# for emacs: -*- mode: sh; -*-
#
#	the above keeps emacs happy while working with this text document

# This file describes how we made the browser database on the
# Rattus norvegicus genome, March 2012 update (Rnor5.0) from Baylor.

#	http://www.ncbi.nlm.nih.gov/bioproject/16219
#	http://www.ncbi.nlm.nih.gov/genome/73
#	http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AABR06
#	Genome Coverage : 3x BAC; 6x WGS ABI Sanger reads
#	chrMt: NC_001665.2

#	DATE:   08-Mar-2012
#	ORGANISM:       Rattus norvegicus
#	TAXID:  10116
#	ASSEMBLY LONG NAME:     Rnor_5.0
#	ASSEMBLY SHORT NAME:    Rnor_5.0
#	ASSEMBLY SUBMITTER:     Rat Genome Sequencing Consortium
#	ASSEMBLY TYPE:  Haploid
#	NUMBER OF ASSEMBLY-UNITS:       1
#	ASSEMBLY ACCESSION:     GCA_000001895.3
#	FTP-RELEASE DATE: 19-Mar-2012

#########################################################################
## Download sequence (DONE - 2012-03-19 - Hiram)
    mkdir /hive/data/genomes/rn5
    mkdir /hive/data/genomes/rn5/genbank
    cd /hive/data/genomes/rn5/genbank

    rsync -a -P \
rsync://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Rattus_norvegicus/Rnor_5.0/ ./

    faSize Primary_Assembly/assembled_chromosomes/FASTA/chr*.fa.gz
# 2902588968 bases (334517722 N's 2568071246 real 2568071246 upper 0 lower)
#	in 21 sequences in 21 files
# Total size: mean 138218522.3 sd 67159802.9
#	min 54450796 (gi|380690185|gb|CM000083.4|)
#	max 290094216 (gi|380690196|gb|CM000072.4|) median 118718031

    faSize Primary_Assembly/unlocalized_scaffolds/FASTA/*.fa.gz
# 4156200 bases (1012688 N's 3143512 real 3143512 upper 0 lower)
#	in 1278 sequences in 21 files
# Total size: mean 3252.1 sd 8429.6
#	min 500 (gi|380099756|gb|AABR06109458.1|)
#	max 227955 (gi|380099484|gb|AABR06109730.1|) median 2219

    faSize Primary_Assembly/unplaced_scaffolds/FASTA/*.fa.gz
# 2937457 bases (1314805 N's 1622652 real 1622652 upper 0 lower)
#	in 1439 sequences in 1 files
# Total size: mean 2041.3 sd 5072.3 min 280 (gi|380097677|gb|AABR06111537.1|)
#	max 73090 (gi|380452989|gb|JH620568.1|) median 723

    # and all together:
    faSize Primary_Assembly/assembled_chromosomes/FASTA/chr*.fa.gz \
Primary_Assembly/unlocalized_scaffolds/FASTA/*.fa.gz \
Primary_Assembly/unplaced_scaffolds/FASTA/*.fa.gz
# 2909682625 bases (336845215 N's 2572837410 real 2572837410 upper 0 lower)
#	in 2738 sequences in 43 files
# Total size: mean 1062703.7 sd 13357023.2
#	min 280 (gi|380097677|gb|AABR06111537.1|)
#	max 290094216 (gi|380690196|gb|CM000072.4|) median 1018

#########################################################################
# fixup names for UCSC standards (DONE - 2012-03-19 - Hiram)
    mkdir /hive/data/genomes/rn5/ucsc
    cd /hive/data/genomes/rn5/ucsc

    ########################  Assembled Chromosomes
    cat << '_EOF_' > toUcsc.pl
#!/bin/env perl

use strict;
use warnings;

my %accToChr;

open (FH, "<../genbank/Primary_Assembly/assembled_chromosomes/chr2acc") or
        die "can not read Primary_Assembly/assembled_chromosomes/chr2acc";
while (my $line = <FH>) {
    next if ($line =~ m/^#/);
    chomp $line;
    my ($chrN, $acc) = split('\s+', $line);
    $accToChr{$acc} = $chrN;
}
close (FH);

foreach my $acc (keys %accToChr) {
    my $chrN =  $accToChr{$acc};
    print "$acc $accToChr{$acc}\n";
    open (FH, "zcat ../genbank/Primary_Assembly/assembled_chromosomes/AGP/chr${chrN}.agp.gz|") or die "can not read chr${chrN}.agp.gz";
    open (UC, ">chr${chrN}.agp") or die "can not write to chr${chrN}.agp";
    while (my $line = <FH>) {
        if ($line =~ m/^#/) {
            print UC $line;
        } else {
            $line =~ s/^$acc/chr${chrN}/;
            print UC $line;
        }
    }
    close (FH);
    close (UC);
    open (FH, "zcat ../genbank/Primary_Assembly/assembled_chromosomes/FASTA/chr${chrN}.fa.gz|") or die "can not read chr${chrN}.fa.gz";
    open (UC, ">chr${chrN}.fa") or die "can not write to chr${chrN}.fa";
    while (my $line = <FH>) {
        if ($line =~ m/^>/) {
            printf UC ">chr${chrN}\n";
        } else {
            print UC $line;
        }
    }
    close (FH);
    close (UC);
}
'_EOF_'
    # << happy emacs
    chmod +x toUcsc.pl
    time ./toUcsc.pl
    #	real    0m50.678s
    time gzip *.fa *.agp
    #	real    12m46.877s
    faSize chr*.fa.gz
    #	2725521370 bases (77999939 N's 2647521431 real 2647521431 upper 0
    #	lower) in 21 sequences in 21 files
    #	Total size: mean 129786731.9 sd 33408399.1 min 61431566 (chr19)
    #	max 195471971 (chr1) median 124902244

    ########################  Unplaced scaffolds
    cat << '_EOF_' > unplaced.pl
#!/bin/env perl

use strict;
use warnings;

my $agpFile =  "../genbank/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz";
my $fastaFile =  "../genbank/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz";
open (FH, "zcat $agpFile|") or die "can not read $agpFile";
open (UC, ">unplaced.agp") or die "can not write to unplaced.agp";
while (my $line = <FH>) {
    if ($line =~ m/^#/) {
        print UC $line;
    } else {
        $line =~ s/\.1//;    
        printf UC "chrUn_%s", $line;
    }
}
close (FH);
close (UC);

open (FH, "zcat $fastaFile|") or die "can not read $fastaFile";
open (UC, ">unplaced.fa") or die "can not write to unplaced.fa";
while (my $line = <FH>) {
    if ($line =~ m/^>/) {
        chomp $line;
        $line =~ s/.*gb\|//;
        $line =~ s/\.1\|.*//;
        printf UC ">chrUn_$line\n";
    } else {
        print UC $line;
    }
}
close (FH);
close (UC);
'_EOF_'
    # << happy emacs
    chmod +x unplaced.pl
    time ./unplaced.pl
    #	real    0m0.131s
    # make sure none of the names got to be over 31 characers long:
    grep -v "^#" unplaced.agp | cut -f1 | sort | uniq -c | sort -rn
    gzip *.fa *.agp
    # not much in that sequence:
    faSize unplaced.fa.gz
# 2937457 bases (1314805 N's 1622652 real 1622652 upper 0 lower)
#	in 1439 sequences in 1 files
# Total size: mean 2041.3 sd 5072.3 min 280 (chrUn_AABR06111537)
#	max 73090 (chrUn_JH620568) median 723

