########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Ancylostoma ceylanicum/A. ceylanicum - ancCey1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzAncCey1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzAncCey1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs ancCey1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Ancylostoma ceylanicum/A. ceylanicum - ancCey1
SEQ2_DIR=/hive/data/genomes/ancCey1/ancCey1.2bit
SEQ2_LEN=/hive/data/genomes/ancCey1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzAncCey1.2015-08-14
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 18m52.311s
    cat fb.cb4.chainAncCey1Link.txt
    # 9557631 bases of 108371485 (8.819%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 ancCey1) > rbest.log 2>&1 &
    # real 0m53.204s

    # and for the swap:
    mkdir /hive/data/genomes/ancCey1/bed/blastz.cb4.swap
    cd /hive/data/genomes/ancCey1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzAncCey1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m24.167s
    cat fb.ancCey1.chainCb4Link.txt
    # 10222024 bases of 300914990 (3.397%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ancCey1 cb4) \
      > rbest.log 2>&1
    # real 1m18.950s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Ascaris suum/Pig roundworm - ascSuu1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzAscSuu1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzAscSuu1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs ascSuu1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Ascaris suum/Pig roundworm - ascSuu1
SEQ2_DIR=/hive/data/genomes/ascSuu1/ascSuu1.2bit
SEQ2_LEN=/hive/data/genomes/ascSuu1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzAscSuu1.2015-08-14
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 23m3.382s
    cat fb.cb4.chainAscSuu1Link.txt
    # 5230043 bases of 108371485 (4.826%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 ascSuu1) > rbest.log 2>&1 &
    # real 0m38.846s

    # and for the swap:
    mkdir /hive/data/genomes/ascSuu1/bed/blastz.cb4.swap
    cd /hive/data/genomes/ascSuu1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzAscSuu1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m10.981s
    cat fb.ascSuu1.chainCb4Link.txt
    # 5339444 bases of 262604320 (2.033%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ascSuu1 cb4) \
      > rbest.log 2>&1
    # real 0m54.982s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Brugia malayi/Filarial worm - bruMal2
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzBruMal2.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzBruMal2.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs bruMal2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Brugia malayi/Filarial worm - bruMal2
SEQ2_DIR=/hive/data/genomes/bruMal2/bruMal2.2bit
SEQ2_LEN=/hive/data/genomes/bruMal2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzBruMal2.2015-08-14
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 14m10.722s
    cat fb.cb4.chainBruMal2Link.txt
    # 4390127 bases of 108371485 (4.051%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 bruMal2) > rbest.log 2>&1 &
    # real 0m35.247s

    # and for the swap:
    mkdir /hive/data/genomes/bruMal2/bed/blastz.cb4.swap
    cd /hive/data/genomes/bruMal2/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzBruMal2.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m33.277s
    cat fb.bruMal2.chainCb4Link.txt
    # 4155614 bases of 87424120 (4.753%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bruMal2 cb4) \
      > rbest.log 2>&1
    # real 0m43.238s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Bursaphelenchus xylophilus/Pine wood nematode - burXyl1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzBurXyl1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzBurXyl1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs burXyl1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# 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=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzBurXyl1.2015-08-14
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 14m6.718s
    cat fb.cb4.chainBurXyl1Link.txt
    # 6267001 bases of 108371485 (5.783%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 burXyl1) > rbest.log 2>&1 &
    # real 0m41.824s

    # and for the swap:
    mkdir /hive/data/genomes/burXyl1/bed/blastz.cb4.swap
    cd /hive/data/genomes/burXyl1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzBurXyl1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m1.619s
    cat fb.burXyl1.chainCb4Link.txt
    # 5843556 bases of 73100506 (7.994%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` burXyl1 cb4) \
      > rbest.log 2>&1
    # real 0m54.764s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Caenorhabditis angaria/C. angaria - caeAng2
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzCaeAng2.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzCaeAng2.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs caeAng2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Caenorhabditis angaria/C. angaria - caeAng2
SEQ2_DIR=/hive/data/genomes/caeAng2/caeAng2.2bit
SEQ2_LEN=/hive/data/genomes/caeAng2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzCaeAng2.2015-08-14
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 27m34.406s
    cat fb.cb4.chainCaeAng2Link.txt
    # 16565079 bases of 108371485 (15.285%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 caeAng2) > rbest.log 2>&1 &
    # real 1m3.116s

