########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Ancylostoma ceylanicum/A. ceylanicum - ancCey1
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzAncCey1.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzAncCey1.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs ancCey1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzAncCey1.2015-08-13
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 24m28.154s
    cat fb.caeRem4.chainAncCey1Link.txt
    # 10989664 bases of 138406203 (7.940%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 ancCey1) > rbest.log 2>&1 &
    # real 0m44.181s

    # and for the swap:
    mkdir /hive/data/genomes/ancCey1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/ancCey1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzAncCey1.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m16.536s
    cat fb.ancCey1.chainCaeRem4Link.txt
    # 11141769 bases of 300914990 (3.703%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ancCey1 caeRem4) \
      > rbest.log 2>&1
    # real 0m58.291s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Ascaris suum/Pig roundworm - ascSuu1
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzAscSuu1.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzAscSuu1.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs ascSuu1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzAscSuu1.2015-08-13
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 29m40.416s
    cat fb.caeRem4.chainAscSuu1Link.txt
    # 5920654 bases of 138406203 (4.278%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 ascSuu1) > rbest.log 2>&1 &
    # real 0m31.225s

    # and for the swap:
    mkdir /hive/data/genomes/ascSuu1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/ascSuu1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzAscSuu1.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m2.959s
    cat fb.ascSuu1.chainCaeRem4Link.txt
    # 5346758 bases of 262604320 (2.036%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ascSuu1 caeRem4) \
      > rbest.log 2>&1
    # real 0m43.593s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Brugia malayi/Filarial worm - bruMal2
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzBruMal2.2015-08-14
    cd /hive/data/genomes/caeRem4/bed/lastzBruMal2.2015-08-14

    cat << '_EOF_' > DEF
# caeRem4 vs bruMal2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/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 22m1.537s
    cat fb.caeRem4.chainBruMal2Link.txt
    # 4998277 bases of 138406203 (3.611%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 bruMal2) > rbest.log 2>&1 &
    # real 0m27.776s

    # and for the swap:
    mkdir /hive/data/genomes/bruMal2/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/bruMal2/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzBruMal2.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m28.825s
    cat fb.bruMal2.chainCaeRem4Link.txt
    # 4431233 bases of 87424120 (5.069%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bruMal2 caeRem4) \
      > rbest.log 2>&1
    # real 0m33.420s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Bursaphelenchus xylophilus/Pine wood nematode - burXyl1
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzBurXyl1.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzBurXyl1.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs burXyl1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzBurXyl1.2015-08-13
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 26m44.330s
    cat fb.caeRem4.chainBurXyl1Link.txt
    # 6911531 bases of 138406203 (4.994%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 burXyl1) > rbest.log 2>&1 &
    # real 0m33.163s

    # and for the swap:
    mkdir /hive/data/genomes/burXyl1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/burXyl1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzBurXyl1.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m54.902s
    cat fb.burXyl1.chainCaeRem4Link.txt
    # 5882820 bases of 73100506 (8.048%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` burXyl1 caeRem4) \
      > rbest.log 2>&1
    # real 0m36.134s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Caenorhabditis angaria/C. angaria - caeAng2
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzCaeAng2.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzCaeAng2.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs caeAng2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzCaeAng2.2015-08-13
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 61m39.769s
    cat fb.caeRem4.chainCaeAng2Link.txt
    # 19565630 bases of 138406203 (14.136%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 caeAng2) > rbest.log 2>&1 &
    # real 0m59.462s

    # and for the swap:
    mkdir /hive/data/genomes/caeAng2/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/caeAng2/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzCaeAng2.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 7m59.041s
    cat fb.caeAng2.chainCaeRem4Link.txt
    # 20022853 bases of 95237926 (21.024%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeAng2 caeRem4) \
      > rbest.log 2>&1
    # real 2m33.908s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Caenorhabditis japonica/C. japonica - caeJap4
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzCaeJap4.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzCaeJap4.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs caeJap4
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzCaeJap4.2015-08-13
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 28m0.148s
    cat fb.caeRem4.chainCaeJap4Link.txt
    # 32136203 bases of 138406203 (23.219%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 caeJap4) > rbest.log 2>&1 &
    # real 1m8.580s

    # and for the swap:
    mkdir /hive/data/genomes/caeJap4/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/caeJap4/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzCaeJap4.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 3m50.517s
    cat fb.caeJap4.chainCaeRem4Link.txt
    # 34607726 bases of 154057934 (22.464%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeJap4 caeRem4) \
      > rbest.log 2>&1
    # real 2m17.022s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Caenorhabditis tropicalis/C. tropicalis - caeSp111
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzCaeSp111.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzCaeSp111.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs caeSp111
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzCaeSp111.2015-08-13
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 11m49.237s
    cat fb.caeRem4.chainCaeSp111Link.txt
    # 48891917 bases of 138406203 (35.325%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 caeSp111) > rbest.log 2>&1 &
    # real 2m4.532s

