########################################################################
# LASTZ Meloidogyne hapla/M. hapla - melHap1 vs.
#       Brugia malayi/Filarial worm - bruMal2
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melHap1/bed/lastzBruMal2.2015-08-17
    cd /hive/data/genomes/melHap1/bed/lastzBruMal2.2015-08-17

    cat << '_EOF_' > DEF
# melHap1 vs bruMal2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne hapla/M. hapla - melHap1
SEQ1_DIR=/hive/data/genomes/melHap1/melHap1.2bit
SEQ1_LEN=/hive/data/genomes/melHap1/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/melHap1/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 3m24.527s
    cat fb.melHap1.chainBruMal2Link.txt
    # 3900049 bases of 53017507 (7.356%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melHap1 bruMal2) > rbest.log 2>&1 &
    # real 0m20.867s

    # and for the swap:
    mkdir /hive/data/genomes/bruMal2/bed/blastz.melHap1.swap
    cd /hive/data/genomes/bruMal2/bed/blastz.melHap1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melHap1/bed/lastzBruMal2.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m19.481s
    cat fb.bruMal2.chainMelHap1Link.txt
    # 4113522 bases of 87424120 (4.705%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bruMal2 melHap1) \
      > rbest.log 2>&1
    # real 0m27.588s

########################################################################
########################################################################
# LASTZ Meloidogyne hapla/M. hapla - melHap1 vs.
#       Bursaphelenchus xylophilus/Pine wood nematode - burXyl1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melHap1/bed/lastzBurXyl1.2015-08-17
    cd /hive/data/genomes/melHap1/bed/lastzBurXyl1.2015-08-17

    cat << '_EOF_' > DEF
# melHap1 vs burXyl1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne hapla/M. hapla - melHap1
SEQ1_DIR=/hive/data/genomes/melHap1/melHap1.2bit
SEQ1_LEN=/hive/data/genomes/melHap1/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/melHap1/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 3m18.565s
    cat fb.melHap1.chainBurXyl1Link.txt
    # 4297958 bases of 53017507 (8.107%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melHap1 burXyl1) > rbest.log 2>&1 &
    # real 0m24.877s

    # and for the swap:
    mkdir /hive/data/genomes/burXyl1/bed/blastz.melHap1.swap
    cd /hive/data/genomes/burXyl1/bed/blastz.melHap1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melHap1/bed/lastzBurXyl1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m46.678s
    cat fb.burXyl1.chainMelHap1Link.txt
    # 4292114 bases of 73100506 (5.872%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` burXyl1 melHap1) \
      > rbest.log 2>&1
    # real 0m25.689s

########################################################################
########################################################################
# LASTZ Meloidogyne hapla/M. hapla - melHap1 vs.
#       Dirofilaria immitis/Dog heartworm - dirImm1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melHap1/bed/lastzDirImm1.2015-08-17
    cd /hive/data/genomes/melHap1/bed/lastzDirImm1.2015-08-17

    cat << '_EOF_' > DEF
# melHap1 vs dirImm1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne hapla/M. hapla - melHap1
SEQ1_DIR=/hive/data/genomes/melHap1/melHap1.2bit
SEQ1_LEN=/hive/data/genomes/melHap1/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/melHap1/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 3m31.399s
    cat fb.melHap1.chainDirImm1Link.txt
    # 3840076 bases of 53017507 (7.243%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melHap1 dirImm1) > rbest.log 2>&1 &
    # real 0m23.270s

    # and for the swap:
    mkdir /hive/data/genomes/dirImm1/bed/blastz.melHap1.swap
    cd /hive/data/genomes/dirImm1/bed/blastz.melHap1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melHap1/bed/lastzDirImm1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m57.829s
    cat fb.dirImm1.chainMelHap1Link.txt
    # 3864092 bases of 84923352 (4.550%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` dirImm1 melHap1) \
      > rbest.log 2>&1
    # real 0m29.466s

########################################################################
########################################################################
# LASTZ Meloidogyne hapla/M. hapla - melHap1 vs.
#       Loa loa/Eye worm - loaLoa1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melHap1/bed/lastzLoaLoa1.2015-08-17
    cd /hive/data/genomes/melHap1/bed/lastzLoaLoa1.2015-08-17

    cat << '_EOF_' > DEF
# melHap1 vs loaLoa1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne hapla/M. hapla - melHap1
SEQ1_DIR=/hive/data/genomes/melHap1/melHap1.2bit
SEQ1_LEN=/hive/data/genomes/melHap1/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/melHap1/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 3m17.360s
    cat fb.melHap1.chainLoaLoa1Link.txt
    # 3625770 bases of 53017507 (6.839%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melHap1 loaLoa1) > rbest.log 2>&1 &
    # real 0m22.785s

    # and for the swap:
    mkdir /hive/data/genomes/loaLoa1/bed/blastz.melHap1.swap
    cd /hive/data/genomes/loaLoa1/bed/blastz.melHap1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melHap1/bed/lastzLoaLoa1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m48.249s
    cat fb.loaLoa1.chainMelHap1Link.txt
    # 3628034 bases of 87533141 (4.145%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` loaLoa1 melHap1) \
      > rbest.log 2>&1
    # real 0m24.879s

