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# LASTZ dog/felCat8 cat/canFam3 - (DONE - 2014-12-11 - Hiram)
    mkdir /hive/data/genomes/canFam3/bed/lastzFelCat8.2014-12-11
    cd /hive/data/genomes/canFam3/bed/lastzFelCat8.2014-12-11

    cat << '_EOF_' > DEF
# dog vs cat
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/felCat8.canFam3/felCat8.canFam3.tuning.top400.txt

BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=50
BLASTZ_X=950
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/canFam3/bed/lastzFelCat8.2014-12-11/felCat8.canFam3.tuning.Q.txt
#       A     C     G     T
# A    95  -160   -43  -141
# C  -160   100  -121   -43
# G   -43  -121   100  -160
# T  -141   -43  -160    95

# TARGET: dog canFam3
SEQ1_DIR=/hive/data/genomes/canFam3/canFam3.2bit
SEQ1_LEN=/hive/data/genomes/canFam3/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LIMIT=80
SEQ1_LAP=0

# QUERY: cat felCat8
SEQ2_DIR=/hive/data/genomes/felCat8/felCat8.2bit
SEQ2_LEN=/hive/data/genomes/felCat8/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=500
SEQ2_LAP=0

BASE=/hive/data/genomes/canFam3/bed/lastzFelCat8.2014-12-11
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    446m41.291s

    cat fb.canFam3.chainFelCat8Link.txt 
    # 1670282681 bases of 2392715236 (69.807%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` canFam3 felCat8) > rbest.log 2>&1 &
    # real    45m20.309s

    # and for the swap:
    mkdir /hive/data/genomes/felCat8/bed/blastz.canFam3.swap
    cd /hive/data/genomes/felCat8/bed/blastz.canFam3.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/canFam3/bed/lastzFelCat8.2014-12-11/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    421m11.236s

    cat fb.felCat8.chainCanFam3Link.txt 
    # 1727969628 bases of 2599716822 (66.468%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` felCat8 canFam3) > rbest.log 2>&1
    # real    125m28.602s

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