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# LASTZ oncVol1 vs Brugia malayi/bruMal2 - (DONE - 2015-08-11 - Hiram)
    mkdir /hive/data/genomes/oncVol1/bed/lastzBruMal2.2015-08-11
    cd /hive/data/genomes/oncVol1/bed/lastzBruMal2.2015-08-11

    cat << '_EOF_' > DEF
# oncVol1 vs bruMal2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET: Onchocerca volvulus oncVol1
SEQ1_DIR=/hive/data/genomes/oncVol1/oncVol1.2bit
SEQ1_LEN=/hive/data/genomes/oncVol1/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Brugia malayi bruMal2
SEQ2_DIR=/hive/data/genomes/bruMal2/bruMal2.2bit
SEQ2_LEN=/hive/data/genomes/bruMal2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/oncVol1/bed/lastzBruMal2.2015-08-11
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
	-workhorse=hgwdev -bigClusterHub=ku \
	-smallClusterHub=ku -syntenicNet) > do.log 2>&1
    #	real    26m35.083s

    cat fb.oncVol1.chainBruMal2Link.txt
    # 59687716 bases of 94327777 (63.277%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` oncVol1 bruMal2) > rbest.log 2>&1 &
    # real    1m55.440s

    # and for the swap:
    mkdir /hive/data/genomes/bruMal2/bed/blastz.oncVol1.swap
    cd /hive/data/genomes/bruMal2/bed/blastz.oncVol1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/oncVol1/bed/lastzBruMal2.2015-08-11/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    6m42.542s

    cat fb.bruMal2.chainOncVol1Link.txt
    # 61774714 bases of 87424120 (70.661%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bruMal2 oncVol1) \
      > rbest.log 2>&1
    # real    2m57.085s

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