    ########################  Unlocalized scaffolds
    cat << '_EOF_' > unlocalized.pl
#!/bin/env perl

use strict;
use warnings;

my %accToChr;
my %chrNames;

open (FH, "<../genbank/Primary_Assembly/unlocalized_scaffolds/unlocalized.chr2scaf") or
        die "can not read Primary_Assembly/unlocalized_scaffolds/unlocalized.chr2scaf";
while (my $line = <FH>) {
    next if ($line =~ m/^#/);
    chomp $line;
    my ($chrN, $acc) = split('\s+', $line);
    $accToChr{$acc} = $chrN;
    $chrNames{$chrN} += 1;
}
close (FH);

foreach my $chrN (keys %chrNames) {
    my $agpFile =  "../genbank/Primary_Assembly/unlocalized_scaffolds/AGP/chr$chrN.unlocalized.scaf.agp.gz";
    my $fastaFile =  "../genbank/Primary_Assembly/unlocalized_scaffolds/FASTA/chr$chrN.unlocalized.scaf.fa.gz";
    open (FH, "zcat $agpFile|") or die "can not read $agpFile";
    open (UC, ">chr${chrN}_random.agp") or die "can not write to chr${chrN}_random.agp";
    while (my $line = <FH>) {
        if ($line =~ m/^#/) {
            print UC $line;
        } else {
            chomp $line;
            my (@a) = split('\t', $line);
            my $acc = $a[0];
            my $accNo1 = $acc;
            $accNo1 =~ s/.1$//;
            die "ERROR: acc not .1: $acc" if ($accNo1 =~ m/\./);
            die "ERROR: chrN $chrN not correct for $acc"
                if ($accToChr{$acc} ne $chrN);
            my $ucscName = "chr${chrN}_${accNo1}_random";
            printf UC "%s", $ucscName;
            for (my $i = 1; $i < scalar(@a); ++$i) {
                printf UC "\t%s", $a[$i];
            }
            printf UC "\n";
        }
    }
    close (FH);
    close (UC);
    printf "chr%s\n", $chrN;
    open (FH, "zcat $fastaFile|") or die "can not read $fastaFile";
    open (UC, ">chr${chrN}_random.fa") or die "can not write to chr${chrN}_random.fa";
    while (my $line = <FH>) {
        if ($line =~ m/^>/) {
            chomp $line;
            my $acc = $line;
            $acc =~ s/.*gb\|//;
            $acc =~ s/\|.*//;
            my $accNo1 = $acc;
            $accNo1 =~ s/.1$//;
            die "ERROR: acc not .1: $acc" if ($accNo1 =~ m/\./);
            die "ERROR: chrN $chrN not correct for $acc"
                if ($accToChr{$acc} ne $chrN);
            my $ucscName = "chr${chrN}_${accNo1}_random";
            printf UC ">$ucscName\n";
        } else {
            print UC $line;
        }
    }
    close (FH);
    close (UC);
}
'_EOF_'
    # << happy emacs
    chmod +x unlocalized.pl
    time ./unlocalized.pl
    #	real    0m0.592s
    gzip *.fa *.agp

    # verify none of the names are longer than 31 characters:
    zcat *.agp.gz | grep -v "^#" | cut -f1 | sort -u \
	| awk '{print length($1),$1}' | sort -rn | head
25 chr20_AABR06110665_random
25 chr20_AABR06110664_random
...

    faSize chr*_random.fa.gz
# 4156200 bases (1012688 N's 3143512 real 3143512 upper 0 lower)
#	in 1278 sequences in 21 files
# Total size: mean 3252.1 sd 8429.6 min 500 (chr2_AABR06109458_random)
#	max 227955 (chr4_AABR06109730_random) median 2219

    #	verify all the sequence is still here after all this rigamarole:
    time faSize *.fa.gz
# 2909682625 bases (336845215 N's 2572837410 real 2572837410 upper 0 lower)
#	in 2738 sequences in 43 files
# Total size: mean 1062703.7 sd 13357023.2 min 280 (chrUn_AABR06111537)
#	max 290094216 (chr1) median 1018
    # verify same numbers as was in the original files measured above

#########################################################################
# Create .ra file and run makeGenomeDb.pl (DONE - Hiram - 2012-03-19)
    cd /hive/data/genomes/rn5
    cat << '_EOF_' >rn5.config.ra
# Config parameters for makeGenomeDb.pl:
db rn5
clade mammal
scientificName Rattus norvegicus
commonName Rat
assemblyDate Mar. 2012
assemblyLabel RGSC Rnor_5.0 (GCA_000001895.3)
assemblyShortLabel RGSC 5.0
orderKey 1559
mitoAcc NC_001665
fastaFiles /hive/data/genomes/rn5/ucsc/*.fa.gz
agpFiles /hive/data/genomes/rn5/ucsc/*.agp.gz
# qualFiles none
dbDbSpeciesDir rat
ncbiAssemblyId 73
ncbiAssemblyName Rnor_5.0
taxId 10116
'_EOF_'
    # << happy emacs

    #	run agp step first to verify fasta and agp files agree
    makeGenomeDb.pl -stop=agp rn5.config.ra > agp.log 2>&1
    # verify end of agp.log indictates:
# All AGP and FASTA entries agree - both files are valid
    # continue with the build
    time makeGenomeDb.pl -continue=db rn5.config.ra > db.log 2>&1
    #	real    22m39.834s

#########################################################################
# running repeat masker (DONE - 2012-03-19 - Hiram)
    mkdir /hive/data/genomes/rn5/bed/repeatMasker
    cd /hive/data/genomes/rn5/bed/repeatMasker
    time doRepeatMasker.pl -buildDir=`pwd` -noSplit \
	-bigClusterHub=swarm -dbHost=hgwdev -workhorse=hgwdev \
	-smallClusterHub=encodek rn5 > do.log 2>&1 &
    # hgwdev rebooted during kluster run, continuing:
    time doRepeatMasker.pl -buildDir=`pwd` -noSplit \
	-continue=cat -bigClusterHub=swarm -dbHost=hgwdev -workhorse=hgwdev \
	-smallClusterHub=encodek rn5 > cat.log 2>&1 &
    #	real    55m22.186s
    cat faSize.rmsk.txt
    #	2909698938 bases (336845215 N's 2572853723 real 1473277432 upper
    #	1099576291 lower) in 2739 sequences in 1 files
    #	Total size: mean 1062321.6 sd 13354598.7 min 280 (chrUn_AABR06111537)
    #	max 290094216 (chr1) median 1018
    #	%37.79 masked total, %42.74 masked real

    grep -i versi do.log
# RepeatMasker version development-$Id: RepeatMasker,v 1.26 2011/09/26 16:19:44 angie Exp $
#    April 26 2011 (open-3-3-0) version of RepeatMasker

    featureBits -countGaps rn5 rmsk
    #	1100336249 bases of 2909698938 (37.816%) in intersection
    # why is it different than the faSize above ?
    # because rmsk masks out some N's as well as bases, the faSize count above
    #	separates out the N's from the bases, it doesn't show lower case N's

##########################################################################
# running simple repeat (DONE - 2012-03-19 - Hiram)
    mkdir /hive/data/genomes/rn5/bed/simpleRepeat
    cd /hive/data/genomes/rn5/bed/simpleRepeat
    time doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=swarm \
	-dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=encodek \
	rn5 > do.log 2>&1 &
    #	real    14m45.644s

    cat fb.simpleRepeat 
    #	97893561 bases of 2780239565 (3.521%) in intersection

    # add the TRF mask to the rmsk sequence:
    #	it masks more sequence
    cd /hive/data/genomes/rn5
    twoBitMask rn5.rmsk.2bit \
	-add bed/simpleRepeat/trfMask.bed rn5.2bit
    #	you can safely ignore the warning about fields >= 13

    twoBitToFa rn5.2bit stdout | faSize stdin > faSize.rn5.2bit.txt
    cat faSize.rn5.2bit.txt
    #	2909698938 bases (336845215 N's 2572853723 real 1471484052 upper
    #	1101369671 lower) in 2739 sequences in 1 files
    #	Total size: mean 1062321.6 sd 13354598.7 min 280 (chrUn_AABR06111537)
    #	max 290094216 (chr1) median 1018
    #	%37.85 masked total, %42.81 masked real

    #	replace the previous symLink which goes to the unmasked 2bit
    rm /gbdb/rn5/rn5.2bit
    ln -s `pwd`/rn5.2bit /gbdb/rn5/rn5.2bit

#########################################################################
# Verify all gaps are marked, add any N's not in gap as type 'other'
#	(DONE - 2012-03-19 - Hiram)
    mkdir /hive/data/genomes/rn5/bed/gap
    cd /hive/data/genomes/rn5/bed/gap
    time nice -n +19 findMotif -motif=gattaca -verbose=4 \
	-strand=+ ../../rn5.unmasked.2bit > findMotif.txt 2>&1
    #	real    0m35.258s
    grep "^#GAP " findMotif.txt | sed -e "s/^#GAP //" > allGaps.bed
    time featureBits -countGaps rn5 -not gap -bed=notGap.bed
    #	2573362844 bases of 2909698938 (88.441%) in intersection
    #	real    0m14.151s

    time featureBits -countGaps rn5 allGaps.bed notGap.bed -bed=new.gaps.bed
    #	509121 bases of 2909698938 (0.017%) in intersection
    #	real    2m40.070s