########################################################################
########################################################################
# LASTZ Meloidogyne hapla/M. hapla - melHap1 vs.
#       Meloidogyne incognita/M. incognita - melInc2
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melHap1/bed/lastzMelInc2.2015-08-17
    cd /hive/data/genomes/melHap1/bed/lastzMelInc2.2015-08-17

    cat << '_EOF_' > DEF
# melHap1 vs melInc2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne hapla/M. hapla - melHap1
SEQ1_DIR=/hive/data/genomes/melHap1/melHap1.2bit
SEQ1_LEN=/hive/data/genomes/melHap1/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/melHap1/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 5m0.178s
    cat fb.melHap1.chainMelInc2Link.txt
    # 29779257 bases of 53017507 (56.169%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melHap1 melInc2) > rbest.log 2>&1 &
    # real 1m6.702s

    # and for the swap:
    mkdir /hive/data/genomes/melInc2/bed/blastz.melHap1.swap
    cd /hive/data/genomes/melInc2/bed/blastz.melHap1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melHap1/bed/lastzMelInc2.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 3m18.507s
    cat fb.melInc2.chainMelHap1Link.txt
    # 45218946 bases of 82114761 (55.068%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melInc2 melHap1) \
      > rbest.log 2>&1
    # real 1m36.037s

########################################################################
########################################################################
# LASTZ Meloidogyne hapla/M. hapla - melHap1 vs.
#       Onchocerca volvulus/O. volvulus - oncVol1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melHap1/bed/lastzOncVol1.2015-08-17
    cd /hive/data/genomes/melHap1/bed/lastzOncVol1.2015-08-17

    cat << '_EOF_' > DEF
# melHap1 vs oncVol1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne hapla/M. hapla - melHap1
SEQ1_DIR=/hive/data/genomes/melHap1/melHap1.2bit
SEQ1_LEN=/hive/data/genomes/melHap1/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/melHap1/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 2m41.446s
    cat fb.melHap1.chainOncVol1Link.txt
    # 3943793 bases of 53017507 (7.439%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melHap1 oncVol1) > rbest.log 2>&1 &
    # real 0m35.191s

    # and for the swap:
    mkdir /hive/data/genomes/oncVol1/bed/blastz.melHap1.swap
    cd /hive/data/genomes/oncVol1/bed/blastz.melHap1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melHap1/bed/lastzOncVol1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m46.172s
    cat fb.oncVol1.chainMelHap1Link.txt
    # 4053038 bases of 94327777 (4.297%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oncVol1 melHap1) \
      > rbest.log 2>&1
    # real 0m33.245s

########################################################################
########################################################################
# LASTZ Meloidogyne hapla/M. hapla - melHap1 vs.
#       Trichinella spiralis/Trichinella - triSpi1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melHap1/bed/lastzTriSpi1.2015-08-17
    cd /hive/data/genomes/melHap1/bed/lastzTriSpi1.2015-08-17

    cat << '_EOF_' > DEF
# melHap1 vs triSpi1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne hapla/M. hapla - melHap1
SEQ1_DIR=/hive/data/genomes/melHap1/melHap1.2bit
SEQ1_LEN=/hive/data/genomes/melHap1/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/melHap1/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 2m41.012s
    cat fb.melHap1.chainTriSpi1Link.txt
    # 1975831 bases of 53017507 (3.727%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melHap1 triSpi1) > rbest.log 2>&1 &
    # real 0m22.845s

    # and for the swap:
    mkdir /hive/data/genomes/triSpi1/bed/blastz.melHap1.swap
    cd /hive/data/genomes/triSpi1/bed/blastz.melHap1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melHap1/bed/lastzTriSpi1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m43.779s
    cat fb.triSpi1.chainMelHap1Link.txt
    # 2150540 bases of 58558192 (3.672%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSpi1 melHap1) \
      > rbest.log 2>&1
    # real 0m19.363s

########################################################################
########################################################################
# LASTZ Meloidogyne hapla/M. hapla - melHap1 vs.
#       Trichuris suis/Whipworm - triSui1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melHap1/bed/lastzTriSui1.2015-08-17
    cd /hive/data/genomes/melHap1/bed/lastzTriSui1.2015-08-17

    cat << '_EOF_' > DEF
# melHap1 vs triSui1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne hapla/M. hapla - melHap1
SEQ1_DIR=/hive/data/genomes/melHap1/melHap1.2bit
SEQ1_LEN=/hive/data/genomes/melHap1/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/melHap1/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 3m3.627s
    cat fb.melHap1.chainTriSui1Link.txt
    # 1718675 bases of 53017507 (3.242%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melHap1 triSui1) > rbest.log 2>&1 &
    # real 2m19.455s

    # and for the swap:
    mkdir /hive/data/genomes/triSui1/bed/blastz.melHap1.swap
    cd /hive/data/genomes/triSui1/bed/blastz.melHap1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melHap1/bed/lastzTriSui1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m39.921s
    cat fb.triSui1.chainMelHap1Link.txt
    # 1786809 bases of 71825323 (2.488%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSui1 melHap1) \
      > rbest.log 2>&1
    # real 0m17.006s

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