########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Ancylostoma ceylanicum/A. ceylanicum - ancCey1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzAncCey1.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzAncCey1.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs ancCey1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Ancylostoma ceylanicum/A. ceylanicum - ancCey1
SEQ2_DIR=/hive/data/genomes/ancCey1/ancCey1.2bit
SEQ2_LEN=/hive/data/genomes/ancCey1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzAncCey1.2015-08-16
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 4m12.356s
    cat fb.strRat2.chainAncCey1Link.txt
    # 2993561 bases of 43150242 (6.938%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 ancCey1) > rbest.log 2>&1 &
    # real 0m24.513s

    # and for the swap:
    mkdir /hive/data/genomes/ancCey1/bed/blastz.strRat2.swap
    cd /hive/data/genomes/ancCey1/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzAncCey1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m50.699s
    cat fb.ancCey1.chainStrRat2Link.txt
    # 3660266 bases of 300914990 (1.216%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ancCey1 strRat2) \
      > rbest.log 2>&1
    # real 0m33.752s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Ascaris suum/Pig roundworm - ascSuu1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzAscSuu1.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzAscSuu1.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs ascSuu1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Ascaris suum/Pig roundworm - ascSuu1
SEQ2_DIR=/hive/data/genomes/ascSuu1/ascSuu1.2bit
SEQ2_LEN=/hive/data/genomes/ascSuu1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzAscSuu1.2015-08-16
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 3m15.889s
    cat fb.strRat2.chainAscSuu1Link.txt
    # 3147688 bases of 43150242 (7.295%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 ascSuu1) > rbest.log 2>&1 &
    # real 0m25.739s

    # and for the swap:
    mkdir /hive/data/genomes/ascSuu1/bed/blastz.strRat2.swap
    cd /hive/data/genomes/ascSuu1/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzAscSuu1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m56.744s
    cat fb.ascSuu1.chainStrRat2Link.txt
    # 3490561 bases of 262604320 (1.329%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ascSuu1 strRat2) \
      > rbest.log 2>&1
    # real 0m37.372s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Brugia malayi/Filarial worm - bruMal2
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzBruMal2.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzBruMal2.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs bruMal2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Brugia malayi/Filarial worm - bruMal2
SEQ2_DIR=/hive/data/genomes/bruMal2/bruMal2.2bit
SEQ2_LEN=/hive/data/genomes/bruMal2/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzBruMal2.2015-08-16
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 3m2.192s
    cat fb.strRat2.chainBruMal2Link.txt
    # 4175213 bases of 43150242 (9.676%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 bruMal2) > rbest.log 2>&1 &
    # real 0m26.831s

    # and for the swap:
    mkdir /hive/data/genomes/bruMal2/bed/blastz.strRat2.swap
    cd /hive/data/genomes/bruMal2/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzBruMal2.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m25.933s
    cat fb.bruMal2.chainStrRat2Link.txt
    # 4174239 bases of 87424120 (4.775%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bruMal2 strRat2) \
      > rbest.log 2>&1
    # real 0m34.642s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Bursaphelenchus xylophilus/Pine wood nematode - burXyl1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzBurXyl1.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzBurXyl1.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs burXyl1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Bursaphelenchus xylophilus/Pine wood nematode - burXyl1
SEQ2_DIR=/hive/data/genomes/burXyl1/burXyl1.2bit
SEQ2_LEN=/hive/data/genomes/burXyl1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzBurXyl1.2015-08-16
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 3m0.488s
    cat fb.strRat2.chainBurXyl1Link.txt
    # 4615585 bases of 43150242 (10.697%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 burXyl1) > rbest.log 2>&1 &
    # real 0m26.920s

    # and for the swap:
    mkdir /hive/data/genomes/burXyl1/bed/blastz.strRat2.swap
    cd /hive/data/genomes/burXyl1/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzBurXyl1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m50.432s
    cat fb.burXyl1.chainStrRat2Link.txt
    # 4710613 bases of 73100506 (6.444%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` burXyl1 strRat2) \
      > rbest.log 2>&1
    # real 0m34.233s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Dirofilaria immitis/Dog heartworm - dirImm1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzDirImm1.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzDirImm1.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs dirImm1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Dirofilaria immitis/Dog heartworm - dirImm1
SEQ2_DIR=/hive/data/genomes/dirImm1/dirImm1.2bit
SEQ2_LEN=/hive/data/genomes/dirImm1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzDirImm1.2015-08-16
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 3m0.960s
    cat fb.strRat2.chainDirImm1Link.txt
    # 3937991 bases of 43150242 (9.126%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 dirImm1) > rbest.log 2>&1 &
    # real 0m25.286s

