########################################################################
# LASTZ Pristionchus exspectatus/P. exspectatus - priExs1 vs.
#       Brugia malayi/Filarial worm - bruMal2
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/priExs1/bed/lastzBruMal2.2015-08-17
    cd /hive/data/genomes/priExs1/bed/lastzBruMal2.2015-08-17

    cat << '_EOF_' > DEF
# priExs1 vs bruMal2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Pristionchus exspectatus/P. exspectatus - priExs1
SEQ1_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ1_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Brugia malayi/Filarial worm - bruMal2
SEQ2_DIR=/hive/data/genomes/bruMal2/bruMal2.2bit
SEQ2_LEN=/hive/data/genomes/bruMal2/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/priExs1/bed/lastzBruMal2.2015-08-17
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 5m59.806s
    cat fb.priExs1.chainBruMal2Link.txt
    # 3887307 bases of 166917800 (2.329%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` priExs1 bruMal2) > rbest.log 2>&1 &
    # real 0m27.330s

    # and for the swap:
    mkdir /hive/data/genomes/bruMal2/bed/blastz.priExs1.swap
    cd /hive/data/genomes/bruMal2/bed/blastz.priExs1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/priExs1/bed/lastzBruMal2.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m44.795s
    cat fb.bruMal2.chainPriExs1Link.txt
    # 3421161 bases of 87424120 (3.913%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bruMal2 priExs1) \
      > rbest.log 2>&1
    # real 1m55.381s

########################################################################
########################################################################
# LASTZ Pristionchus exspectatus/P. exspectatus - priExs1 vs.
#       Bursaphelenchus xylophilus/Pine wood nematode - burXyl1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/priExs1/bed/lastzBurXyl1.2015-08-17
    cd /hive/data/genomes/priExs1/bed/lastzBurXyl1.2015-08-17

    cat << '_EOF_' > DEF
# priExs1 vs burXyl1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Pristionchus exspectatus/P. exspectatus - priExs1
SEQ1_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ1_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Bursaphelenchus xylophilus/Pine wood nematode - burXyl1
SEQ2_DIR=/hive/data/genomes/burXyl1/burXyl1.2bit
SEQ2_LEN=/hive/data/genomes/burXyl1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/priExs1/bed/lastzBurXyl1.2015-08-17
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 3m43.014s
    cat fb.priExs1.chainBurXyl1Link.txt
    # 4907824 bases of 166917800 (2.940%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` priExs1 burXyl1) > rbest.log 2>&1 &
    # real 0m27.915s

    # and for the swap:
    mkdir /hive/data/genomes/burXyl1/bed/blastz.priExs1.swap
    cd /hive/data/genomes/burXyl1/bed/blastz.priExs1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/priExs1/bed/lastzBurXyl1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m48.742s
    cat fb.burXyl1.chainPriExs1Link.txt
    # 4035610 bases of 73100506 (5.521%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` burXyl1 priExs1) \
      > rbest.log 2>&1
    # real 0m33.566s

########################################################################
########################################################################
# LASTZ Pristionchus exspectatus/P. exspectatus - priExs1 vs.
#       Dirofilaria immitis/Dog heartworm - dirImm1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/priExs1/bed/lastzDirImm1.2015-08-17
    cd /hive/data/genomes/priExs1/bed/lastzDirImm1.2015-08-17

    cat << '_EOF_' > DEF
# priExs1 vs dirImm1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Pristionchus exspectatus/P. exspectatus - priExs1
SEQ1_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ1_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Dirofilaria immitis/Dog heartworm - dirImm1
SEQ2_DIR=/hive/data/genomes/dirImm1/dirImm1.2bit
SEQ2_LEN=/hive/data/genomes/dirImm1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/priExs1/bed/lastzDirImm1.2015-08-17
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 5m41.225s
    cat fb.priExs1.chainDirImm1Link.txt
    # 3730849 bases of 166917800 (2.235%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` priExs1 dirImm1) > rbest.log 2>&1 &
    # real 0m25.818s

    # and for the swap:
    mkdir /hive/data/genomes/dirImm1/bed/blastz.priExs1.swap
    cd /hive/data/genomes/dirImm1/bed/blastz.priExs1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/priExs1/bed/lastzDirImm1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 6m14.115s
    cat fb.dirImm1.chainPriExs1Link.txt
    # 3179503 bases of 84923352 (3.744%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` dirImm1 priExs1) \
      > rbest.log 2>&1
    # real 0m31.009s

