#########################################################################
# LASTZ rat/regenRn1 vs rabbit/oryCun2 - (DONE - 2019-10-11 - Hiram)
    mkdir /hive/data/genomes/regenRn1/bed/lastzOryCun2.2019-10-11
    cd /hive/data/genomes/regenRn1/bed/lastzOryCun2.2019-10-11

    printf '# Rat vs. rabbit
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz

# TARGET: Rat Rn6
SEQ1_DIR=/hive/data/genomes/regenRn1/regenRn1.2bit
SEQ1_LEN=/hive/data/genomes/regenRn1/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=15

# QUERY: rabbit oryCun2
SEQ2_DIR=/hive/data/genomes/oryCun2/oryCun2.2bit
SEQ2_LEN=/hive/data/genomes/oryCun2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=20

BASE=/hive/data/genomes/regenRn1/bed/lastzOryCun2.2019-10-11
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku -noDbNameCheck \
        -smallClusterHub=hgwdev -chainMinScore=3000 -chainLinearGap=medium \
	-syntenicNet) > do.log 2>&1
    # real    184m23.050s

    cat fb.regenRn1.chainOryCun2Link.txt
    # 586652448 bases of 2282482188 (25.702%) in intersection

    cat fb.regenRn1.chainSynOryCun2Link.txt
    # 539247828 bases of 2282482188 (23.625%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` regenRn1 oryCun2) > rbest.log 2>&1 &
    # real    268m49.478s

    cat fb.regenRn1.chainRBest.OryCun2.txt
    # 558355463 bases of 2282482188 (24.463%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/oryCun2/bed/blastz.regenRn1.swap
    cd /hive/data/genomes/oryCun2/bed/blastz.regenRn1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/regenRn1/bed/lastzOryCun2.2019-10-11/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    34m44.321s

    cat fb.oryCun2.chainRegenRn1Link.txt
    # 594376030 bases of 2604023284 (22.825%) in intersection
    cat fb.oryCun2.chainSynRegenRn1Link.txt
    # 537850488 bases of 2604023284 (20.655%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` oryCun2 regenRn1) > rbest.log 2>&1
    # real    287m55.750s

    cat fb.oryCun2.chainRBest.RegenRn1.txt
    # 557937174 bases of 2604023284 (21.426%) in intersection

#########################################################################
# LASTZ rat/regenRn1 vs pig/susScr11 - (DONE - 2019-10-14 - Hiram)
    mkdir /hive/data/genomes/regenRn1/bed/lastzSusScr11.2019-10-14
    cd /hive/data/genomes/regenRn1/bed/lastzSusScr11.2019-10-14

    printf '# Rat vs. pig
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz

# TARGET: Rat Rn6
SEQ1_DIR=/hive/data/genomes/regenRn1/regenRn1.2bit
SEQ1_LEN=/hive/data/genomes/regenRn1/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=5

# QUERY: pig susScr11
SEQ2_DIR=/hive/data/genomes/susScr11/susScr11.2bit
SEQ2_LEN=/hive/data/genomes/susScr11/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=5

BASE=/hive/data/genomes/regenRn1/bed/lastzSusScr11.2019-10-14
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku -noDbNameCheck \
        -smallClusterHub=hgwdev -chainMinScore=3000 -chainLinearGap=medium \
	-syntenicNet) > do.log 2>&1
    # real    226m34.300s

    cat fb.regenRn1.chainSusScr11Link.txt
    # 642554959 bases of 2282482188 (28.152%) in intersection

    cat fb.regenRn1.chainSynSusScr11Link.txt
    # 606015870 bases of 2282482188 (26.551%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` regenRn1 susScr11) > rbest.log 2>&1 &
    # real    224m31.973s

    cat fb.regenRn1.chainRBest.SusScr11.txt
    # 614448249 bases of 2282482188 (26.920%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/susScr11/bed/blastz.regenRn1.swap
    cd /hive/data/genomes/susScr11/bed/blastz.regenRn1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/regenRn1/bed/lastzSusScr11.2019-10-14/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    43m19.318s

    cat fb.susScr11.chainRegenRn1Link.txt
    # 635932961 bases of 2472073034 (25.725%) in intersection
    cat fb.susScr11.chainSynRegenRn1Link.txt
    # 605094540 bases of 2472073034 (24.477%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` susScr11 regenRn1) > rbest.log 2>&1
   # real    195m27.050s

   cat fb.susScr11.chainRBest.RegenRn1.txt
   # 613864682 bases of 2472073034 (24.832%) in intersection

