz5way.maf

    #	before getting to the annotation, load this up so we can get
    #	a first view of the track.  This will be replaced with the annotated
    #	mafs
    ssh hgwdev
    cd /hive/data/genomes/ce7/bed/multiz5way
    mkdir /gbdb/ce7/multiz5way
    ln -s /hive/data/genomes/ce7/bed/multiz5way/multiz5way.maf \
	/gbdb/ce7/multiz5way

    #	this load creates a large file, do that on local disk:
    cd /scratch/tmp
    time nice -n +19 hgLoadMaf ce7 multiz5way
    #	a few seconds to load:
    #	Loaded 327160 mafs in 1 files from /gbdb/ce7/multiz5way

    time nice -n +19 hgLoadMafSummary -minSize=10000 -mergeGap=500 \
	-maxSize=50000 ce7 multiz5waySummary /gbdb/ce7/multiz5way/multiz5way.maf
    #	a few seconds to load:
    #	Created 111894 summary blocks from 849995 components and 327160 mafs
    #	from /gbdb/ce7/multiz5way/multiz5way.maf

    #	remove the temporary .tab files:
    rm multiz5*.tab

############################################################################
# CE7->CE8 LIFTOVER (DONE - 2008-06-24 - Hiram)
    cd /hive/data/genomes/ce7
    #	test procedure with -debug first
    doSameSpeciesLiftOver.pl -bigClusterHub=swarm -workhorse=hgwdev \
	-ooc /hive/data/genomes/ce7/jkStuff/ce7.11.ooc ce7 ce8 -debug
    cd bed/blat.ce8.2009-07-28
    time nice -n +19 doSameSpeciesLiftOver.pl -bigClusterHub=swarm \
	-workhorse=hgwdev \
	-ooc /hive/data/genomes/ce7/jkStuff/ce7.11.ooc ce7 ce8 > do.log 2>&1 &
    #	real    8m10.453s

    #	this takes about 10 minutes
    tail -f do.log
    rm -f /cluster/bluearc/ce6/ce6.2bit

#########################################################################
# reset default position, same as ce4 on the ZC101 / unc-52 locus
    ssh hgwdev
    hgsql -e 'update dbDb set defaultPos="chrII:14646344-14667746"
	where name="ce7";' hgcentraltest

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