    # and for the swap:
    mkdir /hive/data/genomes/caeAng2/bed/blastz.cb4.swap
    cd /hive/data/genomes/caeAng2/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzCaeAng2.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 7m43.269s
    cat fb.caeAng2.chainCb4Link.txt
    # 18681417 bases of 95237926 (19.616%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeAng2 cb4) \
      > rbest.log 2>&1
    # real 2m48.902s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Caenorhabditis japonica/C. japonica - caeJap4
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzCaeJap4.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzCaeJap4.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs caeJap4
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Caenorhabditis japonica/C. japonica - caeJap4
SEQ2_DIR=/hive/data/genomes/caeJap4/caeJap4.2bit
SEQ2_LEN=/hive/data/genomes/caeJap4/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzCaeJap4.2015-08-14
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 23m58.752s
    cat fb.cb4.chainCaeJap4Link.txt
    # 27376096 bases of 108371485 (25.261%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 caeJap4) > rbest.log 2>&1 &
    # real 1m19.958s

    # and for the swap:
    mkdir /hive/data/genomes/caeJap4/bed/blastz.cb4.swap
    cd /hive/data/genomes/caeJap4/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzCaeJap4.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 4m11.948s
    cat fb.caeJap4.chainCb4Link.txt
    # 31956053 bases of 154057934 (20.743%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeJap4 cb4) \
      > rbest.log 2>&1
    # real 2m51.268s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Caenorhabditis tropicalis/C. tropicalis - caeSp111
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzCaeSp111.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzCaeSp111.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs caeSp111
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ2_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ2_LEN=/hive/data/genomes/caeSp111/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzCaeSp111.2015-08-14
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 13m47.142s
    cat fb.cb4.chainCaeSp111Link.txt
    # 39755169 bases of 108371485 (36.684%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 caeSp111) > rbest.log 2>&1 &
    # real 1m55.621s

    # and for the swap:
    mkdir /hive/data/genomes/caeSp111/bed/blastz.cb4.swap
    cd /hive/data/genomes/caeSp111/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzCaeSp111.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 2m54.821s
    cat fb.caeSp111.chainCb4Link.txt
    # 37587659 bases of 76497192 (49.136%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeSp111 cb4) \
      > rbest.log 2>&1
    # real 2m18.905s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Caenorhabditis sp5 ju800/C. sp. 5 ju800 - caeSp51
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzCaeSp51.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzCaeSp51.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs caeSp51
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Caenorhabditis sp5 ju800/C. sp. 5 ju800 - caeSp51
SEQ2_DIR=/hive/data/genomes/caeSp51/caeSp51.2bit
SEQ2_LEN=/hive/data/genomes/caeSp51/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzCaeSp51.2015-08-14
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 21m31.000s
    cat fb.cb4.chainCaeSp51Link.txt
    # 50509882 bases of 108371485 (46.608%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 caeSp51) > rbest.log 2>&1 &
    # real 1m51.859s

    # and for the swap:
    mkdir /hive/data/genomes/caeSp51/bed/blastz.cb4.swap
    cd /hive/data/genomes/caeSp51/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzCaeSp51.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 6m12.384s
    cat fb.caeSp51.chainCb4Link.txt
    # 51406222 bases of 130562982 (39.373%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeSp51 cb4) \
      > rbest.log 2>&1
    # real 3m18.144s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Dirofilaria immitis/Dog heartworm - dirImm1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzDirImm1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzDirImm1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs dirImm1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Dirofilaria immitis/Dog heartworm - dirImm1
SEQ2_DIR=/hive/data/genomes/dirImm1/dirImm1.2bit
SEQ2_LEN=/hive/data/genomes/dirImm1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzDirImm1.2015-08-14
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 34m25.078s
    cat fb.cb4.chainDirImm1Link.txt
    # 4291012 bases of 108371485 (3.960%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 dirImm1) > rbest.log 2>&1 &
    # real 0m33.835s