########################################################################
########################################################################
# LASTZ Pristionchus exspectatus/P. exspectatus - priExs1 vs.
#       Loa loa/Eye worm - loaLoa1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/priExs1/bed/lastzLoaLoa1.2015-08-17
    cd /hive/data/genomes/priExs1/bed/lastzLoaLoa1.2015-08-17

    cat << '_EOF_' > DEF
# priExs1 vs loaLoa1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Pristionchus exspectatus/P. exspectatus - priExs1
SEQ1_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ1_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Loa loa/Eye worm - loaLoa1
SEQ2_DIR=/hive/data/genomes/loaLoa1/loaLoa1.2bit
SEQ2_LEN=/hive/data/genomes/loaLoa1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/priExs1/bed/lastzLoaLoa1.2015-08-17
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 3m38.880s
    cat fb.priExs1.chainLoaLoa1Link.txt
    # 3921358 bases of 166917800 (2.349%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` priExs1 loaLoa1) > rbest.log 2>&1 &
    # real 0m25.149s

    # and for the swap:
    mkdir /hive/data/genomes/loaLoa1/bed/blastz.priExs1.swap
    cd /hive/data/genomes/loaLoa1/bed/blastz.priExs1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/priExs1/bed/lastzLoaLoa1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m47.681s
    cat fb.loaLoa1.chainPriExs1Link.txt
    # 3297574 bases of 87533141 (3.767%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` loaLoa1 priExs1) \
      > rbest.log 2>&1
    # real 0m27.793s

########################################################################
########################################################################
# LASTZ Pristionchus exspectatus/P. exspectatus - priExs1 vs.
#       Meloidogyne hapla/M. hapla - melHap1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/priExs1/bed/lastzMelHap1.2015-08-17
    cd /hive/data/genomes/priExs1/bed/lastzMelHap1.2015-08-17

    cat << '_EOF_' > DEF
# priExs1 vs melHap1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Pristionchus exspectatus/P. exspectatus - priExs1
SEQ1_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ1_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Meloidogyne hapla/M. hapla - melHap1
SEQ2_DIR=/hive/data/genomes/melHap1/melHap1.2bit
SEQ2_LEN=/hive/data/genomes/melHap1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/priExs1/bed/lastzMelHap1.2015-08-17
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 3m17.494s
    cat fb.priExs1.chainMelHap1Link.txt
    # 2263158 bases of 166917800 (1.356%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` priExs1 melHap1) > rbest.log 2>&1 &
    # real 0m18.968s

    # and for the swap:
    mkdir /hive/data/genomes/melHap1/bed/blastz.priExs1.swap
    cd /hive/data/genomes/melHap1/bed/blastz.priExs1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/priExs1/bed/lastzMelHap1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m43.299s
    cat fb.melHap1.chainPriExs1Link.txt
    # 2017630 bases of 53017507 (3.806%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melHap1 priExs1) \
      > rbest.log 2>&1
    # real 0m20.748s

########################################################################
########################################################################
# LASTZ Pristionchus exspectatus/P. exspectatus - priExs1 vs.
#       Meloidogyne incognita/M. incognita - melInc2
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/priExs1/bed/lastzMelInc2.2015-08-17
    cd /hive/data/genomes/priExs1/bed/lastzMelInc2.2015-08-17

    cat << '_EOF_' > DEF
# priExs1 vs melInc2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Pristionchus exspectatus/P. exspectatus - priExs1
SEQ1_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ1_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Meloidogyne incognita/M. incognita - melInc2
SEQ2_DIR=/hive/data/genomes/melInc2/melInc2.2bit
SEQ2_LEN=/hive/data/genomes/melInc2/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/priExs1/bed/lastzMelInc2.2015-08-17
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 3m27.184s
    cat fb.priExs1.chainMelInc2Link.txt
    # 2100626 bases of 166917800 (1.258%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` priExs1 melInc2) > rbest.log 2>&1 &
    # real 0m19.183s

    # and for the swap:
    mkdir /hive/data/genomes/melInc2/bed/blastz.priExs1.swap
    cd /hive/data/genomes/melInc2/bed/blastz.priExs1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/priExs1/bed/lastzMelInc2.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m46.274s
    cat fb.melInc2.chainPriExs1Link.txt
    # 2590854 bases of 82114761 (3.155%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melInc2 priExs1) \
      > rbest.log 2>&1
    # real 0m22.887s

########################################################################
########################################################################
# LASTZ Pristionchus exspectatus/P. exspectatus - priExs1 vs.
#       Onchocerca volvulus/O. volvulus - oncVol1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/priExs1/bed/lastzOncVol1.2015-08-17
    cd /hive/data/genomes/priExs1/bed/lastzOncVol1.2015-08-17

    cat << '_EOF_' > DEF
# priExs1 vs oncVol1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Pristionchus exspectatus/P. exspectatus - priExs1
SEQ1_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ1_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Onchocerca volvulus/O. volvulus - oncVol1
SEQ2_DIR=/hive/data/genomes/oncVol1/oncVol1.2bit
SEQ2_LEN=/hive/data/genomes/oncVol1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/priExs1/bed/lastzOncVol1.2015-08-17
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 4m1.659s
    cat fb.priExs1.chainOncVol1Link.txt
    # 3883679 bases of 166917800 (2.327%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` priExs1 oncVol1) > rbest.log 2>&1 &
    # real 0m41.518s