    #	what is the highest index in the existing gap table:
    hgsql -N -e "select ix from gap;" rn5 | sort -n | tail -1
    #	22612
    cat << '_EOF_' > mkGap.pl
#!/bin/env perl

use strict;
use warnings;

my $ix=`hgsql -N -e "select ix from gap;" rn5 | sort -n | tail -1`;
chomp $ix;

open (FH,"<new.gaps.bed") or die "can not read new.gaps.bed";
while (my $line = <FH>) {
    my ($chrom, $chromStart, $chromEnd, $rest) = split('\s+', $line);
    ++$ix;
    printf "%s\t%d\t%d\t%d\tN\t%d\tother\tyes\n", $chrom, $chromStart,
        $chromEnd, $ix, $chromEnd-$chromStart;
}
close (FH);
'_EOF_'
    # << happy emacs
    chmod +x ./mkGap.pl
    ./mkGap.pl > other.bed
    featureBits -countGaps rn5 other.bed
    #	509121 bases of 2909698938 (0.017%) in intersection
    wc -l other.bed
    #	148489
    # verify no mistake here:
    featureBits -countGaps rn5 gap other.bed
    #	0 bases of 2909698938 (0.000%) in intersection

    hgLoadBed -sqlTable=$HOME/kent/src/hg/lib/gap.sql \
	-noLoad rn5 otherGap other.bed
    #	starting with this many
    hgsql -e "select count(*) from gap;" rn5
    #	109913
    hgsql rn5 -e 'load data local infile "bed.tab" into table gap;'
    #	result count:
    hgsql -e "select count(*) from gap;" rn5
    #	258402
    calc 109913 \+ 148489
    #	109913 + 148489 = 258402

    # verify we aren't adding gaps where gaps already exist
    # this would output errors if that were true:
    gapToLift -minGap=1 rn5 nonBridged.lift -bedFile=nonBridged.bed
    # see example in danRer7.txt when problems arise

    # there are no non-bridged gaps here:
    hgsql -N -e "select bridge from gap;" rn5 | sort | uniq -c
    #	8109 no
    #	101804 yes

##########################################################################
## WINDOWMASKER (DONE - 2012-03-19 - Hiram)
    mkdir /hive/data/genomes/rn5/bed/windowMasker
    cd /hive/data/genomes/rn5/bed/windowMasker
    time nice -n +19 doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
	-dbHost=hgwdev rn5 > do.log 2>&1 &
    #	real    231m12.464s

    # Masking statistics
    twoBitToFa rn5.wmsk.2bit stdout | faSize stdin
    #	2909698938 bases (336845215 N's 2572853723 real 1725214664 upper
    #	847639059 lower) in 2739 sequences in 1 files
    #	Total size: mean 1062321.6 sd 13354598.7 min 280 (chrUn_AABR06111537)
    #	max 290094216 (chr1) median 1018
    #	%29.13 masked total, %32.95 masked real

    twoBitToFa rn5.wmsk.sdust.2bit stdout | faSize stdin
    #	2909698938 bases (336845215 N's 2572853723 real 1710265619 upper
    #	862588104 lower) in 2739 sequences in 1 files
    #	Total size: mean 1062321.6 sd 13354598.7 min 280 (chrUn_AABR06111537)
    #	max 290094216 (chr1) median 1018
    #	%29.65 masked total, %33.53 masked real

    hgLoadBed rn5 windowmaskerSdust windowmasker.sdust.bed.gz
    #	Loaded 13855996 elements of size 3

    featureBits -countGaps rn5 windowmaskerSdust
    #	1199303584 bases of 2909698938 (41.217%) in intersection

    #	eliminate the gaps from the masking
    featureBits rn5 -not gap -bed=notGap.bed
    #	2572853723 bases of 2572853723 (100.000%) in intersection
    time nice -n +19 featureBits rn5 windowmaskerSdust notGap.bed \
        -bed=stdout | gzip -c > cleanWMask.bed.gz
    #	862588104 bases of 2572853723 (33.527%) in intersection
    #	real    3m53.016s

    #	reload track to get it clean
    hgLoadBed rn5 windowmaskerSdust cleanWMask.bed.gz
    #	Loaded 13904385 elements of size 4
    time featureBits -countGaps rn5 windowmaskerSdust
    #	862588104 bases of 2909698938 (29.645%) in intersection
    #	real    1m26.398s

    #	mask with this clean result
    zcat cleanWMask.bed.gz \
	| twoBitMask ../../rn5.unmasked.2bit stdin \
	    -type=.bed rn5.cleanWMSdust.2bit
    twoBitToFa rn5.cleanWMSdust.2bit stdout | faSize stdin \
        > rn5.cleanWMSdust.faSize.txt
    cat rn5.cleanWMSdust.faSize.txt
    #	2909698938 bases (336845215 N's 2572853723 real 1710265619 upper
    #	862588104 lower) in 2739 sequences in 1 files
    #	Total size: mean 1062321.6 sd 13354598.7 min 280 (chrUn_AABR06111537)
    #	max 290094216 (chr1) median 1018
    #	%29.65 masked total, %33.53 masked real

    # how much does this window masker and repeat masker overlap:
    featureBits -countGaps rn5 rmsk windowmaskerSdust
    #	648600018 bases of 2909698938 (22.291%) in intersection

#########################################################################
# MASK SEQUENCE WITH WM+TRF
    # not running this since RM + TRF is plenty of masking
#    cd /hive/data/genomes/rn5
#    twoBitMask -add bed/windowMasker/rn5.cleanWMSdust.2bit \
#	bed/simpleRepeat/trfMask.bed rn5.2bit
    #	safe to ignore the warnings about BED file with >=13 fields
#    twoBitToFa rn5.2bit stdout | faSize stdin > faSize.rn5.txt
#    cat faSize.rn5.txt

    #	create symlink to gbdb
#    ssh hgwdev
#    rm /gbdb/rn5/rn5.2bit
#    ln -s `pwd`/rn5.2bit /gbdb/rn5/rn5.2bit

#########################################################################
# PREPARE LINEAGE SPECIFIC REPEAT FILES FOR BLASTZ (DONE - 2012-03-23 - Hiram)
    ssh encodek
    mkdir /hive/data/genomes/rn5/bed/linSpecRep
    cd /hive/data/genomes/rn5/bed/linSpecRep

    # split the RM output by chromosome name into separate files
    mkdir rmsk dateRepeats
    head -3 ../repeatMasker/rn5.sorted.fa.out > rmsk.header.txt
    headRest 3 ../repeatMasker/rn5.sorted.fa.out \
	| splitFileByColumn -ending=.out -col=5 -head=rmsk.header.txt stdin rmsk

    ls -1S rmsk/* > rmOut.list
    wc -l rmOut.list
    #	2382 rmOut.list

    cat << '_EOF_' > mkLSR
#!/bin/csh -fe
rm -f dateRepeats/$1_homo-sapiens_mus-musculus
/scratch/data/RepeatMasker110426/DateRepeats \
    $1 -query rat -comp human -comp mouse
mv $1_homo-sapiens_mus-musculus dateRepeats
'_EOF_'
    #	<< happy emacs
    chmod +x mkLSR

    cat << '_EOF_' > template
#LOOP
./mkLSR $(path1) {check out line+ dateRepeats/$(file1)_homo-sapiens_mus-musculus}
#ENDLOOP
'_EOF_'
    #	<< happy emacs

    gensub2 rmOut.list single template jobList
    para create jobList
    para try ... check ... push ... etc...
    para time
# Completed: 2382 of 2382 jobs
# CPU time in finished jobs:      37294s     621.57m    10.36h    0.43d  0.001 y
# IO & Wait Time:                  6367s     106.11m     1.77h    0.07d  0.000 y
# Average job time:                  18s       0.31m     0.01h    0.00d
# Longest finished job:              78s       1.30m     0.02h    0.00d
# Submission to last job:          2245s      37.42m     0.62h    0.03d

    mkdir notInHuman notInMouse
    for F in dateRepeats/chr*.out_homo-sapiens*
    do
	B=`basename ${F}`
	B=${B/.out*/}
	echo $B 
        /cluster/bin/scripts/extractRepeats 1 ${F} > \
		notInHuman/${B}.out.spec
        /cluster/bin/scripts/extractRepeats 2 ${F} > \
		notInMouse/${B}.out.spec
    done