    # and for the swap:
    mkdir /hive/data/genomes/dirImm1/bed/blastz.strRat2.swap
    cd /hive/data/genomes/dirImm1/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzDirImm1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m1.174s
    cat fb.dirImm1.chainStrRat2Link.txt
    # 3935087 bases of 84923352 (4.634%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` dirImm1 strRat2) \
      > rbest.log 2>&1
    # real 0m38.462s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Haemonchus contortus/Barber pole worm - haeCon2
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzHaeCon2.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzHaeCon2.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs haeCon2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# 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=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzHaeCon2.2015-08-16
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 3m24.504s
    cat fb.strRat2.chainHaeCon2Link.txt
    # 2969153 bases of 43150242 (6.881%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 haeCon2) > rbest.log 2>&1 &
    # real 0m23.929s

    # and for the swap:
    mkdir /hive/data/genomes/haeCon2/bed/blastz.strRat2.swap
    cd /hive/data/genomes/haeCon2/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzHaeCon2.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m20.610s
    cat fb.haeCon2.chainStrRat2Link.txt
    # 4244128 bases of 346001353 (1.227%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` haeCon2 strRat2) \
      > rbest.log 2>&1
    # real 0m49.338s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Loa loa/Eye worm - loaLoa1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzLoaLoa1.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzLoaLoa1.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs loaLoa1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Loa loa/Eye worm - loaLoa1
SEQ2_DIR=/hive/data/genomes/loaLoa1/loaLoa1.2bit
SEQ2_LEN=/hive/data/genomes/loaLoa1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzLoaLoa1.2015-08-16
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 2m57.260s
    cat fb.strRat2.chainLoaLoa1Link.txt
    # 3782357 bases of 43150242 (8.766%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 loaLoa1) > rbest.log 2>&1 &
    # real 0m25.898s

    # and for the swap:
    mkdir /hive/data/genomes/loaLoa1/bed/blastz.strRat2.swap
    cd /hive/data/genomes/loaLoa1/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzLoaLoa1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m50.535s
    cat fb.loaLoa1.chainStrRat2Link.txt
    # 3615143 bases of 87533141 (4.130%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` loaLoa1 strRat2) \
      > rbest.log 2>&1
    # real 0m31.850s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Meloidogyne hapla/M. hapla - melHap1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzMelHap1.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzMelHap1.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs melHap1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Meloidogyne hapla/M. hapla - melHap1
SEQ2_DIR=/hive/data/genomes/melHap1/melHap1.2bit
SEQ2_LEN=/hive/data/genomes/melHap1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzMelHap1.2015-08-16
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 2m57.702s
    cat fb.strRat2.chainMelHap1Link.txt
    # 5520378 bases of 43150242 (12.793%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 melHap1) > rbest.log 2>&1 &
    # real 0m26.555s

    # and for the swap:
    mkdir /hive/data/genomes/melHap1/bed/blastz.strRat2.swap
    cd /hive/data/genomes/melHap1/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzMelHap1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m56.236s
    cat fb.melHap1.chainStrRat2Link.txt
    # 5246956 bases of 53017507 (9.897%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melHap1 strRat2) \
      > rbest.log 2>&1
    # real 0m34.342s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Meloidogyne incognita/M. incognita - melInc2
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzMelInc2.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzMelInc2.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs melInc2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Meloidogyne incognita/M. incognita - melInc2
SEQ2_DIR=/hive/data/genomes/melInc2/melInc2.2bit
SEQ2_LEN=/hive/data/genomes/melInc2/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzMelInc2.2015-08-16
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 2m27.195s
    cat fb.strRat2.chainMelInc2Link.txt
    # 3639872 bases of 43150242 (8.435%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 melInc2) > rbest.log 2>&1 &
    # real 0m23.589s

