#########################################################################
# SWAP lastz zebrafish danRer10 (DONE - 2015-09-18 - Hiram)
    # the primary alignment on mm10
    cd /hive/data/genomes/mm10/bed/lastzDanRer10.2015-09-11
    cat fb.mm10.chainDanRer10Link.txt
    #	73464192 bases of 2652783500 (2.769%) in intersection

    #	and for the swap
    mkdir /hive/data/genomes/danRer10/bed/blastz.mm10.swap
    cd /hive/data/genomes/danRer10/bed/blastz.mm10.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/mm10/bed/lastzDanRer10.2015-09-11/DEF \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -swap -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 &
    #	real    16m8.387s

    cat  fb.danRer10.chainMm10Link.txt
    #	71611488 bases of 1369683683 (5.228%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` danRer10 mm10) > rbest.log 2>&1
    #    real    7m34.259s

#########################################################################
# LASTZ Xenopus xenTro7 (DONE - 2017-02-09 - Hiram)
    mkdir /hive/data/genomes/danRer10/bed/lastzXenTro7.2017-02-09
    cd /hive/data/genomes/danRer10/bed/lastzXenTro7.2017-02-09

    printf '# zebrafish vs. X. tropicalis
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254

BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_Q=/scratch/data/blastz/HoxD55.q

# TARGET: Zebrafish danRer10
SEQ1_DIR=/hive/data/genomes/danRer10/danRer10.2bit
SEQ1_LEN=/hive/data/genomes/danRer10/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=5

# QUERY: X. tropicalis xenTro7
SEQ2_DIR=/hive/data/genomes/xenTro7/xenTro7.2bit
SEQ2_LEN=/hive/data/genomes/xenTro7/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=40

BASE=/hive/data/genomes/danRer10/bed/lastzXenTro7.2017-02-09
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen
    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -chainMinScore=5000 -chainLinearGap=loose \
          -syntenicNet -workhorse=hgwdev -smallClusterHub=ku \
            -bigClusterHub=ku) > do.log 2>&1
    #	lost tty connection

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -chainMinScore=5000 -chainLinearGap=loose \
          -syntenicNet -workhorse=hgwdev -smallClusterHub=ku \
            -continue=cat -bigClusterHub=ku) > cat.log 2>&1
    # real    136m6.704s

    cat fb.danRer10.chainXenTro7Link.txt
    #	90862965 bases of 1369683683 (6.634%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` danRer10 xenTro7) \
          > rbest.log 2>&1 &
    # real    387m16.949s

    # and for the swap:
    mkdir /hive/data/genomes/xenTro7/bed/blastz.danRer10.swap
    cd /hive/data/genomes/xenTro7/bed/blastz.danRer10.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/danRer10/bed/lastzXenTro7.2017-02-09/DEF \
	-chainMinScore=5000 -chainLinearGap=loose \
	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
	-syntenicNet -swap) > swap.log 2>&1
    #	real    30m3.142s

    cat fb.xenTro7.chainDanRer10Link.txt
    #	96433154 bases of 1365936747 (7.060%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` xenTro7 danRer10) \
          > rbest.log 2>&1
    # real    408m19.596s

########################################################################
# LASTZ green spotted puffer tetNig2 (DONE - 2017-02-09 - Hiram)
    screen -S danRer10TetNig2
    mkdir /hive/data/genomes/danRer10/bed/lastzTetNig2.2017-02-09
    cd /hive/data/genomes/danRer10/bed/lastzTetNig2.2017-02-09

    printf '# zebrafish vs. green spotted puffer
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254

BLASTZ_H=2000
BLASTZ_Y=9400
BLASTZ_L=3000
BLASTZ_K=3000
BLASTZ_Q=/scratch/data/blastz/HoxD55.q

# TARGET: Zebrafish danRer10
SEQ1_DIR=/hive/data/genomes/danRer10/danRer10.2bit
SEQ1_LEN=/hive/data/genomes/danRer10/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=1

# QUERY: green spotted puffer tetNig2
SEQ2_DIR=/hive/data/genomes/tetNig2/tetNig2.2bit
SEQ2_LEN=/hive/data/genomes/tetNig2/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=1