    #	Verify that these two things are actually different
    #	To check identical
    find ./notInHuman ./notInMouse -name "*.out.spec" | \
	while read FN; do echo `cat ${FN} | sum -r` ${FN}; done \
	| sort -k1,1n | sort -t"/" -k3,3 > check.same
    # some of them are the same, but not all:
    sed -e 's#./notInHuman/##; s#./notInMouse/##' check.same \
	| sort | uniq -c | sort -rn | less
    # you will see a count of two at the beginning, but it becomes one soon

    #	Copy to data/staging for cluster replication
    mkdir /hive/data/staging/data/rn5
    rsync -a -P ./notInMouse/ /hive/data/staging/data/rn5/notInMouse/
    rsync -a -P ./notInHuman/ /hive/data/staging/data/rn5/notInHuman/

    # We also need the nibs for the lastz runs with lineage specific repeats
    mkdir /hive/data/staging/data/rn5/nib
    mkdir /hive/data/genomes/rn5/nib
    cd /hive/data/genomes/rn5
    cut -f1 chrom.sizes | while read C
do
    twoBitToFa -seq=${C} rn5.2bit stdout | faToNib -softMask stdin nib/${C}.nib
    ls -og nib/$C.nib
done
    # verify one is properly masked:
    nibFrag -masked nib/chrM.nib 0 `grep -w chrM chrom.sizes | cut -f2` + \
	stdout | faSize stdin
    #	16313 bases (0 N's 16313 real 15922 upper 391 lower)
    #	in 1 sequences in 1 files
    #	%2.40 masked total, %2.40 masked real
    # compare to:
    twoBitToFa -seq=chrM rn5.2bit stdout | faSize stdin
    #	16313 bases (0 N's 16313 real 15922 upper 391 lower)
    #	in 1 sequences in 1 files
    #	%2.40 masked total, %2.40 masked real

    #	Copy to data/genomes staging for cluster replication
    rsync -a -P ./nib/ /hive/data/staging/data/rn5/nib/

#########################################################################
# cpgIslands - (DONE - 2011-04-20 - Hiram)
    mkdir /hive/data/genomes/rn5/bed/cpgIslands
    cd /hive/data/genomes/rn5/bed/cpgIslands
    time doCpgIslands.pl rn5 > do.log 2>&1
    #   Elapsed time: 11m10s

    cat fb.rn5.cpgIslandExt.txt
    #   10377460 bases of 2572853723 (0.403%) in intersection

#########################################################################
# genscan - (DONE - 2011-04-25 - Hiram)
    mkdir /hive/data/genomes/rn5/bed/genscan
    cd /hive/data/genomes/rn5/bed/genscan
    time doGenscan.pl rn5 > do.log 2>&1
    #   real    104m9.716s
    # a number of jobs did not finish, rerunning with window size 2000000
    #   only chr7 completed at 15000000
    # rerunning with window size of 1000000
    #   real    78m10.904s
    # rerunning with window size of 500000
    # rerunning with window size of 250000
    # rerunning with window size of 100000
    #   real    85m5.776s
    # rerunning with window size of 50000
    #   real    86m57.706s
    #   This is not working.  Need to run these split
    mkdir /hive/data/genomes/rn5/bed/genscan/splitRun
    cd /hive/data/genomes/rn5/bed/genscan/splitRun
    gapToLift rn5 rn5.nonBridged.lift -bedFile=rn5.nonBridged.bed

    for C in 2 3 4 5 6 7 11 13 15 19
do
    echo chr${C}
    cd /hive/data/genomes/rn5/bed/genscan/splitRun
    grep -w "chr${C}" rn5.nonBridged.lift | grep -v random \
        | sed -e "s/chr${C}./chr${C}_/" > chr${C}.nonBridged.lift
    mkdir chr${C}
    faToTwoBit ../hardMaskedFa/000/chr${C}.fa chr${C}/chr${C}.2bit
    ~/kent/src/hg/utils/lft2BitToFa.pl chr${C}/chr${C}.2bit \
        chr${C}.nonBridged.lift > chr${C}/chr${C}.nonBridged.fa
    cd /hive/data/genomes/rn5/bed/genscan/splitRun/chr${C}
    mkdir split${C}
    faSplit sequence chr${C}.nonBridged.fa 100 split${C}/chr${C}_
done

    for C in 2 3 4 5 6 7 11 13 15 19
do
    grep -w "chr${C}" rn5.nonBridged.lift | grep -v random \
        | sed -e "s/chr${C}./chr${C}_/" > chr${C}.nonBridged.lift
done

    for C in 2 3 4 5 6 7 11 13 15 19
do
    echo chr${C}
    cd /hive/data/genomes/rn5/bed/genscan/splitRun/chr${C}
    echo '#!/bin/sh' > cmdList.sh
    export NL=-1
    ls split${C} | while read F
  do
  NL=`echo $NL | awk '{print $1+1}'`
  if [ "${NL}" -gt 7 ]; then
    NL=0
    echo "echo waiting before $F" >> cmdList.sh
    echo wait >> cmdList.sh
  fi
  echo "/cluster/bin/x86_64/gsBig split${C}/${F} gtf/${F}.gtf -trans=pep/${F}.pep -subopt=subopt/${F}.bed -exe=/scratch/data/genscan/genscan -par=/scratch/data/genscan/HumanIso.smat -tmp=/dev/shm -window=2400000 &" 
  done >> cmdList.sh
    echo "echo waiting at end" >> cmdList.sh
    echo "wait" >> cmdList.sh
    chmod +x cmdList.sh
    rm -fr gtf pep subopt
    mkdir gtf pep subopt
done

# running chr15 - real    345m30.138s
    # running them all:
    time ./runAll.sh > runAll.log 2>&1
    #   real    458m23.357s

    # collecting the results:
for C in chr2 chr3 chr4 chr5 chr6 chr7 chr11 chr13 chr15 chr19
do
    cd /hive/data/genomes/rn5/bed/genscan/splitRun/${C}
    cat gtf/${C}_*.gtf | liftUp -type=.gtf stdout ../${C}.nonBridged.lift error stdin \
        | sed -e "s/${C}_0\([0-4]\)\./${C}.\1/g" > ${C}.gtf
cat subopt/${C}_*.bed | liftUp -type=.bed stdout ../${C}.nonBridged.lift error stdin \
        | sed -e "s/${C}_0\([0-4]\)\./${C}.\1/g" > ${C}.subopt.bed
cat pep/${C}_*.pep | sed -e "s/${C}_0\([0-4]\)\./${C}.\1/g" > ${C}.pep
ls -l ../../gtf/00?/${C}.gtf ../../pep/00?/${C}.pep ../../subopt/00?/${C}.bed
ls -l ${C}.gtf ${C}.pep ${C}.subopt.bed
done

    # after verifying the sizes of the files seem same compared to what
    #   happened in the main run:
for C in chr2 chr3 chr4 chr5 chr6 chr7 chr11 chr13 chr15 chr19
do
    cd /hive/data/genomes/rn5/bed/genscan/splitRun/${C}
   ls -l ../../gtf/00?/${C}.gtf ../../pep/00?/${C}.pep ../../subopt/00?/${C}.bed
    ls -l ${C}.gtf ${C}.pep ${C}.subopt.bed
    cd /hive/data/genomes/rn5/bed/genscan/splitRun
done