########################################################################
 LASTZ rat/regenRn1 vs dog/canFam3 - (DONE - 2019-10-14 - Hiram)
   mkdir /hive/data/genomes/regenRn1/bed/lastzCanFam3.2019-10-14
   cd /hive/data/genomes/regenRn1/bed/lastzCanFam3.2019-10-14

   printf '# Rat vs. dog
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz

# TARGET: Rat Rn6
SEQ1_DIR=/hive/data/genomes/regenRn1/regenRn1.2bit
SEQ1_LEN=/hive/data/genomes/regenRn1/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=5

# QUERY: dog canFam3
SEQ2_DIR=/hive/data/genomes/canFam3/canFam3.2bit
SEQ2_LEN=/hive/data/genomes/canFam3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=25

BASE=/hive/data/genomes/regenRn1/bed/lastzCanFam3.2019-10-14
TMPDIR=/dev/shm
' > DEF

   time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
       -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku -noDbNameCheck \
       -smallClusterHub=hgwdev -chainMinScore=3000 -chainLinearGap=medium \
       -syntenicNet) > do.log 2>&1
   # real    219m7.084s

   cat fb.regenRn1.chainCanFam3Link.txt
   # 678205600 bases of 2282482188 (29.714%) in intersection

   cat fb.regenRn1.chainSynCanFam3Link.txt
   # 644550064 bases of 2282482188 (28.239%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` regenRn1 canFam3) > rbest.log 2>&1 &
    # real    186m51.804s

    cat fb.regenRn1.chainRBest.CanFam3.txt
    # 651971618 bases of 2282482188 (28.564%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/canFam3/bed/blastz.regenRn1.swap
    cd /hive/data/genomes/canFam3/bed/blastz.regenRn1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/regenRn1/bed/lastzCanFam3.2019-10-14/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    39m44.272s

    cat fb.canFam3.chainRegenRn1Link.txt
    # 672809905 bases of 2392715236 (28.119%) in intersection
    cat fb.canFam3.chainSynRegenRn1Link.txt
    # 642327040 bases of 2392715236 (26.845%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` canFam3 regenRn1) > rbest.log 2>&1
    # real    162m51.212s

    cat fb.canFam3.chainRBest.RegenRn1.txt
    # 651196229 bases of 2392715236 (27.216%) in intersection

#########################################################################
 LASTZ rat/regenRn1 vs crab-eating macaque/macFas5 - (DONE - 2019-10-14 - Hiram)
   mkdir /hive/data/genomes/regenRn1/bed/lastzMacFas5.2019-10-14
   cd /hive/data/genomes/regenRn1/bed/lastzMacFas5.2019-10-14

   printf '# Rat vs. crab-eating macaque
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz

# TARGET: Rat Rn6
SEQ1_DIR=/hive/data/genomes/regenRn1/regenRn1.2bit
SEQ1_LEN=/hive/data/genomes/regenRn1/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=5

# QUERY: crab-eating macaque macFas5
SEQ2_DIR=/hive/data/genomes/macFas5/macFas5.2bit
SEQ2_LEN=/hive/data/genomes/macFas5/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=25

BASE=/hive/data/genomes/regenRn1/bed/lastzMacFas3.2019-10-14
TMPDIR=/dev/shm
' > DEF

# note mistake in BASE directory name, changed directory name after
# the run was complete, and the DEF file was altered to MacFas5
# and the symlinks fixed in htdocs-hgdownload

   time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
       -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku -noDbNameCheck \
       -smallClusterHub=hgwdev -chainMinScore=3000 -chainLinearGap=medium \
       -syntenicNet) > do.log 2>&1
   # real    256m56.897s

   cat fb.regenRn1.chainMacFas5Link.txt
   # 815551694 bases of 2282482188 (35.731%) in intersection

   cat fb.regenRn1.chainSynMacFas5Link.txt
   # 774681241 bases of 2282482188 (33.940%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` regenRn1 macFas5) > rbest.log 2>&1 &
    # real    282m53.369s

    cat fb.regenRn1.chainRBest.MacFas5.txt
    # 782563616 bases of 2282482188 (34.286%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/macFas5/bed/blastz.regenRn1.swap
    cd /hive/data/genomes/macFas5/bed/blastz.regenRn1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/regenRn1/bed/lastzMacFas5.2019-10-14/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    55m38.846s

    cat fb.macFas5.chainRegenRn1Link.txt
    # 811540597 bases of 2803866698 (28.944%) in intersection
    cat fb.macFas5.chainSynRegenRn1Link.txt
    # 771643309 bases of 2803866698 (27.521%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` macFas5 regenRn1) > rbest.log 2>&1
    # real    271m41.030s

    cat fb.macFas5.chainRBest.RegenRn1.txt
    # 781449190 bases of 2803866698 (27.870%) in intersection

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