########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Ascaris suum/Pig roundworm - ascSuu1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzAscSuu1.2015-08-16
    cd /hive/data/genomes/necAme1/bed/lastzAscSuu1.2015-08-16

    cat << '_EOF_' > DEF
# necAme1 vs ascSuu1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Ascaris suum/Pig roundworm - ascSuu1
SEQ2_DIR=/hive/data/genomes/ascSuu1/ascSuu1.2bit
SEQ2_LEN=/hive/data/genomes/ascSuu1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/necAme1/bed/lastzAscSuu1.2015-08-16
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 8m37.442s
    cat fb.necAme1.chainAscSuu1Link.txt
    # 6515063 bases of 208187215 (3.129%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 ascSuu1) > rbest.log 2>&1 &
    # real 0m38.856s

    # and for the swap:
    mkdir /hive/data/genomes/ascSuu1/bed/blastz.necAme1.swap
    cd /hive/data/genomes/ascSuu1/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzAscSuu1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m6.586s
    cat fb.ascSuu1.chainNecAme1Link.txt
    # 6291196 bases of 262604320 (2.396%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ascSuu1 necAme1) \
      > rbest.log 2>&1
    # real 0m47.705s

########################################################################
########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Brugia malayi/Filarial worm - bruMal2
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzBruMal2.2015-08-17
    cd /hive/data/genomes/necAme1/bed/lastzBruMal2.2015-08-17

    cat << '_EOF_' > DEF
# necAme1 vs bruMal2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/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/necAme1/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 5m37.563s
    cat fb.necAme1.chainBruMal2Link.txt
    # 5289476 bases of 208187215 (2.541%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 bruMal2) > rbest.log 2>&1 &
    # real 0m32.442s

    # and for the swap:
    mkdir /hive/data/genomes/bruMal2/bed/blastz.necAme1.swap
    cd /hive/data/genomes/bruMal2/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzBruMal2.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m35.867s
    cat fb.bruMal2.chainNecAme1Link.txt
    # 5414787 bases of 87424120 (6.194%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bruMal2 necAme1) \
      > rbest.log 2>&1
    # real 0m37.781s

########################################################################
########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Bursaphelenchus xylophilus/Pine wood nematode - burXyl1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzBurXyl1.2015-08-17
    cd /hive/data/genomes/necAme1/bed/lastzBurXyl1.2015-08-17

    cat << '_EOF_' > DEF
# necAme1 vs burXyl1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/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/necAme1/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 4m42.354s
    cat fb.necAme1.chainBurXyl1Link.txt
    # 5035251 bases of 208187215 (2.419%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 burXyl1) > rbest.log 2>&1 &
    # real 0m43.599s

    # and for the swap:
    mkdir /hive/data/genomes/burXyl1/bed/blastz.necAme1.swap
    cd /hive/data/genomes/burXyl1/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzBurXyl1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m51.794s
    cat fb.burXyl1.chainNecAme1Link.txt
    # 4679604 bases of 73100506 (6.402%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` burXyl1 necAme1) \
      > rbest.log 2>&1
    # real 0m35.511s

########################################################################
########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Dirofilaria immitis/Dog heartworm - dirImm1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzDirImm1.2015-08-17
    cd /hive/data/genomes/necAme1/bed/lastzDirImm1.2015-08-17

    cat << '_EOF_' > DEF
# necAme1 vs dirImm1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/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/necAme1/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 5m45.566s
    cat fb.necAme1.chainDirImm1Link.txt
    # 5158372 bases of 208187215 (2.478%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 dirImm1) > rbest.log 2>&1 &
    # real 0m32.728s

    # and for the swap:
    mkdir /hive/data/genomes/dirImm1/bed/blastz.necAme1.swap
    cd /hive/data/genomes/dirImm1/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzDirImm1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m5.470s
    cat fb.dirImm1.chainNecAme1Link.txt
    # 5006918 bases of 84923352 (5.896%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` dirImm1 necAme1) \
      > rbest.log 2>&1
    # real 0m41.121s

