########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Ancylostoma ceylanicum/A. ceylanicum - ancCey1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzAncCey1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzAncCey1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs ancCey1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzAncCey1.2015-08-15
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 20m31.696s
    cat fb.caeSp111.chainAncCey1Link.txt
    # 8741749 bases of 76497192 (11.428%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 ancCey1) > rbest.log 2>&1 &
    # real 0m49.194s

    # and for the swap:
    mkdir /hive/data/genomes/ancCey1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/ancCey1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzAncCey1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m19.699s
    cat fb.ancCey1.chainCaeSp111Link.txt
    # 10007715 bases of 300914990 (3.326%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ancCey1 caeSp111) \
      > rbest.log 2>&1
    # real 1m14.322s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Ascaris suum/Pig roundworm - ascSuu1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzAscSuu1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzAscSuu1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs ascSuu1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzAscSuu1.2015-08-15
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 29m8.636s
    cat fb.caeSp111.chainAscSuu1Link.txt
    # 4871761 bases of 76497192 (6.369%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 ascSuu1) > rbest.log 2>&1 &
    # real 0m37.332s

    # and for the swap:
    mkdir /hive/data/genomes/ascSuu1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/ascSuu1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzAscSuu1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m9.398s
    cat fb.ascSuu1.chainCaeSp111Link.txt
    # 5096630 bases of 262604320 (1.941%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ascSuu1 caeSp111) \
      > rbest.log 2>&1
    # real 0m56.970s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Brugia malayi/Filarial worm - bruMal2
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzBruMal2.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzBruMal2.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs bruMal2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzBruMal2.2015-08-15
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 15m30.110s
    cat fb.caeSp111.chainBruMal2Link.txt
    # 4231724 bases of 76497192 (5.532%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 bruMal2) > rbest.log 2>&1 &
    # real 0m35.904s

    # and for the swap:
    mkdir /hive/data/genomes/bruMal2/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/bruMal2/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzBruMal2.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 3m5.891s
    cat fb.bruMal2.chainCaeSp111Link.txt
    # 4146475 bases of 87424120 (4.743%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bruMal2 caeSp111) \
      > rbest.log 2>&1
    # real 3m48.434s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Bursaphelenchus xylophilus/Pine wood nematode - burXyl1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzBurXyl1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzBurXyl1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs burXyl1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzBurXyl1.2015-08-15
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 12m29.006s
    cat fb.caeSp111.chainBurXyl1Link.txt
    # 5799971 bases of 76497192 (7.582%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 burXyl1) > rbest.log 2>&1 &
    # real 0m37.308s

    # and for the swap:
    mkdir /hive/data/genomes/burXyl1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/burXyl1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzBurXyl1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m1.017s
    cat fb.burXyl1.chainCaeSp111Link.txt
    # 5738266 bases of 73100506 (7.850%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` burXyl1 caeSp111) \
      > rbest.log 2>&1
    # real 0m53.216s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Caenorhabditis angaria/C. angaria - caeAng2
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzCaeAng2.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzCaeAng2.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs caeAng2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzCaeAng2.2015-08-15
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 40m54.252s
    cat fb.caeSp111.chainCaeAng2Link.txt
    # 15971454 bases of 76497192 (20.878%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 caeAng2) > rbest.log 2>&1 &
    # real 1m9.198s

    # and for the swap:
    mkdir /hive/data/genomes/caeAng2/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/caeAng2/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzCaeAng2.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 9m38.965s
    cat fb.caeAng2.chainCaeSp111Link.txt
    # 18687865 bases of 95237926 (19.622%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeAng2 caeSp111) \
      > rbest.log 2>&1
    # real 2m56.553s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Caenorhabditis sp5 ju800/C. sp. 5 ju800 - caeSp51
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzCaeSp51.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzCaeSp51.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs caeSp51
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzCaeSp51.2015-08-15
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 32m12.464s
    cat fb.caeSp111.chainCaeSp51Link.txt
    # 40001139 bases of 76497192 (52.291%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 caeSp51) > rbest.log 2>&1 &
    # real 1m40.938s

    # and for the swap:
    mkdir /hive/data/genomes/caeSp51/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/caeSp51/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzCaeSp51.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 6m50.031s
    cat fb.caeSp51.chainCaeSp111Link.txt
    # 43114193 bases of 130562982 (33.022%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeSp51 caeSp111) \
      > rbest.log 2>&1
    # real 9m37.381s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Dirofilaria immitis/Dog heartworm - dirImm1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzDirImm1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzDirImm1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs dirImm1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzDirImm1.2015-08-15
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 17m0.022s
    cat fb.caeSp111.chainDirImm1Link.txt
    # 4148770 bases of 76497192 (5.423%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 dirImm1) > rbest.log 2>&1 &
    # real 0m35.488s

