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# LASTZ Brugia malayi/Filarial worm - bruMal2 vs.
#       Trichinella spiralis/Trichinella - triSpi1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/bruMal2/bed/lastzTriSpi1.2015-08-17
    cd /hive/data/genomes/bruMal2/bed/lastzTriSpi1.2015-08-17

    cat << '_EOF_' > DEF
# bruMal2 vs triSpi1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Brugia malayi/Filarial worm - bruMal2
SEQ1_DIR=/hive/data/genomes/bruMal2/bruMal2.2bit
SEQ1_LEN=/hive/data/genomes/bruMal2/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/bruMal2/bed/lastzTriSpi1.2015-08-17
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 3m42.746s
    cat fb.bruMal2.chainTriSpi1Link.txt
    # 2897180 bases of 87424120 (3.314%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` bruMal2 triSpi1) > rbest.log 2>&1 &
    # real 0m24.703s

    # and for the swap:
    mkdir /hive/data/genomes/triSpi1/bed/blastz.bruMal2.swap
    cd /hive/data/genomes/triSpi1/bed/blastz.bruMal2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/bruMal2/bed/lastzTriSpi1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m47.155s
    cat fb.triSpi1.chainBruMal2Link.txt
    # 3015360 bases of 58558192 (5.149%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSpi1 bruMal2) \
      > rbest.log 2>&1
    # real 0m24.485s

########################################################################
########################################################################
# LASTZ Brugia malayi/Filarial worm - bruMal2 vs.
#       Trichuris suis/Whipworm - triSui1
# (DONE - 2015-08-17 - Hiram)
    mkdir /hive/data/genomes/bruMal2/bed/lastzTriSui1.2015-08-17
    cd /hive/data/genomes/bruMal2/bed/lastzTriSui1.2015-08-17

    cat << '_EOF_' > DEF
# bruMal2 vs triSui1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_H=2000
BLASTZ_M=50

# TARGET:Brugia malayi/Filarial worm - bruMal2
SEQ1_DIR=/hive/data/genomes/bruMal2/bruMal2.2bit
SEQ1_LEN=/hive/data/genomes/bruMal2/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/bruMal2/bed/lastzTriSui1.2015-08-17
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 4m48.258s
    cat fb.bruMal2.chainTriSui1Link.txt
    # 2399958 bases of 87424120 (2.745%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` bruMal2 triSui1) > rbest.log 2>&1 &
    # real 0m21.478s

    # and for the swap:
    mkdir /hive/data/genomes/triSui1/bed/blastz.bruMal2.swap
    cd /hive/data/genomes/triSui1/bed/blastz.bruMal2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/bruMal2/bed/lastzTriSui1.2015-08-17/DEF \
        -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real 0m42.179s
    cat fb.triSui1.chainBruMal2Link.txt
    # 2314529 bases of 71825323 (3.222%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSui1 bruMal2) \
      > rbest.log 2>&1
    # real 0m21.462s

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