    # and for the swap:
    mkdir /hive/data/genomes/oncVol1/bed/blastz.priExs1.swap
    cd /hive/data/genomes/oncVol1/bed/blastz.priExs1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/priExs1/bed/lastzOncVol1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 3m56.976s
    cat fb.oncVol1.chainPriExs1Link.txt
    # 3317528 bases of 94327777 (3.517%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oncVol1 priExs1) \
      > rbest.log 2>&1
    # real 0m34.149s

########################################################################
########################################################################
# LASTZ Pristionchus exspectatus/P. exspectatus - priExs1 vs.
#       Pristionchus pacificus/P. pacificus - priPac3
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/priExs1/bed/lastzPriPac3.2015-08-17
    cd /hive/data/genomes/priExs1/bed/lastzPriPac3.2015-08-17

    cat << '_EOF_' > DEF
# priExs1 vs priPac3
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Pristionchus exspectatus/P. exspectatus - priExs1
SEQ1_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ1_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Pristionchus pacificus/P. pacificus - priPac3
SEQ2_DIR=/hive/data/genomes/priPac3/priPac3.2bit
SEQ2_LEN=/hive/data/genomes/priPac3/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/priExs1/bed/lastzPriPac3.2015-08-17
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 12m45.418s
    cat fb.priExs1.chainPriPac3Link.txt
    # 129023524 bases of 166917800 (77.298%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` priExs1 priPac3) > rbest.log 2>&1 &
    # real 3m15.932s

    # and for the swap:
    mkdir /hive/data/genomes/priPac3/bed/blastz.priExs1.swap
    cd /hive/data/genomes/priPac3/bed/blastz.priExs1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/priExs1/bed/lastzPriPac3.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 8m40.726s
    cat fb.priPac3.chainPriExs1Link.txt
    # 116836391 bases of 153238914 (76.245%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priPac3 priExs1) \
      > rbest.log 2>&1
    # real 5m10.285s

########################################################################
########################################################################
# LASTZ Pristionchus exspectatus/P. exspectatus - priExs1 vs.
#       Trichinella spiralis/Trichinella - triSpi1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/priExs1/bed/lastzTriSpi1.2015-08-17
    cd /hive/data/genomes/priExs1/bed/lastzTriSpi1.2015-08-17

    cat << '_EOF_' > DEF
# priExs1 vs triSpi1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Pristionchus exspectatus/P. exspectatus - priExs1
SEQ1_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ1_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Trichinella spiralis/Trichinella - triSpi1
SEQ2_DIR=/hive/data/genomes/triSpi1/triSpi1.2bit
SEQ2_LEN=/hive/data/genomes/triSpi1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/priExs1/bed/lastzTriSpi1.2015-08-17
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 3m4.655s
    cat fb.priExs1.chainTriSpi1Link.txt
    # 1833902 bases of 166917800 (1.099%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` priExs1 triSpi1) > rbest.log 2>&1 &
    # real 0m21.331s

    # and for the swap:
    mkdir /hive/data/genomes/triSpi1/bed/blastz.priExs1.swap
    cd /hive/data/genomes/triSpi1/bed/blastz.priExs1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/priExs1/bed/lastzTriSpi1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m42.093s
    cat fb.triSpi1.chainPriExs1Link.txt
    # 1694507 bases of 58558192 (2.894%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSpi1 priExs1) \
      > rbest.log 2>&1
    # real 0m20.242s

########################################################################
########################################################################
# LASTZ Pristionchus exspectatus/P. exspectatus - priExs1 vs.
#       Trichuris suis/Whipworm - triSui1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/priExs1/bed/lastzTriSui1.2015-08-17
    cd /hive/data/genomes/priExs1/bed/lastzTriSui1.2015-08-17

    cat << '_EOF_' > DEF
# priExs1 vs triSui1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Pristionchus exspectatus/P. exspectatus - priExs1
SEQ1_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ1_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Trichuris suis/Whipworm - triSui1
SEQ2_DIR=/hive/data/genomes/triSui1/triSui1.2bit
SEQ2_LEN=/hive/data/genomes/triSui1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/priExs1/bed/lastzTriSui1.2015-08-17
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 3m31.116s
    cat fb.priExs1.chainTriSui1Link.txt
    # 2166782 bases of 166917800 (1.298%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` priExs1 triSui1) > rbest.log 2>&1 &
    # real 0m21.665s

    # and for the swap:
    mkdir /hive/data/genomes/triSui1/bed/blastz.priExs1.swap
    cd /hive/data/genomes/triSui1/bed/blastz.priExs1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/priExs1/bed/lastzTriSui1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m9.994s
    cat fb.triSui1.chainPriExs1Link.txt
    # 2050588 bases of 71825323 (2.855%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSui1 priExs1) \
      > rbest.log 2>&1
    # real 1m12.574s

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