    # and for the swap:
    mkdir /hive/data/genomes/dirImm1/bed/blastz.cb4.swap
    cd /hive/data/genomes/dirImm1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzDirImm1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m5.599s
    cat fb.dirImm1.chainCb4Link.txt
    # 3967148 bases of 84923352 (4.671%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` dirImm1 cb4) \
      > rbest.log 2>&1
    # real 0m46.684s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Haemonchus contortus/Barber pole worm - haeCon2
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzHaeCon2.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzHaeCon2.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs haeCon2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# 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=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzHaeCon2.2015-08-14
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 28m16.853s
    cat fb.cb4.chainHaeCon2Link.txt
    # 8647640 bases of 108371485 (7.980%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 haeCon2) > rbest.log 2>&1 &
    # real 0m47.676s

    # and for the swap:
    mkdir /hive/data/genomes/haeCon2/bed/blastz.cb4.swap
    cd /hive/data/genomes/haeCon2/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzHaeCon2.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 2m19.535s
    cat fb.haeCon2.chainCb4Link.txt
    # 12125398 bases of 346001353 (3.504%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` haeCon2 cb4) \
      > rbest.log 2>&1
    # real 1m47.729s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzHetBac1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzHetBac1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs hetBac1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1
SEQ2_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit
SEQ2_LEN=/hive/data/genomes/hetBac1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzHetBac1.2015-08-14
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 9m6.174s
    cat fb.cb4.chainHetBac1Link.txt
    # 10100734 bases of 108371485 (9.320%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 hetBac1) > rbest.log 2>&1 &
    # real 0m46.141s

    # and for the swap:
    mkdir /hive/data/genomes/hetBac1/bed/blastz.cb4.swap
    cd /hive/data/genomes/hetBac1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzHetBac1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m13.854s
    cat fb.hetBac1.chainCb4Link.txt
    # 9594114 bases of 74374900 (12.900%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hetBac1 cb4) \
      > rbest.log 2>&1
    # real 1m1.073s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Loa loa/Eye worm - loaLoa1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzLoaLoa1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzLoaLoa1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs loaLoa1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Loa loa/Eye worm - loaLoa1
SEQ2_DIR=/hive/data/genomes/loaLoa1/loaLoa1.2bit
SEQ2_LEN=/hive/data/genomes/loaLoa1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzLoaLoa1.2015-08-14
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 10m45.502s
    cat fb.cb4.chainLoaLoa1Link.txt
    # 4428332 bases of 108371485 (4.086%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 loaLoa1) > rbest.log 2>&1 &
    # real 0m33.370s

    # and for the swap:
    mkdir /hive/data/genomes/loaLoa1/bed/blastz.cb4.swap
    cd /hive/data/genomes/loaLoa1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzLoaLoa1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m54.892s
    cat fb.loaLoa1.chainCb4Link.txt
    # 4025438 bases of 87533141 (4.599%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` loaLoa1 cb4) \
      > rbest.log 2>&1
    # real 0m39.613s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Meloidogyne hapla/M. hapla - melHap1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzMelHap1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzMelHap1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs melHap1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Meloidogyne hapla/M. hapla - melHap1
SEQ2_DIR=/hive/data/genomes/melHap1/melHap1.2bit
SEQ2_LEN=/hive/data/genomes/melHap1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzMelHap1.2015-08-14
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 6m38.291s
    cat fb.cb4.chainMelHap1Link.txt
    # 3509385 bases of 108371485 (3.238%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 melHap1) > rbest.log 2>&1 &
    # real 0m27.404s

    # and for the swap:
    mkdir /hive/data/genomes/melHap1/bed/blastz.cb4.swap
    cd /hive/data/genomes/melHap1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzMelHap1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m52.361s
    cat fb.melHap1.chainCb4Link.txt
    # 3276376 bases of 53017507 (6.180%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melHap1 cb4) \
      > rbest.log 2>&1
    # real 0m32.503s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Meloidogyne incognita/M. incognita - melInc2
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzMelInc2.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzMelInc2.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs melInc2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Meloidogyne incognita/M. incognita - melInc2
SEQ2_DIR=/hive/data/genomes/melInc2/melInc2.2bit
SEQ2_LEN=/hive/data/genomes/melInc2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzMelInc2.2015-08-14
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 8m55.401s
    cat fb.cb4.chainMelInc2Link.txt
    # 3269265 bases of 108371485 (3.017%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 melInc2) > rbest.log 2>&1 &
    # real 0m27.713s

