########################################################################
# LASTZ Meloidogyne incognita/M. incognita - melInc2 vs.
#       Brugia malayi/Filarial worm - bruMal2
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melInc2/bed/lastzBruMal2.2015-08-17
    cd /hive/data/genomes/melInc2/bed/lastzBruMal2.2015-08-17

    cat << '_EOF_' > DEF
# melInc2 vs bruMal2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne incognita/M. incognita - melInc2
SEQ1_DIR=/hive/data/genomes/melInc2/melInc2.2bit
SEQ1_LEN=/hive/data/genomes/melInc2/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/melInc2/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 3m27.516s
    cat fb.melInc2.chainBruMal2Link.txt
    # 4994915 bases of 82114761 (6.083%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melInc2 bruMal2) > rbest.log 2>&1 &
    # real 2m24.748s

    # and for the swap:
    mkdir /hive/data/genomes/bruMal2/bed/blastz.melInc2.swap
    cd /hive/data/genomes/bruMal2/bed/blastz.melInc2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melInc2/bed/lastzBruMal2.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m19.399s
    cat fb.bruMal2.chainMelInc2Link.txt
    # 3880673 bases of 87424120 (4.439%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bruMal2 melInc2) \
      > rbest.log 2>&1
    # real 0m26.762s

########################################################################
########################################################################
# LASTZ Meloidogyne incognita/M. incognita - melInc2 vs.
#       Bursaphelenchus xylophilus/Pine wood nematode - burXyl1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melInc2/bed/lastzBurXyl1.2015-08-17
    cd /hive/data/genomes/melInc2/bed/lastzBurXyl1.2015-08-17

    cat << '_EOF_' > DEF
# melInc2 vs burXyl1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne incognita/M. incognita - melInc2
SEQ1_DIR=/hive/data/genomes/melInc2/melInc2.2bit
SEQ1_LEN=/hive/data/genomes/melInc2/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/melInc2/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 3m20.509s
    cat fb.melInc2.chainBurXyl1Link.txt
    # 5517514 bases of 82114761 (6.719%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melInc2 burXyl1) > rbest.log 2>&1 &
    # real 0m31.924s

    # and for the swap:
    mkdir /hive/data/genomes/burXyl1/bed/blastz.melInc2.swap
    cd /hive/data/genomes/burXyl1/bed/blastz.melInc2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melInc2/bed/lastzBurXyl1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m46.238s
    cat fb.burXyl1.chainMelInc2Link.txt
    # 3825759 bases of 73100506 (5.234%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` burXyl1 melInc2) \
      > rbest.log 2>&1
    # real 0m25.939s

########################################################################
########################################################################
# LASTZ Meloidogyne incognita/M. incognita - melInc2 vs.
#       Dirofilaria immitis/Dog heartworm - dirImm1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melInc2/bed/lastzDirImm1.2015-08-17
    cd /hive/data/genomes/melInc2/bed/lastzDirImm1.2015-08-17

    cat << '_EOF_' > DEF
# melInc2 vs dirImm1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne incognita/M. incognita - melInc2
SEQ1_DIR=/hive/data/genomes/melInc2/melInc2.2bit
SEQ1_LEN=/hive/data/genomes/melInc2/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/melInc2/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 3m26.513s
    cat fb.melInc2.chainDirImm1Link.txt
    # 4915473 bases of 82114761 (5.986%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melInc2 dirImm1) > rbest.log 2>&1 &
    # real 2m32.223s

    # and for the swap:
    mkdir /hive/data/genomes/dirImm1/bed/blastz.melInc2.swap
    cd /hive/data/genomes/dirImm1/bed/blastz.melInc2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melInc2/bed/lastzDirImm1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m58.626s
    cat fb.dirImm1.chainMelInc2Link.txt
    # 3538919 bases of 84923352 (4.167%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` dirImm1 melInc2) \
      > rbest.log 2>&1
    # real 0m30.773s

########################################################################
########################################################################
# LASTZ Meloidogyne incognita/M. incognita - melInc2 vs.
#       Loa loa/Eye worm - loaLoa1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melInc2/bed/lastzLoaLoa1.2015-08-17
    cd /hive/data/genomes/melInc2/bed/lastzLoaLoa1.2015-08-17

    cat << '_EOF_' > DEF
# melInc2 vs loaLoa1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne incognita/M. incognita - melInc2
SEQ1_DIR=/hive/data/genomes/melInc2/melInc2.2bit
SEQ1_LEN=/hive/data/genomes/melInc2/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/melInc2/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 3m18.964s
    cat fb.melInc2.chainLoaLoa1Link.txt
    # 4806271 bases of 82114761 (5.853%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melInc2 loaLoa1) > rbest.log 2>&1 &
    # real 2m22.988s

