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# LASTZ prarie vole/micOch1 vs. Chinese hamster - (DONE - 2014-05-18 - Hiram)
    mkdir /hive/data/genomes/micOch1/bed/lastzCriGri1.2014-05-18
    cd /hive/data/genomes/micOch1/bed/lastzCriGri1.2014-05-18

    printf '# Praire vole vs. Chinese hamster
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/micOch1.criGri1/micOch1.criGri1.tuning.top400.txt

BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.52/bin/lastz
BLASTZ_M=50
BLASTZ_O=400
BLASTZ_E=30

BLASTZ_T=2
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_K=3000
BLASTZ_L=3000
BLASTZ_Q=/hive/data/genomes/micOch1/bed/lastzCriGri1.2014-05-27/micOch1.criGri1.tuning.Q.txt
#       A     C     G     T
# A   100  -177   -63  -166
# C  -177    95  -183   -63
# G   -63  -183    95  -177
# T  -166   -63  -177   100

# TARGET: Praire vole micOch1
SEQ1_DIR=/hive/data/genomes/micOch1/micOch1.wmTrf.2bit
SEQ1_LEN=/hive/data/genomes/micOch1/chrom.sizes
SEQ1_CHUNK=10000000
SEQ1_LAP=10000
SEQ1_LIMIT=200

# QUERY: Chinese hamster criGri1
SEQ2_DIR=/hive/data/genomes/criGri1/criGri1.wmTrf.2bit
SEQ2_LEN=/hive/data/genomes/criGri1/chrom.sizes
SEQ2_CHUNK=5000000
SEQ2_LAP=0
SEQ2_LIMIT=600

BASE=/hive/data/genomes/micOch1/bed/lastzCriGri1.2014-05-27
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl \
      -verbose=2 `pwd`/DEF \
         -chainMinScore=5000 -chainLinearGap=medium \
            -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
             -syntenicNet) > do.log 2>&1
    # real    415m37.964s

    cat fb.micOch1.chainCriGri1Link.txt
    #  1589566722 bases of 2104321675 (75.538%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` micOch1 criGri1) \
          > rbest.log 2>&1 &
    #  real    68m5.404s

    # and for the swap:
    mkdir /hive/data/genomes/criGri1/bed/blastz.micOch1.swap
    cd /hive/data/genomes/criGri1/bed/blastz.micOch1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/micOch1/bed/lastzCriGri1.2014-05-27/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #	real    140m58.824s

    cat fb.criGri1.chainMicOch1Link.txt
    # 1624868863 bases of 2301325917 (70.606%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` criGri1 micOch1) \
       > rbest.log 2>&1
    # real    392m21.459s

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