    # and for the swap:
    mkdir /hive/data/genomes/caeSp111/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/caeSp111/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzCaeSp111.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 2m54.033s
    cat fb.caeSp111.chainCaeRem4Link.txt
    # 41468674 bases of 76497192 (54.209%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeSp111 caeRem4) \
      > rbest.log 2>&1
    # real 1m59.189s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Caenorhabditis sp5 ju800/C. sp. 5 ju800 - caeSp51
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzCaeSp51.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzCaeSp51.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs caeSp51
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzCaeSp51.2015-08-13
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 166m19.789s
    cat fb.caeRem4.chainCaeSp51Link.txt
    # 56378074 bases of 138406203 (40.734%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 caeSp51) > rbest.log 2>&1 &
    # real 1m50.955s

    # and for the swap:
    mkdir /hive/data/genomes/caeSp51/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/caeSp51/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzCaeSp51.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 5m56.194s
    cat fb.caeSp51.chainCaeRem4Link.txt
    # 51633913 bases of 130562982 (39.547%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeSp51 caeRem4) \
      > rbest.log 2>&1
    # real 2m45.025s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Caenorhabditis briggsae/C. briggsae - cb4
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzCb4.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzCb4.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs cb4
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/chrom.sizes
SEQ1_CHUNK=1000000
SEQ1_LAP=10000

# QUERY: Caenorhabditis briggsae/C. briggsae - cb4
SEQ2_DIR=/hive/data/genomes/cb4/cb4.2bit
SEQ2_LEN=/hive/data/genomes/cb4/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/caeRem4/bed/lastzCb4.2015-08-13
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 13m10.751s
    cat fb.caeRem4.chainCb4Link.txt
    # 50799321 bases of 138406203 (36.703%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 cb4) > rbest.log 2>&1 &
    # real 1m55.376s

    # and for the swap:
    mkdir /hive/data/genomes/cb4/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/cb4/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzCb4.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 3m25.219s
    cat fb.cb4.chainCaeRem4Link.txt
    # 45892158 bases of 108371485 (42.347%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` cb4 caeRem4) \
      > rbest.log 2>&1
    # real 2m10.789s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Dirofilaria immitis/Dog heartworm - dirImm1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzDirImm1.2015-08-14
    cd /hive/data/genomes/caeRem4/bed/lastzDirImm1.2015-08-14

    cat << '_EOF_' > DEF
# caeRem4 vs dirImm1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/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 43m20.604s
    cat fb.caeRem4.chainDirImm1Link.txt
    # 4875771 bases of 138406203 (3.523%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 dirImm1) > rbest.log 2>&1 &
    # real 0m27.084s

    # and for the swap:
    mkdir /hive/data/genomes/dirImm1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/dirImm1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzDirImm1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m1.701s
    cat fb.dirImm1.chainCaeRem4Link.txt
    # 4122885 bases of 84923352 (4.855%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` dirImm1 caeRem4) \
      > rbest.log 2>&1
    # real 0m36.908s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Haemonchus contortus/Barber pole worm - haeCon2
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzHaeCon2.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzHaeCon2.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs haeCon2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzHaeCon2.2015-08-13
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 34m23.121s
    cat fb.caeRem4.chainHaeCon2Link.txt
    # 10038770 bases of 138406203 (7.253%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 haeCon2) > rbest.log 2>&1 &
    # real 0m42.028s

    # and for the swap:
    mkdir /hive/data/genomes/haeCon2/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/haeCon2/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzHaeCon2.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 2m21.128s
    cat fb.haeCon2.chainCaeRem4Link.txt
    # 13415380 bases of 346001353 (3.877%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` haeCon2 caeRem4) \
      > rbest.log 2>&1
    # real 1m26.806s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzHetBac1.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzHetBac1.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs hetBac1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzHetBac1.2015-08-13
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 11m46.225s
    cat fb.caeRem4.chainHetBac1Link.txt
    # 11240749 bases of 138406203 (8.122%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 hetBac1) > rbest.log 2>&1 &
    # real 0m38.747s