    # this is tricky, it is counting on the file existing, empty or otherwise
for C in chr2 chr3 chr4 chr5 chr6 chr7 chr11 chr13 chr15 chr19
do
    cd /hive/data/genomes/rn5/bed/genscan/splitRun/${C}
    D=`ls ../../gtf/00?/${C}.gtf`
    rm -f "${D}"
    cp -p ${C}.gtf "${D}"
    D=`ls ../../pep/00?/${C}.pep`
    rm -f "${D}"
    cp -p ${C}.pep "${D}"
    D=`ls ../../subopt/00?/${C}.bed`
    rm -f "${D}"
    cp -p ${C}.subopt.bed "${D}"
    cd /hive/data/genomes/rn5/bed/genscan/splitRun
done

    # Now, we can continue
    cd /hive/data/genomes/rn5/bed/genscan
    time doGenscan.pl -continue=makeBed -workhorse=hgwdev -dbHost=hgwdev \
        rn5 > makeBed.log 2>&1
    #   real    1m51.711s

    cat fb.rn5.genscan.txt
    #   56153914 bases of 2572853723 (2.183%) in intersection
    cat fb.rn5.genscanSubopt.txt
    #   59799363 bases of 2572853723 (2.324%) in intersection

#########################################################################
# MAKE 11.OOC FILE FOR BLAT/GENBANK (DONE - 2012-05-04 - Hiram)
    # Use -repMatch=900, based on size -- for human we use 1024
    # use the "real" number from the faSize measurement,
    # hg19 is 2897316137, calculate the ratio factor for 1024:
    calc \( 2572837410 / 2897316137 \) \* 1024
    #	( 2572837410 / 2897316137 ) * 1024 = 909.319309

    # round up to 950  (rn4 was 1024)

    cd /hive/data/genomes/rn5
    time blat rn5.2bit /dev/null /dev/null -tileSize=11 \
      -makeOoc=jkStuff/rn5.11.ooc -repMatch=800
    #   Wrote 34513 overused 11-mers to jkStuff/rn5.11.ooc
    #   rn4 had: Wrote 25608 overused 11-mers to /cluster/bluearc/rn4/11.ooc
    #	real     1m13.627s

    # there are non-bridged gaps, create lift file needed for genbank
    hgsql -N -e "select bridge from gap;" rn5 | sort | uniq -c
    #   8109 no
    #   250293 yes

    cd /hive/data/genomes/rn5/jkStuff
    gapToLift rn5 rn5.nonBridged.lift -bedFile=rn5.nonBridged.bed
    # largest non-bridged contig:
    awk '{print $3-$2,$0}' rn5.nonBridged.bed | sort -nr | head
    #   13151837 chr10  48884958        62036795        chr10.150

#########################################################################
# AUTO UPDATE GENBANK (DONE - 2012-05-04 - Hiram)
    # examine the file:
    /cluster/data/genbank/data/organism.lst
    # for your species to see what counts it has for:
# organism       mrnaCnt estCnt  refSeqCnt
# Rattus norvegicus	123478	1103589	16820
    # to decide which "native" mrna or ests you want to specify in genbank.conf

    ssh hgwdev  
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # edit etc/genbank.conf to add:
# rn5 (rat)
rn5.serverGenome = /hive/data/genomes/rn5/rn5.2bit
rn5.clusterGenome = /hive/data/genomes/rn5/rn5.2bit
rn5.ooc = /hive/data/genomes/rn5/jkStuff/rn5.11.ooc
rn5.lift = /hive/data/genomes/rn5/jkStuff/rn5.nonBridged.lift
rn5.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
rn5.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
rn5.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
rn5.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
rn5.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
rn5.downloadDir = rn5
rn5.refseq.mrna.xeno.load  = yes
rn5.refseq.mrna.xeno.loadDesc = yes
rn5.perChromTables = no
rn5.mgc = yes
# rn5.upstreamGeneTbl = refGene
# rn5.upstreamMaf = multiz9way /hive/data/genomes/rn5/bed/multiz9way/species.lst

    # end of section added to etc/genbank.conf
    git commit -m "adding rn5 rat" etc/genbank.conf
    git push
    make etc-update

    ssh hgwdev			# used to do this on "genbank" machine
    screen -S rn5           # long running job managed in screen
    cd /cluster/data/genbank
    time nice -n +19 ./bin/gbAlignStep -initial rn5 &
    #	var/build/logs/2012.05.04-10:28:06.rn5.initalign.log
    #   real    1166m46.194s

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time nice -n +19 ./bin/gbDbLoadStep -drop -initialLoad rn5 &
    #	logFile: var/dbload/hgwdev/logs/2012.05.07-13:39:54.dbload.log
    #   real    63m53.369s

    # enable daily alignment and update of hgwdev (DONE - 2012-02-09 - Hiram)
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add rn5 to:
        etc/align.dbs etc/hgwdev.dbs
    git commit -m "Added rn5." etc/align.dbs etc/hgwdev.dbs
    git push
    make etc-update

#########################################################################
# constructing downloads
    # first add rn5 to all.joiner and make sure joinerCheck is clean on it
    cd /hive/data/genomes/rn5
    time makeDownloads.pl -workhorse=hgwdev -dbHost=hgwdev rn5 \
        > downloads.log 2>&1
    #   real    24m32.649s
    # need to edit the README.txt files to make sure they are correct.

##########################################################################
# create pushQ entry (DONE - 2012-05-23 - Hiram)
    # first make sure all.joiner is up to date and has this new organism
    # a keys check should be clean:
    cd ~/kent/src/hg/makeDb/schema
    joinerCheck -database=rn5 -keys all.joiner

    mkdir /hive/data/genomes/rn5/pushQ
    cd /hive/data/genomes/rn5/pushQ
    makePushQSql.pl rn5 > rn5.sql 2> stderr.out
    # check stderr.out for no significant problems, it is common to see:
# WARNING: hgwdev does not have /gbdb/rn5/wib/gc5Base.wib
# WARNING: hgwdev does not have /gbdb/rn5/wib/quality.wib
# WARNING: hgwdev does not have /gbdb/rn5/bbi/quality.bw
# WARNING: rn5 does not have seq
# WARNING: rn5 does not have extFile
    # which are no real problem
    # if some tables are not identified:
# WARNING: Could not tell (from trackDb, all.joiner and hardcoded lists of
# supporting and genbank tables) which tracks to assign these tables to:
#	<some table list ... >
    # put them in manually after loading the pushQ entry
    scp -p rn5.sql hgwbeta:/tmp
    ssh hgwbeta
    cd /tmp
    hgsql qapushq < rn5.sql

#########################################################################
# fixup search rule for assembly track/gold table (DONE - 2012-06-07 - Hiram)
    hgsql -N -e "select frag from gold;" rn5 | sort | head -1
AABR06000001.1
    hgsql -N -e "select frag from gold;" rn5 | sort | tail -2
AABR06112651.1
NC_001665

    # to test the rule:
    hgsql -N -e "select frag from gold;" rn5 | wc -l
    #   112652
    # should find all:
    hgsql -N -e "select frag from gold;" rn5 \
        | egrep -e '[AN][AC][B_][R0]0[0-9]+(\.1)?' | wc -l
    #   112652
    # or exclude all:
    hgsql -N -e "select frag from gold;" rn5 \
        | egrep -v -e '[AN][AC][B_][R0]0[0-9]+(\.1)?' | wc -l
    #   0

    # hence, add to trackDb/rat/rn5/trackDb.ra
searchTable gold
shortCircuit 1
termRegex [AN][AC][B_][R0]0[0-9]+(\.1)?
query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
searchPriority 8

#########################################################################
# chain/net hg19 (DONE - 2012-06-28 - Hiram)
    # the original alignment to human:
    cd /hive/data/genomes/hg19/bed/lastzRn5.2012-06-27
    cat fb.hg19.chainRn5Link.txt
    #   917356917 bases of 2897316137 (31.662%) in intersection

    #	running the swap - DONE - 2012-06-28
    mkdir /hive/data/genomes/rn5/bed/blastz.hg19.swap
    cd /hive/data/genomes/rn5/bed/blastz.hg19.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/hg19/bed/lastzRn5.2012-06-27/DEF \
	-swap -noLoadChainSplit \
	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
	-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
    #   real    66m53.095s
    cat fb.rn5.chainHg19Link.txt
    #	933922552 bases of 2572853723 (36.299%) in intersection

