########################################################################
# LASTZ Dirofilaria immitis/Dog heartworm - dirImm1 vs.
#       Brugia malayi/Filarial worm - bruMal2
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/dirImm1/bed/lastzBruMal2.2015-08-17
    cd /hive/data/genomes/dirImm1/bed/lastzBruMal2.2015-08-17

    cat << '_EOF_' > DEF
# dirImm1 vs bruMal2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Dirofilaria immitis/Dog heartworm - dirImm1
SEQ1_DIR=/hive/data/genomes/dirImm1/dirImm1.2bit
SEQ1_LEN=/hive/data/genomes/dirImm1/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/dirImm1/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 8m34.892s
    cat fb.dirImm1.chainBruMal2Link.txt
    # 52062904 bases of 84923352 (61.306%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` dirImm1 bruMal2) > rbest.log 2>&1 &
    # real 1m53.341s

    # and for the swap:
    mkdir /hive/data/genomes/bruMal2/bed/blastz.dirImm1.swap
    cd /hive/data/genomes/bruMal2/bed/blastz.dirImm1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/dirImm1/bed/lastzBruMal2.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 5m39.813s
    cat fb.bruMal2.chainDirImm1Link.txt
    # 54553847 bases of 87424120 (62.401%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bruMal2 dirImm1) \
      > rbest.log 2>&1
    # real 2m27.411s

########################################################################
########################################################################
# LASTZ Dirofilaria immitis/Dog heartworm - dirImm1 vs.
#       Loa loa/Eye worm - loaLoa1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/dirImm1/bed/lastzLoaLoa1.2015-08-17
    cd /hive/data/genomes/dirImm1/bed/lastzLoaLoa1.2015-08-17

    cat << '_EOF_' > DEF
# dirImm1 vs loaLoa1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Dirofilaria immitis/Dog heartworm - dirImm1
SEQ1_DIR=/hive/data/genomes/dirImm1/dirImm1.2bit
SEQ1_LEN=/hive/data/genomes/dirImm1/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/dirImm1/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 8m27.843s
    cat fb.dirImm1.chainLoaLoa1Link.txt
    # 57910879 bases of 84923352 (68.192%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` dirImm1 loaLoa1) > rbest.log 2>&1 &
    # real 9m56.032s

    # and for the swap:
    mkdir /hive/data/genomes/loaLoa1/bed/blastz.dirImm1.swap
    cd /hive/data/genomes/loaLoa1/bed/blastz.dirImm1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/dirImm1/bed/lastzLoaLoa1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 3m56.954s
    cat fb.loaLoa1.chainDirImm1Link.txt
    # 57351893 bases of 87533141 (65.520%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` loaLoa1 dirImm1) \
      > rbest.log 2>&1
    # real 2m25.452s

########################################################################
########################################################################
# LASTZ Dirofilaria immitis/Dog heartworm - dirImm1 vs.
#       Onchocerca volvulus/O. volvulus - oncVol1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/dirImm1/bed/lastzOncVol1.2015-08-17
    cd /hive/data/genomes/dirImm1/bed/lastzOncVol1.2015-08-17

    cat << '_EOF_' > DEF
# dirImm1 vs oncVol1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Dirofilaria immitis/Dog heartworm - dirImm1
SEQ1_DIR=/hive/data/genomes/dirImm1/dirImm1.2bit
SEQ1_LEN=/hive/data/genomes/dirImm1/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/dirImm1/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 8m35.470s
    cat fb.dirImm1.chainOncVol1Link.txt
    # 65488529 bases of 84923352 (77.115%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` dirImm1 oncVol1) > rbest.log 2>&1 &
    # real 2m23.783s

    # and for the swap:
    mkdir /hive/data/genomes/oncVol1/bed/blastz.dirImm1.swap
    cd /hive/data/genomes/oncVol1/bed/blastz.dirImm1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/dirImm1/bed/lastzOncVol1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 4m8.923s
    cat fb.oncVol1.chainDirImm1Link.txt
    # 66237166 bases of 94327777 (70.220%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oncVol1 dirImm1) \
      > rbest.log 2>&1
    # real 2m44.746s

########################################################################
########################################################################
# LASTZ Dirofilaria immitis/Dog heartworm - dirImm1 vs.
#       Trichinella spiralis/Trichinella - triSpi1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/dirImm1/bed/lastzTriSpi1.2015-08-17
    cd /hive/data/genomes/dirImm1/bed/lastzTriSpi1.2015-08-17

    cat << '_EOF_' > DEF
# dirImm1 vs triSpi1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Dirofilaria immitis/Dog heartworm - dirImm1
SEQ1_DIR=/hive/data/genomes/dirImm1/dirImm1.2bit
SEQ1_LEN=/hive/data/genomes/dirImm1/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/dirImm1/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 4m15.938s
    cat fb.dirImm1.chainTriSpi1Link.txt
    # 2710536 bases of 84923352 (3.192%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` dirImm1 triSpi1) > rbest.log 2>&1 &
    # real 0m25.726s

    # and for the swap:
    mkdir /hive/data/genomes/triSpi1/bed/blastz.dirImm1.swap
    cd /hive/data/genomes/triSpi1/bed/blastz.dirImm1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/dirImm1/bed/lastzTriSpi1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m46.203s
    cat fb.triSpi1.chainDirImm1Link.txt
    # 2958673 bases of 58558192 (5.053%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSpi1 dirImm1) \
      > rbest.log 2>&1
    # real 0m24.870s

########################################################################
########################################################################
# LASTZ Dirofilaria immitis/Dog heartworm - dirImm1 vs.
#       Trichuris suis/Whipworm - triSui1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/dirImm1/bed/lastzTriSui1.2015-08-17
    cd /hive/data/genomes/dirImm1/bed/lastzTriSui1.2015-08-17

    cat << '_EOF_' > DEF
# dirImm1 vs triSui1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Dirofilaria immitis/Dog heartworm - dirImm1
SEQ1_DIR=/hive/data/genomes/dirImm1/dirImm1.2bit
SEQ1_LEN=/hive/data/genomes/dirImm1/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/dirImm1/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 4m51.646s
    cat fb.dirImm1.chainTriSui1Link.txt
    # 2223232 bases of 84923352 (2.618%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` dirImm1 triSui1) > rbest.log 2>&1 &
    # real 0m21.450s

    # and for the swap:
    mkdir /hive/data/genomes/triSui1/bed/blastz.dirImm1.swap
    cd /hive/data/genomes/triSui1/bed/blastz.dirImm1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/dirImm1/bed/lastzTriSui1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m41.397s
    cat fb.triSui1.chainDirImm1Link.txt
    # 2223506 bases of 71825323 (3.096%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSui1 dirImm1) \
      > rbest.log 2>&1
    # real 0m20.240s

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