    # and for the swap:
    mkdir /hive/data/genomes/melInc2/bed/blastz.strRat2.swap
    cd /hive/data/genomes/melInc2/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzMelInc2.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m56.416s
    cat fb.melInc2.chainStrRat2Link.txt
    # 4936952 bases of 82114761 (6.012%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melInc2 strRat2) \
      > rbest.log 2>&1
    # real 0m34.500s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Necator americanus/N. americanus - necAme1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzNecAme1.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzNecAme1.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs necAme1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Necator americanus/N. americanus - necAme1
SEQ2_DIR=/hive/data/genomes/necAme1/necAme1.2bit
SEQ2_LEN=/hive/data/genomes/necAme1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzNecAme1.2015-08-16
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 3m13.818s
    cat fb.strRat2.chainNecAme1Link.txt
    # 3059487 bases of 43150242 (7.090%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 necAme1) > rbest.log 2>&1 &
    # real 0m25.146s

    # and for the swap:
    mkdir /hive/data/genomes/necAme1/bed/blastz.strRat2.swap
    cd /hive/data/genomes/necAme1/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzNecAme1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m58.876s
    cat fb.necAme1.chainStrRat2Link.txt
    # 3351287 bases of 208187215 (1.610%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` necAme1 strRat2) \
      > rbest.log 2>&1
    # real 0m37.128s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Onchocerca volvulus/O. volvulus - oncVol1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzOncVol1.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzOncVol1.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs oncVol1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Onchocerca volvulus/O. volvulus - oncVol1
SEQ2_DIR=/hive/data/genomes/oncVol1/oncVol1.2bit
SEQ2_LEN=/hive/data/genomes/oncVol1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzOncVol1.2015-08-16
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 3m1.911s
    cat fb.strRat2.chainOncVol1Link.txt
    # 4337430 bases of 43150242 (10.052%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 oncVol1) > rbest.log 2>&1 &
    # real 0m37.848s

    # and for the swap:
    mkdir /hive/data/genomes/oncVol1/bed/blastz.strRat2.swap
    cd /hive/data/genomes/oncVol1/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzOncVol1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m47.675s
    cat fb.oncVol1.chainStrRat2Link.txt
    # 4183657 bases of 94327777 (4.435%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oncVol1 strRat2) \
      > rbest.log 2>&1
    # real 0m41.733s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Panagrellus redivivus/Microworm - panRed1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzPanRed1.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzPanRed1.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs panRed1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Panagrellus redivivus/Microworm - panRed1
SEQ2_DIR=/hive/data/genomes/panRed1/panRed1.2bit
SEQ2_LEN=/hive/data/genomes/panRed1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzPanRed1.2015-08-16
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 5m47.770s
    cat fb.strRat2.chainPanRed1Link.txt
    # 4723823 bases of 43150242 (10.947%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 panRed1) > rbest.log 2>&1 &
    # real 0m27.682s

    # and for the swap:
    mkdir /hive/data/genomes/panRed1/bed/blastz.strRat2.swap
    cd /hive/data/genomes/panRed1/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzPanRed1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 1m31.730s
    cat fb.panRed1.chainStrRat2Link.txt
    # 4944725 bases of 62228262 (7.946%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` panRed1 strRat2) \
      > rbest.log 2>&1
    # real 3m26.454s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Pristionchus exspectatus/P. exspectatus - priExs1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzPriExs1.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzPriExs1.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs priExs1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Pristionchus exspectatus/P. exspectatus - priExs1
SEQ2_DIR=/hive/data/genomes/priExs1/priExs1.2bit
SEQ2_LEN=/hive/data/genomes/priExs1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzPriExs1.2015-08-16
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 3m0.692s
    cat fb.strRat2.chainPriExs1Link.txt
    # 2098934 bases of 43150242 (4.864%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 priExs1) > rbest.log 2>&1 &
    # real 0m20.272s

