##############################################################################
# SWAP from chimp/rheMac8 Lastz run (DONE - 2016-08-27 - Hiram)

    # primary alignment
    cd /hive/data/genomes/rheMac8/bed/lastzChlSab2.2016-08-27

    cat fb.rheMac8.chainChlSab2Link.txt
    # 2674926475 bases of 3142093174 (85.132%) in intersection

    # running the swap
    mkdir /hive/data/genomes/chlSab2/bed/blastz.rheMac8.swap
    cd /hive/data/genomes/chlSab2/bed/blastz.rheMac8.swap
    time (doBlastzChainNet.pl -verbose=2 \
        -swap /hive/data/genomes/rheMac8/bed/lastzChlSab2.2016-08-27/DEF \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > swap.log 2>&1
    # real    89m19.998s

    cat fb.chlSab2.chainRheMac8Link.txt
    # 2596129666 bases of 2752019208 (94.335%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        chlSab2 rheMac8) > rbest.log 2>&1
    # real    278m9.306s

#############################################################################
# chimp/rheMac2 <-> Chlorocebus sabaeus/Green monkey Lastz run (DONE - 2015-01-28 - Brian)
    screen -S chlSab2RheMac2  # use a screen to manage this longish running job
    mkdir /hive/data/genomes/chlSab2/bed/lastzRheMac2.2015-01-28
    cd /hive/data/genomes/chlSab2/bed/lastzRheMac2.2015-01-28

    # always set the BLASTZ program so we know what version was used
    printf "# vervet vs macaca mulatta
BLASTZ=lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
# and place those items here
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: Human Hg19
SEQ1_DIR=/hive/data/genomes/chlSab2/chlSab2.2bit
SEQ1_LEN=/hive/data/genomes/chlSab2/chrom.sizes
SEQ1_CHUNK=10000000
SEQ1_LAP=10000
SEQ1_IN_CONTIGS=0

# QUERY: Macaca Mulatta RheMac2
SEQ2_DIR=/scratch/data/rheMac2/rheMac2.2bit
SEQ2_LEN=/scratch/data/rheMac2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/chlSab2/bed/lastzRheMac2.2015-01-28
TMPDIR=/scratch/tmp
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > do.log 2>&1
    # Elapsed time: 346m35s

    cat fb.hg38.chainChlSab2Link.txt
    # 2480180858 bases of 2752019208 (90.122%) in intersection

    # filter with doRecipBest.pl
    doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        hg38 chlSab2
    # about 45 minutes

    # running the swap
    mkdir /hive/data/genomes/rheMac2/bed/blastz.chlSab2.swap
    cd /hive/data/genomes/rheMac2/bed/blastz.chlSab2.swap
    time (doBlastzChainNet.pl -verbose=2 \
        -swap /hive/data/genomes/chlSab2/bed/lastzRheMac2.2015-01-28/DEF \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > swap.log 2>&1
XXX - running - Wed Sep 28 10:01:36 PDT 2016
    # Elapsed time: 88m48s

    cat fb.chlSab2.chainHg38Link.txt
    # 2429053010 bases of 2752019208 (88.264%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        chlSab2 hg38) > rbest.log 2>&1
    # real    240m25.264s

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