    # and for the swap:
    mkdir /hive/data/genomes/melInc2/bed/blastz.cb4.swap
    cd /hive/data/genomes/melInc2/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzMelInc2.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m58.548s
    cat fb.melInc2.chainCb4Link.txt
    # 4159538 bases of 82114761 (5.066%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melInc2 cb4) \
      > rbest.log 2>&1
    # real 0m39.684s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Necator americanus/N. americanus - necAme1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzNecAme1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzNecAme1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs necAme1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Necator americanus/N. americanus - necAme1
SEQ2_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ2_LEN=/hive/data/genomes/necAme1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzNecAme1.2015-08-14
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 19m23.484s
    cat fb.cb4.chainNecAme1Link.txt
    # 8586092 bases of 108371485 (7.923%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 necAme1) > rbest.log 2>&1 &
    # real 0m47.285s

    # and for the swap:
    mkdir /hive/data/genomes/necAme1/bed/blastz.cb4.swap
    cd /hive/data/genomes/necAme1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzNecAme1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m28.729s
    cat fb.necAme1.chainCb4Link.txt
    # 8450113 bases of 208187215 (4.059%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` necAme1 cb4) \
      > rbest.log 2>&1
    # real 1m17.113s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Onchocerca volvulus/O. volvulus - oncVol1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzOncVol1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzOncVol1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs oncVol1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Onchocerca volvulus/O. volvulus - oncVol1
SEQ2_DIR=/hive/data/genomes/oncVol1/oncVol1.2bit
SEQ2_LEN=/hive/data/genomes/oncVol1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzOncVol1.2015-08-14
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 9m45.232s
    cat fb.cb4.chainOncVol1Link.txt
    # 4482337 bases of 108371485 (4.136%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 oncVol1) > rbest.log 2>&1 &
    # real 0m45.962s

    # and for the swap:
    mkdir /hive/data/genomes/oncVol1/bed/blastz.cb4.swap
    cd /hive/data/genomes/oncVol1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzOncVol1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m51.498s
    cat fb.oncVol1.chainCb4Link.txt
    # 4151033 bases of 94327777 (4.401%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oncVol1 cb4) \
      > rbest.log 2>&1
    # real 0m51.808s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Panagrellus redivivus/Microworm - panRed1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzPanRed1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzPanRed1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs panRed1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Panagrellus redivivus/Microworm - panRed1
SEQ2_DIR=/hive/data/genomes/panRed1/panRed1.2bit
SEQ2_LEN=/hive/data/genomes/panRed1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzPanRed1.2015-08-14
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 7m5.146s
    cat fb.cb4.chainPanRed1Link.txt
    # 6678544 bases of 108371485 (6.163%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 panRed1) > rbest.log 2>&1 &
    # real 0m38.093s

    # and for the swap:
    mkdir /hive/data/genomes/panRed1/bed/blastz.cb4.swap
    cd /hive/data/genomes/panRed1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzPanRed1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m0.898s
    cat fb.panRed1.chainCb4Link.txt
    # 6349768 bases of 62228262 (10.204%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` panRed1 cb4) \
      > rbest.log 2>&1
    # real 0m48.872s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Pristionchus exspectatus/P. exspectatus - priExs1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzPriExs1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzPriExs1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs priExs1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Pristionchus exspectatus/P. exspectatus - priExs1
SEQ2_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ2_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzPriExs1.2015-08-14
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 10m45.214s
    cat fb.cb4.chainPriExs1Link.txt
    # 6129158 bases of 108371485 (5.656%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 priExs1) > rbest.log 2>&1 &
    # real 0m41.845s