########################################################################
########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Haemonchus contortus/Barber pole worm - haeCon2
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzHaeCon2.2015-08-16
    cd /hive/data/genomes/necAme1/bed/lastzHaeCon2.2015-08-16

    cat << '_EOF_' > DEF
# necAme1 vs haeCon2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Haemonchus contortus/Barber pole worm - haeCon2
SEQ2_DIR=/hive/data/genomes/haeCon2/haeCon2.2bit
SEQ2_LEN=/hive/data/genomes/haeCon2/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/necAme1/bed/lastzHaeCon2.2015-08-16
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 13m35.193s
    cat fb.necAme1.chainHaeCon2Link.txt
    # 29177064 bases of 208187215 (14.015%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 haeCon2) > rbest.log 2>&1 &
    # real 1m24.226s

    # and for the swap:
    mkdir /hive/data/genomes/haeCon2/bed/blastz.necAme1.swap
    cd /hive/data/genomes/haeCon2/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzHaeCon2.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 5m11.770s
    cat fb.haeCon2.chainNecAme1Link.txt
    # 42769920 bases of 346001353 (12.361%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` haeCon2 necAme1) \
      > rbest.log 2>&1
    # real 2m48.118s

########################################################################
########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Loa loa/Eye worm - loaLoa1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzLoaLoa1.2015-08-17
    cd /hive/data/genomes/necAme1/bed/lastzLoaLoa1.2015-08-17

    cat << '_EOF_' > DEF
# necAme1 vs loaLoa1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/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/necAme1/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 5m16.166s
    cat fb.necAme1.chainLoaLoa1Link.txt
    # 5434476 bases of 208187215 (2.610%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 loaLoa1) > rbest.log 2>&1 &
    # real 0m32.142s

    # and for the swap:
    mkdir /hive/data/genomes/loaLoa1/bed/blastz.necAme1.swap
    cd /hive/data/genomes/loaLoa1/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzLoaLoa1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m55.240s
    cat fb.loaLoa1.chainNecAme1Link.txt
    # 5118183 bases of 87533141 (5.847%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` loaLoa1 necAme1) \
      > rbest.log 2>&1
    # real 0m34.349s

########################################################################
########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Meloidogyne hapla/M. hapla - melHap1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzMelHap1.2015-08-17
    cd /hive/data/genomes/necAme1/bed/lastzMelHap1.2015-08-17

    cat << '_EOF_' > DEF
# necAme1 vs melHap1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/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/necAme1/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 3m47.971s
    cat fb.necAme1.chainMelHap1Link.txt
    # 3069272 bases of 208187215 (1.474%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 melHap1) > rbest.log 2>&1 &
    # real 0m29.791s

    # and for the swap:
    mkdir /hive/data/genomes/melHap1/bed/blastz.necAme1.swap
    cd /hive/data/genomes/melHap1/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzMelHap1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m47.464s
    cat fb.melHap1.chainNecAme1Link.txt
    # 2935804 bases of 53017507 (5.537%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melHap1 necAme1) \
      > rbest.log 2>&1
    # real 0m25.202s

########################################################################
########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Meloidogyne incognita/M. incognita - melInc2
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzMelInc2.2015-08-17
    cd /hive/data/genomes/necAme1/bed/lastzMelInc2.2015-08-17

    cat << '_EOF_' > DEF
# necAme1 vs melInc2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/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/necAme1/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 4m3.474s
    cat fb.necAme1.chainMelInc2Link.txt
    # 2942687 bases of 208187215 (1.413%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 melInc2) > rbest.log 2>&1 &
    # real 0m31.129s

    # and for the swap:
    mkdir /hive/data/genomes/melInc2/bed/blastz.necAme1.swap
    cd /hive/data/genomes/melInc2/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzMelInc2.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m51.706s
    cat fb.melInc2.chainNecAme1Link.txt
    # 3870419 bases of 82114761 (4.713%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melInc2 necAme1) \
      > rbest.log 2>&1
    # real 0m28.679s

########################################################################
########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Onchocerca volvulus/O. volvulus - oncVol1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzOncVol1.2015-08-17
    cd /hive/data/genomes/necAme1/bed/lastzOncVol1.2015-08-17

    cat << '_EOF_' > DEF
# necAme1 vs oncVol1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/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/necAme1/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 5m15.022s
    cat fb.necAme1.chainOncVol1Link.txt
    # 5425777 bases of 208187215 (2.606%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 oncVol1) > rbest.log 2>&1 &
    # real 0m48.683s

