#########################################################################
# LASTZ Golden snub-nosed monkey/rhiRox1 - Tarsier TarSyr2 (DONE - 2015-02-23 - Hiram)
    mkdir /hive/data/genomes/rhiRox1/bed/lastzTarSyr2.2015-02-23
    cd /hive/data/genomes/rhiRox1/bed/lastzTarSyr2.2015-02-23

    cat << '_EOF_' > DEF
# Golden snub-nosed monkey vs tarsier
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/rhiRox1.tarSyr2/rhiRox1.tarSyr2.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=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/rhiRox1/bed/lastzTarSyr2.2015-02-23/rhiRox1.tarSyr2.tuning.Q.txt
#       A     C     G     T
# A   100  -173   -26  -121
# C  -173    96  -172   -26
# G   -26  -172    96  -173
# T  -121   -26  -173   100

# TARGET: Golden snub-nosed monkey rhiRox1
SEQ1_DIR=/hive/data/genomes/rhiRox1/rhiRox1.2bit
SEQ1_LEN=/hive/data/genomes/rhiRox1/chrom.sizes
SEQ1_CHUNK=40000000
SEQ1_LIMIT=500
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/rhiRox1/bed/lastzTarSyr2.2015-02-23
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    235m57.597s

    cat fb.rhiRox1.chainTarSyr2Link.txt 
    # 1614951617 bases of 2856044136 (56.545%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` rhiRox1 tarSyr2) \
       > rbest.log 2>&1 &
    # real    72m29.259s

    # and for the swap:
    mkdir /hive/data/genomes/tarSyr2/bed/blastz.rhiRox1.swap
    cd /hive/data/genomes/tarSyr2/bed/blastz.rhiRox1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/rhiRox1/bed/lastzTarSyr2.2015-02-23/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    372m37.027s

    cat fb.tarSyr2.chainRhiRox1Link.txt 
    # 1755301727 bases of 3405755564 (51.539%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` tarSyr2 rhiRox1) \
       > rbest.log 2>&1 &
    # real    148m53.108s

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