    # and for the swap:
    mkdir /hive/data/genomes/dirImm1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/dirImm1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzDirImm1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 4m4.836s
    cat fb.dirImm1.chainCaeSp111Link.txt
    # 3958648 bases of 84923352 (4.661%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` dirImm1 caeSp111) \
      > rbest.log 2>&1
    # real 2m46.733s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Haemonchus contortus/Barber pole worm - haeCon2
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzHaeCon2.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzHaeCon2.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs haeCon2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzHaeCon2.2015-08-15
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 47m29.734s
    cat fb.caeSp111.chainHaeCon2Link.txt
    # 7936931 bases of 76497192 (10.375%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 haeCon2) > rbest.log 2>&1 &
    # real 0m50.920s

    # and for the swap:
    mkdir /hive/data/genomes/haeCon2/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/haeCon2/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzHaeCon2.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 2m22.553s
    cat fb.haeCon2.chainCaeSp111Link.txt
    # 11930405 bases of 346001353 (3.448%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` haeCon2 caeSp111) \
      > rbest.log 2>&1
    # real 1m55.447s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzHetBac1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzHetBac1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs hetBac1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzHetBac1.2015-08-15
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 13m15.916s
    cat fb.caeSp111.chainHetBac1Link.txt
    # 9439008 bases of 76497192 (12.339%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 hetBac1) > rbest.log 2>&1 &
    # real 0m46.034s

    # and for the swap:
    mkdir /hive/data/genomes/hetBac1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/hetBac1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzHetBac1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m33.541s
    cat fb.hetBac1.chainCaeSp111Link.txt
    # 9496128 bases of 74374900 (12.768%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hetBac1 caeSp111) \
      > rbest.log 2>&1
    # real 1m1.502s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Loa loa/Eye worm - loaLoa1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzLoaLoa1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzLoaLoa1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs loaLoa1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzLoaLoa1.2015-08-15
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 13m2.438s
    cat fb.caeSp111.chainLoaLoa1Link.txt
    # 4226914 bases of 76497192 (5.526%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 loaLoa1) > rbest.log 2>&1 &
    # real 0m31.107s

    # and for the swap:
    mkdir /hive/data/genomes/loaLoa1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/loaLoa1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzLoaLoa1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m56.240s
    cat fb.loaLoa1.chainCaeSp111Link.txt
    # 3949632 bases of 87533141 (4.512%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` loaLoa1 caeSp111) \
      > rbest.log 2>&1
    # real 0m42.963s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Meloidogyne hapla/M. hapla - melHap1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzMelHap1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzMelHap1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs melHap1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzMelHap1.2015-08-15
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 8m2.451s
    cat fb.caeSp111.chainMelHap1Link.txt
    # 3467147 bases of 76497192 (4.532%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 melHap1) > rbest.log 2>&1 &
    # real 0m25.812s

    # and for the swap:
    mkdir /hive/data/genomes/melHap1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/melHap1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzMelHap1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m53.782s
    cat fb.melHap1.chainCaeSp111Link.txt
    # 3416461 bases of 53017507 (6.444%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melHap1 caeSp111) \
      > rbest.log 2>&1
    # real 0m35.847s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Meloidogyne incognita/M. incognita - melInc2
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzMelInc2.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzMelInc2.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs melInc2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzMelInc2.2015-08-15
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 8m32.150s
    cat fb.caeSp111.chainMelInc2Link.txt
    # 3077248 bases of 76497192 (4.023%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 melInc2) > rbest.log 2>&1 &
    # real 0m27.273s

    # and for the swap:
    mkdir /hive/data/genomes/melInc2/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/melInc2/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzMelInc2.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m58.949s
    cat fb.melInc2.chainCaeSp111Link.txt
    # 4294620 bases of 82114761 (5.230%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melInc2 caeSp111) \
      > rbest.log 2>&1
    # real 0m38.864s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Necator americanus/N. americanus - necAme1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzNecAme1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzNecAme1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs necAme1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzNecAme1.2015-08-15
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 23m40.093s
    cat fb.caeSp111.chainNecAme1Link.txt
    # 7968401 bases of 76497192 (10.417%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 necAme1) > rbest.log 2>&1 &
    # real 0m46.675s

    # and for the swap:
    mkdir /hive/data/genomes/necAme1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/necAme1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzNecAme1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m22.535s
    cat fb.necAme1.chainCaeSp111Link.txt
    # 8378681 bases of 208187215 (4.025%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` necAme1 caeSp111) \
      > rbest.log 2>&1
    # real 1m15.042s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Onchocerca volvulus/O. volvulus - oncVol1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzOncVol1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzOncVol1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs oncVol1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzOncVol1.2015-08-15
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 12m9.190s
    cat fb.caeSp111.chainOncVol1Link.txt
    # 4301507 bases of 76497192 (5.623%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 oncVol1) > rbest.log 2>&1 &
    # real 0m45.441s

