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# LASTZ Mouse lemur/micMur2 - Tarsier TarSyr2 (DONE - 2015-05-29 - Hiram)
    mkdir /hive/data/genomes/micMur2/bed/lastzTarSyr2.2015-05-29
    cd /hive/data/genomes/micMur2/bed/lastzTarSyr2.2015-05-29

    cp -p /hive/users/hiram/multiz/100way/micMur1.tarSyr2/micMur1.tarSyr2.tuning.top400.txt \
      ./micMur1.tarSyr2.tuning.Q.txt

    cat << '_EOF_' > DEF
# Mouse lemur vs tarsier
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/micMur1.tarSyr2/micMur1.tarSyr2.tuning.top400.txt
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz

BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=50
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/micMur2/bed/lastzTarSyr2.2015-05-29/micMur1.tarSyr2.tuning.Q.txt
#       A     C     G     T
# A   100  -170   -29  -137
# C  -170    97  -194   -29
# G   -29  -194    97  -170
# T  -137   -29  -170   100

# TARGET: Mouse lemur micMur2
SEQ1_DIR=/hive/data/genomes/micMur2/micMur2.2bit
SEQ1_LEN=/hive/data/genomes/micMur2/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LIMIT=200
SEQ1_LAP=10000

# QUERY: Tarsier tarSyr2
SEQ2_DIR=/hive/data/genomes/tarSyr2/tarSyr2.2bit
SEQ2_LEN=/hive/data/genomes/tarSyr2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=1000
SEQ2_LAP=0

BASE=/hive/data/genomes/micMur2/bed/lastzTarSyr2.2015-05-29
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
    # broken cluster run completed, then continuing:
    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -continue=cat -workhorse=hgwdev -smallClusterHub=ku \
           -bigClusterHub=ku -syntenicNet) > cat.log 2>&1
    # real    127m41.210s

    cat fb.micMur2.chainTarSyr2Link.txt
    # 1517068571 bases of 2377775715 (63.802%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` micMur2 tarSyr2) > rbest.log 2>&1 &
    # real    35m35.833s

    # and for the swap:
    mkdir /hive/data/genomes/tarSyr2/bed/blastz.micMur2.swap
    cd /hive/data/genomes/tarSyr2/bed/blastz.micMur2.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/micMur2/bed/lastzTarSyr2.2015-05-29/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    314m3.377s

    cat fb.tarSyr2.chainMicMur2Link.txt
    # 1628005062 bases of 3405755564 (47.802%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` tarSyr2 micMur2) > rbest.log 2>&1
    # real    82m56.253s

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