    # and for the swap:
    mkdir /hive/data/genomes/hetBac1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/hetBac1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzHetBac1.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m5.125s
    cat fb.hetBac1.chainCaeRem4Link.txt
    # 9871731 bases of 74374900 (13.273%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hetBac1 caeRem4) \
      > rbest.log 2>&1
    # real 0m43.849s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Loa loa/Eye worm - loaLoa1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzLoaLoa1.2015-08-14
    cd /hive/data/genomes/caeRem4/bed/lastzLoaLoa1.2015-08-14

    cat << '_EOF_' > DEF
# caeRem4 vs loaLoa1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/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 16m23.334s
    cat fb.caeRem4.chainLoaLoa1Link.txt
    # 4977657 bases of 138406203 (3.596%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 loaLoa1) > rbest.log 2>&1 &
    # real 0m28.681s

    # and for the swap:
    mkdir /hive/data/genomes/loaLoa1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/loaLoa1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzLoaLoa1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m51.285s
    cat fb.loaLoa1.chainCaeRem4Link.txt
    # 4141306 bases of 87533141 (4.731%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` loaLoa1 caeRem4) \
      > rbest.log 2>&1
    # real 0m31.033s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Meloidogyne hapla/M. hapla - melHap1
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzMelHap1.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzMelHap1.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs melHap1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzMelHap1.2015-08-13
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 9m59.922s
    cat fb.caeRem4.chainMelHap1Link.txt
    # 4066777 bases of 138406203 (2.938%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 melHap1) > rbest.log 2>&1 &
    # real 0m23.673s

    # and for the swap:
    mkdir /hive/data/genomes/melHap1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/melHap1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzMelHap1.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m48.783s
    cat fb.melHap1.chainCaeRem4Link.txt
    # 3476425 bases of 53017507 (6.557%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melHap1 caeRem4) \
      > rbest.log 2>&1
    # real 0m26.294s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Meloidogyne incognita/M. incognita - melInc2
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzMelInc2.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzMelInc2.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs melInc2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzMelInc2.2015-08-13
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 12m6.789s
    cat fb.caeRem4.chainMelInc2Link.txt
    # 3739627 bases of 138406203 (2.702%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 melInc2) > rbest.log 2>&1 &
    # real 0m24.776s

    # and for the swap:
    mkdir /hive/data/genomes/melInc2/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/melInc2/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzMelInc2.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m52.460s
    cat fb.melInc2.chainCaeRem4Link.txt
    # 4482338 bases of 82114761 (5.459%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melInc2 caeRem4) \
      > rbest.log 2>&1
    # real 0m28.855s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Necator americanus/N. americanus - necAme1
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzNecAme1.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzNecAme1.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs necAme1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzNecAme1.2015-08-13
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 25m59.341s
    cat fb.caeRem4.chainNecAme1Link.txt
    # 9831415 bases of 138406203 (7.103%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 necAme1) > rbest.log 2>&1 &
    # real 0m38.421s

    # and for the swap:
    mkdir /hive/data/genomes/necAme1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/necAme1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzNecAme1.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m20.780s
    cat fb.necAme1.chainCaeRem4Link.txt
    # 8904532 bases of 208187215 (4.277%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` necAme1 caeRem4) \
      > rbest.log 2>&1
    # real 0m56.713s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Onchocerca volvulus/O. volvulus - oncVol1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzOncVol1.2015-08-14
    cd /hive/data/genomes/caeRem4/bed/lastzOncVol1.2015-08-14

    cat << '_EOF_' > DEF
# caeRem4 vs oncVol1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/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 13m31.117s
    cat fb.caeRem4.chainOncVol1Link.txt
    # 5118944 bases of 138406203 (3.698%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 oncVol1) > rbest.log 2>&1 &
    # real 0m44.013s

    # and for the swap:
    mkdir /hive/data/genomes/oncVol1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/oncVol1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzOncVol1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m47.519s
    cat fb.oncVol1.chainCaeRem4Link.txt
    # 4333907 bases of 94327777 (4.595%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oncVol1 caeRem4) \
      > rbest.log 2>&1
    # real 0m43.563s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Panagrellus redivivus/Microworm - panRed1
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzPanRed1.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzPanRed1.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs panRed1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzPanRed1.2015-08-13
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 8m17.363s
    cat fb.caeRem4.chainPanRed1Link.txt
    # 7379417 bases of 138406203 (5.332%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 panRed1) > rbest.log 2>&1 &
    # real 0m30.637s