    # and for the swap:
    mkdir /hive/data/genomes/oncVol1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/oncVol1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzOncVol1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 3m6.947s
    cat fb.oncVol1.chainCaeSp111Link.txt
    # 4117539 bases of 94327777 (4.365%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oncVol1 caeSp111) \
      > rbest.log 2>&1
    # real 4m40.471s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Panagrellus redivivus/Microworm - panRed1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzPanRed1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzPanRed1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs panRed1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzPanRed1.2015-08-15
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 8m57.926s
    cat fb.caeSp111.chainPanRed1Link.txt
    # 6199853 bases of 76497192 (8.105%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 panRed1) > rbest.log 2>&1 &
    # real 0m36.528s

    # and for the swap:
    mkdir /hive/data/genomes/panRed1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/panRed1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzPanRed1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m59.049s
    cat fb.panRed1.chainCaeSp111Link.txt
    # 6254068 bases of 62228262 (10.050%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` panRed1 caeSp111) \
      > rbest.log 2>&1
    # real 0m52.194s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Pristionchus exspectatus/P. exspectatus - priExs1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzPriExs1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzPriExs1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs priExs1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzPriExs1.2015-08-15
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 13m28.290s
    cat fb.caeSp111.chainPriExs1Link.txt
    # 5668073 bases of 76497192 (7.410%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 priExs1) > rbest.log 2>&1 &
    # real 0m42.910s

    # and for the swap:
    mkdir /hive/data/genomes/priExs1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/priExs1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzPriExs1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 2m20.097s
    cat fb.priExs1.chainCaeSp111Link.txt
    # 6810121 bases of 166917800 (4.080%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priExs1 caeSp111) \
      > rbest.log 2>&1
    # real 1m3.248s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Pristionchus pacificus/P. pacificus - priPac3
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzPriPac3.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzPriPac3.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs priPac3
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzPriPac3.2015-08-15
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 23m16.286s
    cat fb.caeSp111.chainPriPac3Link.txt
    # 5703029 bases of 76497192 (7.455%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 priPac3) > rbest.log 2>&1 &
    # real 0m42.158s

    # and for the swap:
    mkdir /hive/data/genomes/priPac3/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/priPac3/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzPriPac3.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m17.598s
    cat fb.priPac3.chainCaeSp111Link.txt
    # 6600980 bases of 153238914 (4.308%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priPac3 caeSp111) \
      > rbest.log 2>&1
    # real 1m5.033s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Strongyloides ratti/Threadworm - strRat2
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzStrRat2.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzStrRat2.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs strRat2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzStrRat2.2015-08-15
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 6m19.930s
    cat fb.caeSp111.chainStrRat2Link.txt
    # 5128065 bases of 76497192 (6.704%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 strRat2) > rbest.log 2>&1 &
    # real 0m36.859s

    # and for the swap:
    mkdir /hive/data/genomes/strRat2/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/strRat2/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzStrRat2.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m50.835s
    cat fb.strRat2.chainCaeSp111Link.txt
    # 4823918 bases of 43150242 (11.179%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` strRat2 caeSp111) \
      > rbest.log 2>&1
    # real 0m43.297s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Trichinella spiralis/Trichinella - triSpi1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzTriSpi1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzTriSpi1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs triSpi1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzTriSpi1.2015-08-15
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 16m13.603s
    cat fb.caeSp111.chainTriSpi1Link.txt
    # 2577883 bases of 76497192 (3.370%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 triSpi1) > rbest.log 2>&1 &
    # real 0m29.222s

    # and for the swap:
    mkdir /hive/data/genomes/triSpi1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/triSpi1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzTriSpi1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 2m9.702s
    cat fb.triSpi1.chainCaeSp111Link.txt
    # 2680173 bases of 58558192 (4.577%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSpi1 caeSp111) \
      > rbest.log 2>&1
    # real 0m30.055s

########################################################################
########################################################################
# LASTZ Caenorhabditis tropicalis/C. tropicalis - caeSp111 vs.
#       Trichuris suis/Whipworm - triSui1
# (DONE - 2015-08-15 - Hiram)
    mkdir /hive/data/genomes/caeSp111/bed/lastzTriSui1.2015-08-15
    cd /hive/data/genomes/caeSp111/bed/lastzTriSui1.2015-08-15

    cat << '_EOF_' > DEF
# caeSp111 vs triSui1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis tropicalis/C. tropicalis - caeSp111
SEQ1_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit
SEQ1_LEN=/hive/data/genomes/caeSp111/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/caeSp111/bed/lastzTriSui1.2015-08-15
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 12m55.181s
    cat fb.caeSp111.chainTriSui1Link.txt
    # 2693509 bases of 76497192 (3.521%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeSp111 triSui1) > rbest.log 2>&1 &
    # real 0m24.775s

    # and for the swap:
    mkdir /hive/data/genomes/triSui1/bed/blastz.caeSp111.swap
    cd /hive/data/genomes/triSui1/bed/blastz.caeSp111.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeSp111/bed/lastzTriSui1.2015-08-15/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m47.199s
    cat fb.triSui1.chainCaeSp111Link.txt
    # 2708498 bases of 71825323 (3.771%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSui1 caeSp111) \
      > rbest.log 2>&1
    # real 0m29.369s

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