##############################################################################
# make refSeq amino acid fasta file for use with mm10 UCSC genes
#
#  downloaded rn5.refGenePepProtNames.faa.gz using table browser, selecting
#  refGene, download sequence, and clicking the "protein" radio button.
#  This generates a file with the protein id's, whereas as we want the NM_*
#  id's for the blastp process to work

zcat rn5.refGenePepProtNames.faa.gz | awk '/^>/ {print buf; buf=$1 " "} ! /^>/ {buf=buf $1}' | tr -d '>' | sed 's/\.[0-9] / /' | sort > tmp1

echo "select refGene.name,refLink.protAcc from refGene,refLink where refGene.name=refLink.mrnaAcc and refLink.protAcc != ''" | hgsql rn5 | tail -n +2 | awk '{print $2,$1}' | sort > tmp2

join tmp1 tmp2 | awk '{printf ">%s\n%s\n",$3,$2}' > rn5.refGenePep.faa
rm tmp1 tmp2

#########################################################################
# LASTZ Macaca rheMac3 (DONE - 2012-07-10 - Chin)
    screen -S rheMac3-rn5
    mkdir /cluster/data/rn5/bed/lastz.rheMac3.2012-07-10
    cd /cluster/data/rn5/bed/lastz.rheMac3.2012-07-10

    # adjust the SEQ2_LIMIT with -stop=partition to get a reasonable
    #   number of jobs, 50,000 to something under 100,000

    cat << '_EOF_' > DEF
# rat vs. macacque
BLASTZ_M=254

# TARGET: Rat Rn5
SEQ1_DIR=/cluster/data/rn5/rn5.2bit
SEQ1_LEN=/cluster/data/rn5/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Macaca Mulatta RheMac3
SEQ2_DIR=/cluster/data/rheMac3/rheMac3.2bit
SEQ2_LEN=/cluster/data/rheMac3/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=1000

BASE=/cluster/data/rn5/bed/lastz.rheMac3.2012-07-10
'_EOF_'
    # << happy emacs

    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
      -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
      -chainMinScore=3000 -chainLinearGap=medium \
      -syntenicNet `pwd`/DEF > do.log 2>&1 &
    #   real    1526m4.274s
    cat fb.rn5.chainRheMac3Link.txt
    # 896256761 bases of 2572853723 (34.835%) in intersection
    cd /hive/data/genomes/rn5/bed
    ln -s lastz.rheMac3.2012-07-10 lastz.rheMac3

    # then swap
    mkdir /cluster/data/rheMac3/bed/blastz.rn5.swap
    cd /cluster/data/rheMac3/bed/blastz.rn5.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
        /cluster/data/rn5/bed/lastz.rheMac3.2012-07-10/DEF \
        -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
        -chainMinScore=3000 -chainLinearGap=medium \
        -swap -syntenicNet > swap.log 2>&1 &
    #   real    69m12.752s
    cat fb.rheMac3.chainRn5Link.txt
    # 858153767 bases of 2639145830 (32.516%) in intersection
    cd /hive/data/genomes/rheMac3/bed
    ln -s blastz.rn5.swap lastz.rn5

##############################################################################
# LIFTOVER TO rn4 (DONE - 2012-11-01 - Hiram)
    mkdir /hive/data/genomes/rn5/bed/blat.rn4.2012-11-01
    cd /hive/data/genomes/rn5/bed/blat.rn4.2012-11-01
    # -debug run to create run dir, preview scripts...
    doSameSpeciesLiftOver.pl -debug \
	-bigClusterHub=swarm -dbHost=hgwdev -workhorse=hgwdev \
        -ooc /hive/data/genomes/rn5/jkStuff/rn5.11.ooc rn5 rn4
    # Real run:
    time nice -n +19 doSameSpeciesLiftOver.pl -verbose=2 \
	-bigClusterHub=swarm -dbHost=hgwdev -workhorse=hgwdev \
        -ooc /hive/data/genomes/rn5/jkStuff/rn5.11.ooc rn5 rn4 > do.log 2>&1
    #	real    114m49.176s

    # test the browser on hgwdev to see if it can convert from rn5 to rn4

#############################################################################
# lastz zebrafish danRer7 (DONE - 2012-11-13,14 - Hiram)
    # establish a screen to control this job with a name to indicate what it is
    screen -S rn5DanRer7
    mkdir /hive/data/genomes/rn5/bed/lastzDanRer7.2012-11-13
    cd /hive/data/genomes/rn5/bed/lastzDanRer7.2012-11-13

    cat << '_EOF_' > DEF
# Rat vs. zebrafish
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.02/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_Q=/scratch/data/blastz/HoxD55.q

# TARGET: Rat Rn5
SEQ1_DIR=/hive/data/genomes/rn5/rn5.2bit
SEQ1_LEN=/hive/data/genomes/rn5/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=15

# QUERY: zebrafish danRer7
SEQ2_DIR=/scratch/data/danRer7/danRer7.2bit
SEQ2_LEN=/scratch/data/danRer7/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=10

BASE=/hive/data/genomes/rn5/bed/lastzDanRer7.2012-11-13
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    # adjust the SEQ2_LIMIT with -stop=partition to get a reasonable
    #	number of jobs, 50,000 to something under 100,000
    # when not present, SEQ2_LIMIT is a default 100
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
        `pwd`/DEF \
        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
        -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 &
    #	real    1099m42.792s
    cat fb.rn5.chainDanRer7Link.txt
    #	66573209 bases of 2572853723 (2.588%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/rn5/bed
    ln -s lastzDanRer7.2012-11-13 lastz.danRer7

    #	and for the swap
    mkdir /hive/data/genomes/danRer7/bed/blastz.rn5.swap
    cd /hive/data/genomes/danRer7/bed/blastz.rn5.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/rn5/bed/lastzDanRer7.2012-11-13/DEF \
        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
        -swap -chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
    #	real    15m5.664s
    cat  fb.danRer7.chainRn5Link.txt
    #	68007020 bases of 1409770109 (4.824%) in intersection

    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/danRer7/bed
    ln -s blastz.rn5.swap lastz.rn5

#########################################################################
# lastz frog xenTro3 (DONE - 2012-11-13,14 - Hiram)
    # establish a screen to control this job with a name to indicate what it is
    screen -S rn5XenTro3
    mkdir /hive/data/genomes/rn5/bed/lastzXenTro3.2012-11-13
    cd /hive/data/genomes/rn5/bed/lastzXenTro3.2012-11-13

    cat << '_EOF_' > DEF
# Rat vs. frog
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.02/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_Q=/scratch/data/blastz/HoxD55.q

# TARGET: Rat Rn5
SEQ1_DIR=/hive/data/genomes/rn5/rn5.2bit
SEQ1_LEN=/hive/data/genomes/rn5/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=30

# QUERY: frog xenTro3
SEQ2_DIR=/scratch/data/xenTro3/xenTro3.2bit
SEQ2_LEN=/scratch/data/xenTro3/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=80

BASE=/hive/data/genomes/rn5/bed/lastzXenTro3.2012-11-13
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    # adjust the SEQ2_LIMIT with -stop=partition to get a reasonable
    #	number of jobs, 50,000 to something under 100,000
    # when not present, SEQ2_LIMIT is a default 100
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
        `pwd`/DEF \
        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
        -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 &
    #	real    1307m43.094s
    cat fb.rn5.chainXenTro3Link.txt
    #	82011038 bases of 2572853723 (3.188%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/rn5/bed
    ln -s lastzXenTro3.2012-11-13 lastz.xenTro3

    #	and for the swap
    mkdir /hive/data/genomes/xenTro3/bed/blastz.rn5.swap
    cd /hive/data/genomes/xenTro3/bed/blastz.rn5.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/rn5/bed/lastzXenTro3.2012-11-13/DEF \
        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
        -swap -chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
    #	real    25m43.688s

    cat  fb.xenTro3.chainRn5Link.txt
    #	87276772 bases of 1358334882 (6.425%) in intersection

    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/xenTro3/bed
    ln -s blastz.rn5.swap lastz.rn5

#########################################################################
# lastz turkey melGal1 (DONE - 2012-11-13,14 - Hiram)
    # establish a screen to control this job with a name to indicate what it is
    screen -S rn5MelGal1
    mkdir /hive/data/genomes/rn5/bed/lastzMelGal1.2012-11-13
    cd /hive/data/genomes/rn5/bed/lastzMelGal1.2012-11-13

    cat << '_EOF_' > DEF
# Rat vs. turkey
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.02/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_Q=/scratch/data/blastz/HoxD55.q