    # and for the swap:
    mkdir /hive/data/genomes/priExs1/bed/blastz.strRat2.swap
    cd /hive/data/genomes/priExs1/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzPriExs1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m47.411s
    cat fb.priExs1.chainStrRat2Link.txt
    # 2426876 bases of 166917800 (1.454%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priExs1 strRat2) \
      > rbest.log 2>&1
    # real 0m27.678s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Pristionchus pacificus/P. pacificus - priPac3
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzPriPac3.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzPriPac3.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs priPac3
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Pristionchus pacificus/P. pacificus - priPac3
SEQ2_DIR=/hive/data/genomes/priPac3/priPac3.2bit
SEQ2_LEN=/hive/data/genomes/priPac3/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzPriPac3.2015-08-16
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 3m38.907s
    cat fb.strRat2.chainPriPac3Link.txt
    # 2091531 bases of 43150242 (4.847%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 priPac3) > rbest.log 2>&1 &
    # real 0m21.386s

    # and for the swap:
    mkdir /hive/data/genomes/priPac3/bed/blastz.strRat2.swap
    cd /hive/data/genomes/priPac3/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzPriPac3.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m52.542s
    cat fb.priPac3.chainStrRat2Link.txt
    # 2391493 bases of 153238914 (1.561%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priPac3 strRat2) \
      > rbest.log 2>&1
    # real 0m28.782s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Trichinella spiralis/Trichinella - triSpi1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzTriSpi1.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzTriSpi1.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs triSpi1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Trichinella spiralis/Trichinella - triSpi1
SEQ2_DIR=/hive/data/genomes/triSpi1/triSpi1.2bit
SEQ2_LEN=/hive/data/genomes/triSpi1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzTriSpi1.2015-08-16
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 2m23.938s
    cat fb.strRat2.chainTriSpi1Link.txt
    # 2379633 bases of 43150242 (5.515%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 triSpi1) > rbest.log 2>&1 &
    # real 0m21.912s

    # and for the swap:
    mkdir /hive/data/genomes/triSpi1/bed/blastz.strRat2.swap
    cd /hive/data/genomes/triSpi1/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzTriSpi1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m45.395s
    cat fb.triSpi1.chainStrRat2Link.txt
    # 2532808 bases of 58558192 (4.325%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSpi1 strRat2) \
      > rbest.log 2>&1
    # real 0m23.597s

########################################################################
########################################################################
# LASTZ Strongyloides ratti/Threadworm - strRat2 vs.
#       Trichuris suis/Whipworm - triSui1
# (DONE - 2015-08-16 - Hiram)
    mkdir /hive/data/genomes/strRat2/bed/lastzTriSui1.2015-08-16
    cd /hive/data/genomes/strRat2/bed/lastzTriSui1.2015-08-16

    cat << '_EOF_' > DEF
# strRat2 vs triSui1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Strongyloides ratti/Threadworm - strRat2
SEQ1_DIR=/hive/data/genomes/strRat2/strRat2.2bit
SEQ1_LEN=/hive/data/genomes/strRat2/chrom.sizes
SEQ1_CHUNK=4000000
SEQ1_LAP=10000
SEQ1_LIMIT=100

# QUERY: Trichuris suis/Whipworm - triSui1
SEQ2_DIR=/hive/data/genomes/triSui1/triSui1.2bit
SEQ2_LEN=/hive/data/genomes/triSui1/chrom.sizes
SEQ2_CHUNK=4000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/strRat2/bed/lastzTriSui1.2015-08-16
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 -workhorse=hgwdev \
      -bigClusterHub=ku -smallClusterHub=ku -syntenicNet) > do.log 2>&1
    # real 3m20.565s
    cat fb.strRat2.chainTriSui1Link.txt
    # 2064924 bases of 43150242 (4.785%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` strRat2 triSui1) > rbest.log 2>&1 &
    # real 0m18.418s

    # and for the swap:
    mkdir /hive/data/genomes/triSui1/bed/blastz.strRat2.swap
    cd /hive/data/genomes/triSui1/bed/blastz.strRat2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/strRat2/bed/lastzTriSui1.2015-08-16/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m41.770s
    cat fb.triSui1.chainStrRat2Link.txt
    # 2121799 bases of 71825323 (2.954%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSui1 strRat2) \
      > rbest.log 2>&1
    # real 0m22.335s

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