    # and for the swap:
    mkdir /hive/data/genomes/loaLoa1/bed/blastz.melInc2.swap
    cd /hive/data/genomes/loaLoa1/bed/blastz.melInc2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melInc2/bed/lastzLoaLoa1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m48.651s
    cat fb.loaLoa1.chainMelInc2Link.txt
    # 3429279 bases of 87533141 (3.918%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` loaLoa1 melInc2) \
      > rbest.log 2>&1
    # real 0m25.774s

########################################################################
########################################################################
# LASTZ Meloidogyne incognita/M. incognita - melInc2 vs.
#       Onchocerca volvulus/O. volvulus - oncVol1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melInc2/bed/lastzOncVol1.2015-08-17
    cd /hive/data/genomes/melInc2/bed/lastzOncVol1.2015-08-17

    cat << '_EOF_' > DEF
# melInc2 vs oncVol1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne incognita/M. incognita - melInc2
SEQ1_DIR=/hive/data/genomes/melInc2/melInc2.2bit
SEQ1_LEN=/hive/data/genomes/melInc2/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/melInc2/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 3m28.649s
    cat fb.melInc2.chainOncVol1Link.txt
    # 5152612 bases of 82114761 (6.275%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melInc2 oncVol1) > rbest.log 2>&1 &
    # real 0m50.924s

    # and for the swap:
    mkdir /hive/data/genomes/oncVol1/bed/blastz.melInc2.swap
    cd /hive/data/genomes/oncVol1/bed/blastz.melInc2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melInc2/bed/lastzOncVol1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m45.895s
    cat fb.oncVol1.chainMelInc2Link.txt
    # 3810539 bases of 94327777 (4.040%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oncVol1 melInc2) \
      > rbest.log 2>&1
    # real 0m38.770s

########################################################################
########################################################################
# LASTZ Meloidogyne incognita/M. incognita - melInc2 vs.
#       Trichinella spiralis/Trichinella - triSpi1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melInc2/bed/lastzTriSpi1.2015-08-17
    cd /hive/data/genomes/melInc2/bed/lastzTriSpi1.2015-08-17

    cat << '_EOF_' > DEF
# melInc2 vs triSpi1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne incognita/M. incognita - melInc2
SEQ1_DIR=/hive/data/genomes/melInc2/melInc2.2bit
SEQ1_LEN=/hive/data/genomes/melInc2/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/melInc2/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 3m14.769s
    cat fb.melInc2.chainTriSpi1Link.txt
    # 2558922 bases of 82114761 (3.116%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melInc2 triSpi1) > rbest.log 2>&1 &
    # real 8m30.225s

    # and for the swap:
    mkdir /hive/data/genomes/triSpi1/bed/blastz.melInc2.swap
    cd /hive/data/genomes/triSpi1/bed/blastz.melInc2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melInc2/bed/lastzTriSpi1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m44.874s
    cat fb.triSpi1.chainMelInc2Link.txt
    # 1995827 bases of 58558192 (3.408%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSpi1 melInc2) \
      > rbest.log 2>&1
    # real 0m19.910s

########################################################################
########################################################################
# LASTZ Meloidogyne incognita/M. incognita - melInc2 vs.
#       Trichuris suis/Whipworm - triSui1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/melInc2/bed/lastzTriSui1.2015-08-17
    cd /hive/data/genomes/melInc2/bed/lastzTriSui1.2015-08-17

    cat << '_EOF_' > DEF
# melInc2 vs triSui1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Meloidogyne incognita/M. incognita - melInc2
SEQ1_DIR=/hive/data/genomes/melInc2/melInc2.2bit
SEQ1_LEN=/hive/data/genomes/melInc2/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/melInc2/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 3m10.677s
    cat fb.melInc2.chainTriSui1Link.txt
    # 2333724 bases of 82114761 (2.842%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melInc2 triSui1) > rbest.log 2>&1 &
    # real 6m19.252s

    # and for the swap:
    mkdir /hive/data/genomes/triSui1/bed/blastz.melInc2.swap
    cd /hive/data/genomes/triSui1/bed/blastz.melInc2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melInc2/bed/lastzTriSui1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m40.836s
    cat fb.triSui1.chainMelInc2Link.txt
    # 1767603 bases of 71825323 (2.461%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSui1 melInc2) \
      > rbest.log 2>&1
    # real 0m18.249s

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