# TARGET: Rat Rn5
SEQ1_DIR=/hive/data/genomes/rn5/rn5.2bit
SEQ1_LEN=/hive/data/genomes/rn5/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=20

# QUERY: turkey melGal1
SEQ2_DIR=/scratch/data/melGal1/melGal1.2bit
SEQ2_LEN=/scratch/data/melGal1/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=30

BASE=/hive/data/genomes/rn5/bed/lastzMelGal1.2012-11-13
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    # adjust the SEQ2_LIMIT with -stop=partition to get a reasonable
    #	number of jobs, 50,000 to something under 100,000
    # when not present, SEQ2_LIMIT is a default 100
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
        `pwd`/DEF \
        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
        -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 &
    #	real    1225m37.742s
    cat fb.rn5.chainMelGal1Link.txt
    #	93392251 bases of 2572853723 (3.630%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/rn5/bed
    ln -s lastzMelGal1.2012-11-13 lastz.melGal1

    #	and for the swap
    mkdir /hive/data/genomes/melGal1/bed/blastz.rn5.swap
    cd /hive/data/genomes/melGal1/bed/blastz.rn5.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/rn5/bed/lastzMelGal1.2012-11-13/DEF \
        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
        -swap -chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
    #	real    10m0.139s
    cat  fb.melGal1.chainRn5Link.txt
    #	74638274 bases of 935922386 (7.975%) in intersection

    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/melGal1/bed
    ln -s blastz.rn5.swap lastz.rn5

#########################################################################
# lastz chicken galGal4 (DONE - 2012-11-29,12-04 - Hiram)
    # establish a screen to control this job with a name to indicate what it is
    screen -S rn5GalGal4
    mkdir /hive/data/genomes/rn5/bed/lastzGalGal4.2012-11-29
    cd /hive/data/genomes/rn5/bed/lastzGalGal4.2012-11-29

    cat << '_EOF_' > DEF
# Rat vs. chicken
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.02/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_Q=/scratch/data/blastz/HoxD55.q

# TARGET: Rat Rn5
SEQ1_DIR=/hive/data/genomes/rn5/rn5.2bit
SEQ1_LEN=/hive/data/genomes/rn5/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=20

# QUERY: chicken galGal4
SEQ2_DIR=/hive/data/genomes/galGal4/galGal4.2bit
SEQ2_LEN=/hive/data/genomes/galGal4/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=60

BASE=/hive/data/genomes/rn5/bed/lastzGalGal4.2012-11-29
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    # adjust the SEQ2_LIMIT with -stop=partition to get a reasonable
    #	number of jobs, 50,000 to something under 100,000
    # when not present, SEQ2_LIMIT is a default 100
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
        `pwd`/DEF \
        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
        -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 &
    #	Elapsed time: 1483m27s
    cat fb.rn5.chainGalGal4Link.txt
    #	97465937 bases of 2572853723 (3.788%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/rn5/bed
    ln -s lastzGalGal4.2012-11-29 lastz.galGal4

    #	and for the swap
    mkdir /hive/data/genomes/galGal4/bed/blastz.rn5.swap
    cd /hive/data/genomes/galGal4/bed/blastz.rn5.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/rn5/bed/lastzGalGal4.2012-11-29/DEF \
        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
        -swap -chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
    #	real    11m49.505s
    cat fb.galGal4.chainRn5Link.txt
    #	81184849 bases of 1032854810 (7.860%) in intersection

    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/galGal4/bed
    ln -s blastz.rn5.swap lastz.rn5

#########################################################################
# lastz Opossum monDom5 (WORKING - 2012-11-29 - Hiram)
    # establish a screen to control this job with a name to indicate what it is
    screen -S rn5MonDom5
    mkdir /hive/data/genomes/rn5/bed/lastzMonDom5.2012-11-29
    cd /hive/data/genomes/rn5/bed/lastzMonDom5.2012-11-29

    cat << '_EOF_' > DEF
# Rat vs. opossum
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.02/bin/lastz
BLASTZ_M=254
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_Q=/scratch/data/blastz/HoxD55.q

# TARGET: Rat Rn5
SEQ1_DIR=/hive/data/genomes/rn5/rn5.2bit
SEQ1_LEN=/hive/data/genomes/rn5/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=20

# QUERY: Opossum monDom5
SEQ2_DIR=/scratch/data/monDom5/monDom5.2bit
SEQ2_LEN=/scratch/data/monDom5/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0

BASE=/hive/data/genomes/rn5/bed/lastzMonDom5.2012-11-29
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    # adjust the SEQ2_LIMIT with -stop=partition to get a reasonable
    #	number of jobs, 50,000 to something under 100,000
    #	Can't do this when there are only the single small set of chroms
     time nice -n +19 doBlastzChainNet.pl -verbose=2 \
        `pwd`/DEF \
        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
        -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 &
    #	real    3213m53.797s
    #   chaining failed, running last two for chr1 and chr3
    ./chain.csh rn5.2bit:chr1: chain/rn5.2bit:chr1:.chain &
    ./chain.csh rn5.2bit:chr3: chain/rn5.2bit:chr3:.chain
    #   real    269m41.974s
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
        -continue=chainMerge `pwd`/DEF \
        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
        -chainMinScore=5000 -chainLinearGap=loose > chainMerge.log 2>&1 &
XXX - running - Tue Dec  4 14:05:34 PST 2012

    cat fb.rn5.chainMonDom5Link.txt
    #	254245903 bases of 2652783500 (9.584%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/rn5/bed
    ln -s lastzMonDom5.2012-11-29 lastz.monDom5

    #	and for the swap
    mkdir /hive/data/genomes/monDom5/bed/blastz.rn5.swap
    cd /hive/data/genomes/monDom5/bed/blastz.rn5.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/rn5/bed/lastzMonDom5.2012-11-29/DEF \
        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
        -swap -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 &
    #	real    73m49.230s
    cat  fb.monDom5.chainRn5Link.txt
    #	252291401 bases of 3501660299 (7.205%) in intersection

    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/monDom5/bed
    ln -s blastz.rn5.swap lastz.rn5

#########################################################################
# LASTZ cow bosTau7 (DONE - 2012-11-29,12-03 - Hiram)
    # establish a screen to control this job with a name to indicate what it is
    screen -S rn5BosTau7
    mkdir /hive/data/genomes/rn5/bed/lastzBosTau7.2012-11-29
    cd /hive/data/genomes/rn5/bed/lastzBosTau7.2012-11-29

    cat << '_EOF_' > DEF
# cow vs mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.02/bin/lastz

# TARGET: Rat Rn5
SEQ1_DIR=/hive/data/genomes/rn5/rn5.2bit
SEQ1_LEN=/hive/data/genomes/rn5/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=20

# QUERY: cow BosTau7
SEQ2_DIR=/scratch/data/bosTau7/bosTau7.2bit
SEQ2_LEN=/scratch/data/bosTau7/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/rn5/bed/lastzBosTau7.2012-11-29
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    # adjust the SEQ2_LIMIT with -stop=partition to get a reasonable
    #	number of jobs, 50,000 to something under 100,000
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	`pwd`/DEF \
	-syntenicNet \
	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
	-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
    #   Elapsed time: 2921m25s
    cat fb.rn5.chainBosTau7Link.txt
    #   690036664 bases of 2572853723 (26.820%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/rn5/bed
    ln -s lastzBosTau7.2012-11-29 lastz.bosTau7

    mkdir /hive/data/genomes/bosTau7/bed/blastz.rn5.swap
    cd /hive/data/genomes/bosTau7/bed/blastz.rn5.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/rn5/bed/lastzBosTau7.2012-11-29/DEF \
	-swap -syntenicNet \
	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
	-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
    #   real    64m20.430s
    cat fb.bosTau7.chainRn5Link.txt
    #	687933878 bases of 2804673174 (24.528%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/bosTau7/bed
    ln -s blastz.rn5.swap lastz.rn5