    # and for the swap:
    mkdir /hive/data/genomes/oncVol1/bed/blastz.necAme1.swap
    cd /hive/data/genomes/oncVol1/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzOncVol1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m50.802s
    cat fb.oncVol1.chainNecAme1Link.txt
    # 5222030 bases of 94327777 (5.536%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oncVol1 necAme1) \
      > rbest.log 2>&1
    # real 0m45.765s

########################################################################
########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Pristionchus exspectatus/P. exspectatus - priExs1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzPriExs1.2015-08-17
    cd /hive/data/genomes/necAme1/bed/lastzPriExs1.2015-08-17

    cat << '_EOF_' > DEF
# necAme1 vs priExs1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Pristionchus exspectatus/P. exspectatus - priExs1
SEQ2_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ2_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/necAme1/bed/lastzPriExs1.2015-08-17
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 6m48.147s
    cat fb.necAme1.chainPriExs1Link.txt
    # 6248632 bases of 208187215 (3.001%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 priExs1) > rbest.log 2>&1 &
    # real 0m36.156s

    # and for the swap:
    mkdir /hive/data/genomes/priExs1/bed/blastz.necAme1.swap
    cd /hive/data/genomes/priExs1/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzPriExs1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m4.450s
    cat fb.priExs1.chainNecAme1Link.txt
    # 7309633 bases of 166917800 (4.379%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priExs1 necAme1) \
      > rbest.log 2>&1
    # real 0m45.953s

########################################################################
########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Pristionchus pacificus/P. pacificus - priPac3
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzPriPac3.2015-08-17
    cd /hive/data/genomes/necAme1/bed/lastzPriPac3.2015-08-17

    cat << '_EOF_' > DEF
# necAme1 vs priPac3
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/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/necAme1/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 8m12.906s
    cat fb.necAme1.chainPriPac3Link.txt
    # 6353102 bases of 208187215 (3.052%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 priPac3) > rbest.log 2>&1 &
    # real 0m52.411s

    # and for the swap:
    mkdir /hive/data/genomes/priPac3/bed/blastz.necAme1.swap
    cd /hive/data/genomes/priPac3/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzPriPac3.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m10.392s
    cat fb.priPac3.chainNecAme1Link.txt
    # 7037296 bases of 153238914 (4.592%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priPac3 necAme1) \
      > rbest.log 2>&1
    # real 0m47.455s

########################################################################
########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Trichinella spiralis/Trichinella - triSpi1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzTriSpi1.2015-08-17
    cd /hive/data/genomes/necAme1/bed/lastzTriSpi1.2015-08-17

    cat << '_EOF_' > DEF
# necAme1 vs triSpi1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/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/necAme1/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 4m18.800s
    cat fb.necAme1.chainTriSpi1Link.txt
    # 2326522 bases of 208187215 (1.118%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 triSpi1) > rbest.log 2>&1 &
    # real 0m26.185s

    # and for the swap:
    mkdir /hive/data/genomes/triSpi1/bed/blastz.necAme1.swap
    cd /hive/data/genomes/triSpi1/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzTriSpi1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m45.081s
    cat fb.triSpi1.chainNecAme1Link.txt
    # 2400189 bases of 58558192 (4.099%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSpi1 necAme1) \
      > rbest.log 2>&1
    # real 0m24.636s

########################################################################
########################################################################
# LASTZ Necator americanus/N. americanus - necAme1 vs.
#       Trichuris suis/Whipworm - triSui1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/lastzTriSui1.2015-08-17
    cd /hive/data/genomes/necAme1/bed/lastzTriSui1.2015-08-17

    cat << '_EOF_' > DEF
# necAme1 vs triSui1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Necator americanus/N. americanus - necAme1
SEQ1_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ1_LEN=/hive/data/genomes/necAme1/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/necAme1/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 4m26.391s
    cat fb.necAme1.chainTriSui1Link.txt
    # 2789972 bases of 208187215 (1.340%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` necAme1 triSui1) > rbest.log 2>&1 &
    # real 0m24.360s

    # and for the swap:
    mkdir /hive/data/genomes/triSui1/bed/blastz.necAme1.swap
    cd /hive/data/genomes/triSui1/bed/blastz.necAme1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/necAme1/bed/lastzTriSui1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m45.476s
    cat fb.triSui1.chainNecAme1Link.txt
    # 2695997 bases of 71825323 (3.754%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSui1 necAme1) \
      > rbest.log 2>&1
    # real 0m23.220s

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