#########################################################################
# LASTZ killer whale/orcOrc1 vs. sheep/oviAri3 - (DONE - 2016-06-03 - Hiram)
    mkdir /hive/data/genomes/orcOrc1/bed/lastzOviAri3.2016-06-03
    cd /hive/data/genomes/orcOrc1/bed/lastzOviAri3.2016-06-03

    printf '# Killer whale vs. Sheep
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254

# the default matrix is:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: Killer whale orcOrc1
SEQ1_DIR=/hive/data/genomes/orcOrc1/orcOrc1.2bit
SEQ1_LEN=/hive/data/genomes/orcOrc1/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=50

# QUERY: Sheep oviAri3
SEQ2_DIR=/hive/data/genomes/oviAri3/oviAri3.wmTrf.2bit
SEQ2_LEN=/hive/data/genomes/oviAri3/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LIMIT=80
SEQ2_LAP=0

BASE=/hive/data/genomes/orcOrc1/bed/lastzOviAri3.2016-06-03
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    284m1.002s

    cat fb.orcOrc1.chainOviAri3Link.txt
    # 1647057996 bases of 2249582125 (73.216%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` orcOrc1 oviAri3) \
        > rbest.log 2>&1 &
    # real    796m36.497s

    # and for the swap:
    mkdir /hive/data/genomes/oviAri3/bed/blastz.orcOrc1.swap
    cd /hive/data/genomes/oviAri3/bed/blastz.orcOrc1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/orcOrc1/bed/lastzOviAri3.2016-06-03/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    268m11.052s

    cat fb.oviAri3.chainOrcOrc1Link.txt
    # 1668855009 bases of 2534335866 (65.850%) in intersection


    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oviAri3 orcOrc1) \
      > rbest.log 2>&1
    # real    908m54.965s

#########################################################################
# LASTZ killer whale/orcOrc1 vs. sheep/turTru2 - (DONE - 2016-06-03 - Hiram)
    mkdir /hive/data/genomes/orcOrc1/bed/lastzTurTru2.2016-06-03
    cd /hive/data/genomes/orcOrc1/bed/lastzTurTru2.2016-06-03

    printf '# Killer whale vs. Dolphin
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254

# the default matrix is:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: Killer whale orcOrc1
SEQ1_DIR=/hive/data/genomes/orcOrc1/orcOrc1.2bit
SEQ1_LEN=/hive/data/genomes/orcOrc1/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=200

# QUERY: Dolphin turTru2
SEQ2_DIR=/hive/data/genomes/turTru2/turTru2.2bit
SEQ2_LEN=/hive/data/genomes/turTru2/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LIMIT=600
SEQ2_LAP=0

BASE=/hive/data/genomes/orcOrc1/bed/lastzTurTru2.2016-06-03
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1109m43.604s

    cat fb.orcOrc1.chainTurTru2Link.txt
    # 2116631228 bases of 2249582125 (94.090%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` orcOrc1 turTru2) \
      > rbest.log 2>&1 &
    # real    103m20.994s

    # and for the swap:
    mkdir /hive/data/genomes/turTru2/bed/blastz.orcOrc1.swap
    cd /hive/data/genomes/turTru2/bed/blastz.orcOrc1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/orcOrc1/bed/lastzTurTru2.2016-06-03/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    857m47.170s

    cat fb.turTru2.chainOrcOrc1Link.txt
    # 2148433509 bases of 2332402443 (92.112%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` turTru2 orcOrc1) \
      > rbest.log 2>&1
    # real    202m56.678s

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