##############################################################################
# LASTZ dog canFam3 (DONE - 2012-11-29,12-04 - Hiram)
    # establish a screen to control this job with a name to indicate what it is
    screen -S rn5CanFam3
    mkdir /hive/data/genomes/rn5/bed/lastzCanFam3.2012-11-29
    cd /hive/data/genomes/rn5/bed/lastzCanFam3.2012-11-29

    cat << '_EOF_' > DEF
# dog vs rat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.02/bin/lastz

# TARGET: Rat Rn5
SEQ1_DIR=/hive/data/genomes/rn5/rn5.2bit
SEQ1_LEN=/hive/data/genomes/rn5/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=20

# QUERY: dog CanFam3
SEQ2_DIR=/hive/data/genomes/canFam3/canFam3.2bit
SEQ2_LEN=/hive/data/genomes/canFam3/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=40

BASE=/hive/data/genomes/rn5/bed/lastzCanFam3.2012-11-29
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    # adjust the SEQ2_LIMIT with -stop=partition to get a reasonable
    #	number of jobs, 50,000 to something under 100,000
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	`pwd`/DEF \
	-syntenicNet \
	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
	-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
    #	real    5963m50.439s
    # there was a hung-up job that prolonged this time
    cat fb.rn5.chainCanFam3Link.txt
    #	768049485 bases of 2572853723 (29.852%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/rn5/bed
    ln -s lastzCanFam3.2012-11-29 lastz.canFam3

    mkdir /hive/data/genomes/canFam3/bed/blastz.rn5.swap
    cd /hive/data/genomes/canFam3/bed/blastz.rn5.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/rn5/bed/lastzCanFam3.2012-11-29/DEF \
	-swap -syntenicNet \
	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
	-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
    #	Elapsed time: 67m13s
    cat fb.canFam3.chainRn5Link.txt
    #	734454555 bases of 2392715236 (30.695%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/canFam3/bed
    ln -s blastz.rn5.swap lastz.rn5

##############################################################################
# LASTZ panda ailMel1 (DONE - 2012-11-29,12-04 - Hiram)
    # establish a screen to control this job with a name to indicate what it is
    screen -S rn5AilMel1
    mkdir /hive/data/genomes/rn5/bed/lastzAilMel1.2012-11-29
    cd /hive/data/genomes/rn5/bed/lastzAilMel1.2012-11-29

    cat << '_EOF_' > DEF
# panda vs rat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.02/bin/lastz

# TARGET: Rat Rn5
SEQ1_DIR=/hive/data/genomes/rn5/rn5.2bit
SEQ1_LEN=/hive/data/genomes/rn5/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=50

# QUERY: panda AilMel1
SEQ2_DIR=/scratch/data/ailMel1/ailMel1.2bit
SEQ2_LEN=/scratch/data/ailMel1/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=350

BASE=/hive/data/genomes/rn5/bed/lastzAilMel1.2012-11-29
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    # adjust the SEQ2_LIMIT with -stop=partition to get a reasonable
    #	number of jobs, 50,000 to something under 100,000
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	`pwd`/DEF \
	-syntenicNet \
	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
	-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
    #	Elapsed time: 2389m42s
    cat fb.rn5.chainAilMel1Link.txt
    #	818618644 bases of 2572853723 (31.818%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/rn5/bed
    ln -s lastzAilMel1.2012-11-29 lastz.ailMel1

    mkdir /hive/data/genomes/ailMel1/bed/blastz.rn5.swap
    cd /hive/data/genomes/ailMel1/bed/blastz.rn5.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/rn5/bed/lastzAilMel1.2012-11-29/DEF \
	-swap -syntenicNet \
	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
	-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
    #	Elapsed time: 72m40.305s
    cat fb.ailMel1.chainRn5Link.txt
    #	776437110 bases of 2245312831 (34.580%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/ailMel1/bed
    ln -s blastz.rn5.swap lastz.rn5

##############################################################################
# LASTZ Chimp PanTro4 (DONE - 2012-11-29,12-04 - Hiram)
    # establish a screen to control this job with a name to indicate what it is
    screen -S rn5PanTro4
    mkdir /hive/data/genomes/rn5/bed/lastzPanTro4.2012-11-29
    cd /hive/data/genomes/rn5/bed/lastzPanTro4.2012-11-29

    cat << '_EOF_' > DEF
# chimp vs rat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.02/bin/lastz

# TARGET: Rat Rn5
SEQ1_DIR=/hive/data/genomes/rn5/rn5.2bit
SEQ1_LEN=/hive/data/genomes/rn5/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: Chimp PanTro4
SEQ2_DIR=/hive/data/genomes/panTro4/panTro4.2bit
SEQ2_LEN=/hive/data/genomes/panTro4/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/rn5/bed/lastzPanTro4.2012-11-29
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	`pwd`/DEF \
	-syntenicNet \
	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
	-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
    #	real    3194m24.511s
    cat fb.rn5.chainPanTro4Link.txt
    #	916343862 bases of 2572853723 (35.616%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/rn5/bed
    ln -s lastzPanTro4.2012-11-29 lastz.panTro4

    mkdir /hive/data/genomes/panTro4/bed/blastz.rn5.swap
    cd /hive/data/genomes/panTro4/bed/blastz.rn5.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/rn5/bed/lastzPanTro4.2012-11-29/DEF \
	-swap -syntenicNet \
	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
	-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
    #	real    85m28.505s
    cat fb.panTro4.chainRn5Link.txt
    #	901495233 bases of 2902338967 (31.061%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/panTro4/bed
    ln -s blastz.rn5.swap lastz.rn5

##############################################################################
# LASTZ guinea pig cavPor3 (DONE - 2012-11-29,12-04 - Hiram)
    # establish a screen to control this job with a name to indicate what it is
    screen -S rn5CavPor3
    mkdir /hive/data/genomes/rn5/bed/lastzCavPor3.2012-11-29
    cd /hive/data/genomes/rn5/bed/lastzCavPor3.2012-11-29

    cat << '_EOF_' > DEF
# guinea pig vs rat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.02/bin/lastz

# TARGET: Rat Rn5
SEQ1_DIR=/hive/data/genomes/rn5/rn5.2bit
SEQ1_LEN=/hive/data/genomes/rn5/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: guinea pig CavPor3
SEQ2_DIR=/scratch/data/cavPor3/cavPor3.2bit
SEQ2_LEN=/scratch/data/cavPor3/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=20

BASE=/hive/data/genomes/rn5/bed/lastzCavPor3.2012-11-29
TMPDIR=/scratch/tmp
'_EOF_'
    # << happy emacs

    # adjust the SEQ2_LIMIT with -stop=partition to get a reasonable
    #	number of jobs, 50,000 to something under 100,000
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	`pwd`/DEF \
	-syntenicNet \
	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
	-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
    #	real    2935m17.649s
    cat fb.rn5.chainCavPor3Link.txt
    #	749383689 bases of 2572853723 (29.127%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/rn5/bed
    ln -s lastzCavPor3.2012-11-29 lastz.cavPor3

    mkdir /hive/data/genomes/cavPor3/bed/blastz.rn5.swap
    cd /hive/data/genomes/cavPor3/bed/blastz.rn5.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/rn5/bed/lastzCavPor3.2012-11-29/DEF \
	-swap -syntenicNet \
	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
	-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
    #	real    82m22.205s
    cat fb.cavPor3.chainRn5Link.txt
    #	750114059 bases of 2663369733 (28.164%) in intersection
    # set sym link to indicate this is the lastz for this genome:
    cd /hive/data/genomes/cavPor3/bed
    ln -s blastz.rn5.swap lastz.rn5

#########################################################################
# construct lift file Ensembl names to UCSC names (DONE 2013-02-19 Chin)
    cd /hive/data/genomes/rn5/jkStuff

cat ../chrom.sizes | while read L
do
ucName=`echo "${L}" | awk '{print $1}'`
ucSize=`echo "${L}" | awk '{print $2}'`
ensName=`echo $L  | sed -e 's/^chrM/MT/; s/^chr[0-9A-Za-z]*_//; s/_random//; s/^chr//; s/^\([JA][HA][B-Z0-9]*\)/\1.1/;' | awk '{print $1}'`
ensSize=`echo $L | awk '{print $2}'`
echo -e "0\t$ensName\t$ensSize\t$ucName\t$ucSize"
done > ensToUcsc.lift

##############################################################################