BASE=/hive/data/genomes/danRer10/bed/lastzTetNig2.2017-02-09
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen
    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -chainMinScore=2000 -chainLinearGap=medium \
          -syntenicNet -workhorse=hgwdev -smallClusterHub=ku \
            -bigClusterHub=ku) > do.log 2>&1
    #	real    97m22.745s

    cat fb.danRer10.chainTetNig2Link.txt
    #	83044644 bases of 1369683683 (6.063%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` danRer10 tetNig2) \
          > rbest.log 2>&1 &
    # real    254m45.837s

    mkdir /hive/data/genomes/tetNig2/bed/blastz.danRer10.swap
    cd /hive/data/genomes/tetNig2/bed/blastz.danRer10.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/danRer10/bed/lastzTetNig2.2017-02-09/DEF \
	-chainMinScore=2000 -chainLinearGap=medium \
	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
	-swap) > swap.log 2>&1
    #	real    6m59.881s

    cat fb.tetNig2.chainDanRer10Link.txt
    #	70573446 bases of 302314788 (23.344%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` tetNig2 danRer10) \
          > rbest.log 2>&1
    # real    228m19.188s

    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/danRer10/bed/lastzTetNig2.2017-02-09/DEF \
	-chainMinScore=2000 -chainLinearGap=medium \
	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
	-continue=syntenicNet -syntenicNet -swap) > synNet.log 2>&1
    # real    0m43.708s

########################################################################
# LASTZ fugu fr3 (DONE - 2017-02-09 - Hiram)
    screen -S danRer10Fr3
    mkdir /hive/data/genomes/danRer10/bed/lastzFr3.2017-02-09
    cd /hive/data/genomes/danRer10/bed/lastzFr3.2017-02-09

    printf '# zebrafish vs. fugu
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254

BLASTZ_H=2000
BLASTZ_Y=9400
BLASTZ_L=3000
BLASTZ_K=3000
BLASTZ_Q=/scratch/data/blastz/HoxD55.q

# TARGET: Zebrafish danRer10
SEQ1_DIR=/hive/data/genomes/danRer10/danRer10.2bit
SEQ1_LEN=/hive/data/genomes/danRer10/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=6

# QUERY: fugu fr3
SEQ2_DIR=/hive/data/genomes/fr3/fr3.2bit
SEQ2_LEN=/hive/data/genomes/fr3/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=30

BASE=/hive/data/genomes/danRer10/bed/lastzFr3.2017-02-09
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen
    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -chainMinScore=2000 -chainLinearGap=medium \
          -syntenicNet -workhorse=hgwdev -smallClusterHub=ku \
            -bigClusterHub=ku) > do.log 2>&1
    #	real    133m18.224s

    cat fb.danRer10.chainFr3Link.txt
    #	96978660 bases of 1369683683 (7.080%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` danRer10 fr3) \
          > rbest.log 2>&1 &
    # real    200m15.132s

    mkdir /hive/data/genomes/fr3/bed/blastz.danRer10.swap
    cd /hive/data/genomes/fr3/bed/blastz.danRer10.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/danRer10/bed/lastzFr3.2017-02-09/DEF \
	-chainMinScore=2000 -chainLinearGap=medium \
	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
	-syntenicNet -swap) > swap.log 2>&1
    #	real    9m31.601s

    cat fb.fr3.chainDanRer10Link.txt
    #	79663999 bases of 350961831 (22.699%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` fr3 danRer10) \
          > rbest.log 2>&1
    # real    181m55.550s

########################################################################
# LASTZ medaka oryLat2 (DONE - 2017-02-09 - Hiram)
    screen -S oryLat2DanRer10
    mkdir /hive/data/genomes/danRer10/bed/lastzOryLat2.2017-02-09
    cd /hive/data/genomes/danRer10/bed/lastzOryLat2.2017-02-09

    printf '# zebrafish vs. medaka
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254

BLASTZ_H=2000
BLASTZ_Y=9400
BLASTZ_L=3000
BLASTZ_K=3000
BLASTZ_Q=/scratch/data/blastz/HoxD55.q