    # and for the swap:
    mkdir /hive/data/genomes/panRed1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/panRed1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzPanRed1.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m53.062s
    cat fb.panRed1.chainCaeRem4Link.txt
    # 6398620 bases of 62228262 (10.282%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` panRed1 caeRem4) \
      > rbest.log 2>&1
    # real 0m35.662s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Pristionchus exspectatus/P. exspectatus - priExs1
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzPriExs1.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzPriExs1.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs priExs1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzPriExs1.2015-08-13
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 17m9.606s
    cat fb.caeRem4.chainPriExs1Link.txt
    # 7044789 bases of 138406203 (5.090%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 priExs1) > rbest.log 2>&1 &
    # real 0m34.236s

    # and for the swap:
    mkdir /hive/data/genomes/priExs1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/priExs1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzPriExs1.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m7.466s
    cat fb.priExs1.chainCaeRem4Link.txt
    # 7256610 bases of 166917800 (4.347%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priExs1 caeRem4) \
      > rbest.log 2>&1
    # real 0m45.548s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Pristionchus pacificus/P. pacificus - priPac3
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzPriPac3.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzPriPac3.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs priPac3
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzPriPac3.2015-08-13
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 27m33.306s
    cat fb.caeRem4.chainPriPac3Link.txt
    # 7203683 bases of 138406203 (5.205%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 priPac3) > rbest.log 2>&1 &
    # real 0m37.228s

    # and for the swap:
    mkdir /hive/data/genomes/priPac3/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/priPac3/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzPriPac3.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m15.329s
    cat fb.priPac3.chainCaeRem4Link.txt
    # 7182416 bases of 153238914 (4.687%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priPac3 caeRem4) \
      > rbest.log 2>&1
    # real 0m51.330s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Strongyloides ratti/Threadworm - strRat2
# (DONE - 2015-08-13 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzStrRat2.2015-08-13
    cd /hive/data/genomes/caeRem4/bed/lastzStrRat2.2015-08-13

    cat << '_EOF_' > DEF
# caeRem4 vs strRat2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/bed/lastzStrRat2.2015-08-13
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 6m20.608s
    cat fb.caeRem4.chainStrRat2Link.txt
    # 5910072 bases of 138406203 (4.270%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 strRat2) > rbest.log 2>&1 &
    # real 0m32.856s

    # and for the swap:
    mkdir /hive/data/genomes/strRat2/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/strRat2/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzStrRat2.2015-08-13/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m46.709s
    cat fb.strRat2.chainCaeRem4Link.txt
    # 4841898 bases of 43150242 (11.221%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` strRat2 caeRem4) \
      > rbest.log 2>&1
    # real 0m31.690s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Trichinella spiralis/Trichinella - triSpi1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzTriSpi1.2015-08-14
    cd /hive/data/genomes/caeRem4/bed/lastzTriSpi1.2015-08-14

    cat << '_EOF_' > DEF
# caeRem4 vs triSpi1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/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 16m49.840s
    cat fb.caeRem4.chainTriSpi1Link.txt
    # 3047352 bases of 138406203 (2.202%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 triSpi1) > rbest.log 2>&1 &
    # real 0m25.404s

    # and for the swap:
    mkdir /hive/data/genomes/triSpi1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/triSpi1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzTriSpi1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m47.642s
    cat fb.triSpi1.chainCaeRem4Link.txt
    # 2773930 bases of 58558192 (4.737%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSpi1 caeRem4) \
      > rbest.log 2>&1
    # real 0m23.956s

########################################################################
########################################################################
# LASTZ Caenorhabditis remanei/C. remanei - caeRem4 vs.
#       Trichuris suis/Whipworm - triSui1
# (DONE - 2015-08-14 - Hiram)
    mkdir /hive/data/genomes/caeRem4/bed/lastzTriSui1.2015-08-14
    cd /hive/data/genomes/caeRem4/bed/lastzTriSui1.2015-08-14

    cat << '_EOF_' > DEF
# caeRem4 vs triSui1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Caenorhabditis remanei/C. remanei - caeRem4
SEQ1_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit
SEQ1_LEN=/hive/data/genomes/caeRem4/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/caeRem4/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 16m38.089s
    cat fb.caeRem4.chainTriSui1Link.txt
    # 3214561 bases of 138406203 (2.323%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` caeRem4 triSui1) > rbest.log 2>&1 &
    # real 0m22.937s

    # and for the swap:
    mkdir /hive/data/genomes/triSui1/bed/blastz.caeRem4.swap
    cd /hive/data/genomes/triSui1/bed/blastz.caeRem4.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/caeRem4/bed/lastzTriSui1.2015-08-14/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m47.853s
    cat fb.triSui1.chainCaeRem4Link.txt
    # 2864101 bases of 71825323 (3.988%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSui1 caeRem4) \
      > rbest.log 2>&1
    # real 0m22.120s

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