    # and for the swap:
    mkdir /hive/data/genomes/priExs1/bed/blastz.cb4.swap
    cd /hive/data/genomes/priExs1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzPriExs1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m16.127s
    cat fb.priExs1.chainCb4Link.txt
    # 6956900 bases of 166917800 (4.168%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priExs1 cb4) \
      > rbest.log 2>&1
    # real 1m3.692s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Pristionchus pacificus/P. pacificus - priPac3
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzPriPac3.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzPriPac3.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs priPac3
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Pristionchus pacificus/P. pacificus - priPac3
SEQ2_DIR=/hive/data/genomes/priPac3/priPac3.2bit
SEQ2_LEN=/hive/data/genomes/priPac3/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzPriPac3.2015-08-14
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 16m41.642s
    cat fb.cb4.chainPriPac3Link.txt
    # 6371378 bases of 108371485 (5.879%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 priPac3) > rbest.log 2>&1 &
    # real 0m41.855s

    # and for the swap:
    mkdir /hive/data/genomes/priPac3/bed/blastz.cb4.swap
    cd /hive/data/genomes/priPac3/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzPriPac3.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m24.497s
    cat fb.priPac3.chainCb4Link.txt
    # 6808980 bases of 153238914 (4.443%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priPac3 cb4) \
      > rbest.log 2>&1
    # real 1m8.306s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Strongyloides ratti/Threadworm - strRat2
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzStrRat2.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzStrRat2.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs strRat2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Strongyloides ratti/Threadworm - strRat2
SEQ2_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ2_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzStrRat2.2015-08-14
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 6m14.097s
    cat fb.cb4.chainStrRat2Link.txt
    # 5096044 bases of 108371485 (4.702%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 strRat2) > rbest.log 2>&1 &
    # real 0m36.900s

    # and for the swap:
    mkdir /hive/data/genomes/strRat2/bed/blastz.cb4.swap
    cd /hive/data/genomes/strRat2/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzStrRat2.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m50.887s
    cat fb.strRat2.chainCb4Link.txt
    # 4635994 bases of 43150242 (10.744%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` strRat2 cb4) \
      > rbest.log 2>&1
    # real 0m42.809s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Trichinella spiralis/Trichinella - triSpi1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzTriSpi1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzTriSpi1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs triSpi1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Trichinella spiralis/Trichinella - triSpi1
SEQ2_DIR=/hive/data/genomes/triSpi1/triSpi1.2bit
SEQ2_LEN=/hive/data/genomes/triSpi1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzTriSpi1.2015-08-14
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 10m6.948s
    cat fb.cb4.chainTriSpi1Link.txt
    # 2674725 bases of 108371485 (2.468%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 triSpi1) > rbest.log 2>&1 &
    # real 0m28.512s

    # and for the swap:
    mkdir /hive/data/genomes/triSpi1/bed/blastz.cb4.swap
    cd /hive/data/genomes/triSpi1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzTriSpi1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m49.594s
    cat fb.triSpi1.chainCb4Link.txt
    # 2638021 bases of 58558192 (4.505%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSpi1 cb4) \
      > rbest.log 2>&1
    # real 0m30.332s

########################################################################
########################################################################
# LASTZ Caenorhabditis briggsae/C. briggsae - cb4 vs.
#       Trichuris suis/Whipworm - triSui1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/cb4/bed/lastzTriSui1.2015-08-14
    cd /hive/data/genomes/cb4/bed/lastzTriSui1.2015-08-14

    cat << '_EOF_' > DEF
# cb4 vs triSui1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis briggsae/C. briggsae - cb4
SEQ1_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ1_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Trichuris suis/Whipworm - triSui1
SEQ2_DIR=/hive/data/genomes/triSui1/triSui1.2bit
SEQ2_LEN=/hive/data/genomes/triSui1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/cb4/bed/lastzTriSui1.2015-08-14
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 10m21.749s
    cat fb.cb4.chainTriSui1Link.txt
    # 2903573 bases of 108371485 (2.679%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cb4 triSui1) > rbest.log 2>&1 &
    # real 0m26.185s

    # and for the swap:
    mkdir /hive/data/genomes/triSui1/bed/blastz.cb4.swap
    cd /hive/data/genomes/triSui1/bed/blastz.cb4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/cb4/bed/lastzTriSui1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m49.589s
    cat fb.triSui1.chainCb4Link.txt
    # 2856164 bases of 71825323 (3.977%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSui1 cb4) \
      > rbest.log 2>&1
    # real 0m31.481s

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