# TARGET: Zebrafish danRer10
SEQ1_DIR=/hive/data/genomes/danRer10/danRer10.2bit
SEQ1_LEN=/hive/data/genomes/danRer10/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=6

# QUERY: medaka oryLat2
SEQ2_DIR=/hive/data/genomes/oryLat2/oryLat2.2bit
SEQ2_LEN=/hive/data/genomes/oryLat2/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=0
SEQ2_LIMIT=30

BASE=/hive/data/genomes/danRer10/bed/lastzOryLat2.2017-02-09
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen
    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -chainMinScore=2000 -chainLinearGap=medium \
          -syntenicNet -workhorse=hgwdev -smallClusterHub=ku \
            -bigClusterHub=ku) > do.log 2>&1
    #	real    202m52.634s

    cat fb.danRer10.chainOryLat2Link.txt
    #	132042172 bases of 1369683683 (9.640%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` danRer10 oryLat2) \
          > rbest.log 2>&1 &
    # real    388m46.359s

    mkdir /hive/data/genomes/oryLat2/bed/blastz.danRer10.swap
    cd /hive/data/genomes/oryLat2/bed/blastz.danRer10.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/danRer10/bed/lastzOryLat2.2017-02-09/DEF \
	-chainMinScore=2000 -chainLinearGap=medium \
	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
	-syntenicNet -swap) > swap.log 2>&1
    #	real    18m21.238s

    cat fb.oryLat2.chainDanRer10Link.txt
    #	123853592 bases of 700386597 (17.684%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oryLat2 danRer10) \
          > rbest.log 2>&1
    # real    370m26.030s

########################################################################
# LASTZ stickleback gasAcu1 (DONE - 2017-02-09 - Hiram)
    screen -S gasAcu1DanRer10
    mkdir /hive/data/genomes/danRer10/bed/lastzGasAcu1.2017-02-09
    cd /hive/data/genomes/danRer10/bed/lastzGasAcu1.2017-02-09

    printf '# zebrafish vs. stickleback
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254

BLASTZ_H=2000
BLASTZ_Y=9400
BLASTZ_L=3000
BLASTZ_K=3000
BLASTZ_Q=/scratch/data/blastz/HoxD55.q

# TARGET: Zebrafish danRer10
SEQ1_DIR=/hive/data/genomes/danRer10/danRer10.2bit
SEQ1_LEN=/hive/data/genomes/danRer10/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=6

# QUERY: stickleback gasAcu1
#  30,000,000 is enough to work with the biggest chrom as one item
SEQ2_DIR=/hive/data/genomes/gasAcu1/gasAcu1.2bit
SEQ2_LEN=/hive/data/genomes/gasAcu1/chrom.sizes
SEQ2_CHUNK=30000000
SEQ2_LAP=0
SEQ2_LIMIT=30

BASE=/hive/data/genomes/danRer10/bed/lastzGasAcu1.2017-02-09
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen
    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -chainMinScore=2000 -chainLinearGap=medium \
          -syntenicNet -workhorse=hgwdev -smallClusterHub=ku \
            -bigClusterHub=ku) > do.log 2>&1
    #	real    766m31.436s

    cat fb.danRer10.chainGasAcu1Link.txt
    #	134422269 bases of 1369683683 (9.814%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` danRer10 gasAcu1) \
          > rbest.log 2>&1 &
    # real    466m55.498s

    mkdir /hive/data/genomes/gasAcu1/bed/blastz.danRer10.swap
    cd /hive/data/genomes/gasAcu1/bed/blastz.danRer10.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/danRer10/bed/lastzGasAcu1.2017-02-09/DEF \
	-chainMinScore=2000 -chainLinearGap=medium \
	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
	-syntenicNet -swap) > swap.log 2>&1
    #	real    26m37.898s

    cat fb.gasAcu1.chainDanRer10Link.txt
    #	123076224 bases of 446627861 (27.557%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` gasAcu1 danRer10) \
          > rbest.log 2>&1
    # real    441m12.898s

########################################################################
# LASTZ Coelacanth latCha1 (DONE - 2020-02-25 - Hiram)
    mkdir /hive/data/genomes/danRer10/bed/lastzLatCha1.2020-02-25
    cd /hive/data/genomes/danRer10/bed/lastzLatCha1.2020-02-25

    printf '# zebrafish vs. Coelacanth
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_M=254

BLASTZ_H=2000
BLASTZ_Y=9400
BLASTZ_L=3000
BLASTZ_K=3000
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: Zebrafish danRer10
SEQ1_DIR=/hive/data/genomes/danRer10/danRer10.2bit
SEQ1_LEN=/hive/data/genomes/danRer10/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=6

# QUERY: Coelacanth latCha1
#  14,000,000 is enough to work with the biggest chrom as one item
SEQ2_DIR=/hive/data/genomes/latCha1/latCha1.2bit
SEQ2_LEN=/hive/data/genomes/latCha1/chrom.sizes
SEQ2_CHUNK=14000000
SEQ2_LAP=0
SEQ2_LIMIT=30

BASE=/hive/data/genomes/danRer10/bed/lastzLatCha1.2020-02-25
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen
    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -chainMinScore=5000 -chainLinearGap=loose \
          -syntenicNet -workhorse=hgwdev -smallClusterHub=ku \
            -bigClusterHub=ku) > do.log 2>&1
    #	real    177m11.851s

    cat fb.danRer10.chainLatCha1Link.txt
    #	86552427 bases of 1369683683 (6.319%) in intersection
    cat fb.danRer10.chainSynLatCha1Link.txt
    #	15892801 bases of 1369683683 (1.160%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
          danRer10 latCha1) > rbest.log 2>&1 &
    # real    71m59.526s

    cat fb.danRer10.chainRBest.LatCha1.txt
    #    56607816 bases of 1369683683 (4.133%) in intersection

    mkdir /hive/data/genomes/latCha1/bed/blastz.danRer10.swap
    cd /hive/data/genomes/latCha1/bed/blastz.danRer10.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/danRer10/bed/lastzLatCha1.2020-02-25/DEF \
	-chainMinScore=5000 -chainLinearGap=loose \
	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
	-syntenicNet -swap) > swap.log 2>&1
    #	real    12m58.361s

    cat fb.latCha1.chainDanRer10Link.txt
    #	98338936 bases of 2183592768 (4.504%) in intersection
    cat fb.latCha1.chainSynDanRer10Link.txt
    #   13550035 bases of 2183592768 (0.621%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
          latCha1 danRer10) > rbest.log 2>&1
    # real    67m29.683s
    cat fb.latCha1.chainRBest.DanRer10.txt
    # 56742837 bases of 2183592768 (2.599%) in intersection

########################################################################
# LASTZ spotted gar lepOcu1 (DONE - 2020-02-25 - Hiram)
    mkdir /hive/data/genomes/danRer10/bed/lastzLepOcu1.2020-02-25
    cd /hive/data/genomes/danRer10/bed/lastzLepOcu1.2020-02-25

    printf '# zebrafish vs. spotted gar
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_M=254

BLASTZ_H=2000
BLASTZ_Y=9400
BLASTZ_L=3000
BLASTZ_K=3000
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: Zebrafish danRer10
SEQ1_DIR=/hive/data/genomes/danRer10/danRer10.2bit
SEQ1_LEN=/hive/data/genomes/danRer10/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=6

# QUERY: spotted gar lepOcu1
SEQ2_DIR=/hive/data/genomes/lepOcu1/lepOcu1.2bit
SEQ2_LEN=/hive/data/genomes/lepOcu1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=30

BASE=/hive/data/genomes/danRer10/bed/lastzLepOcu1.2020-02-25
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen
    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -chainMinScore=5000 -chainLinearGap=loose \
          -syntenicNet -workhorse=hgwdev -smallClusterHub=ku \
            -bigClusterHub=ku) > do.log 2>&1
    #	real    118m59.600s

    cat fb.danRer10.chainLepOcu1Link.txt
    #	115180491 bases of 1369683683 (8.409%) in intersection
    cat fb.danRer10.chainSynLepOcu1Link.txt
    #    58800217 bases of 1369683683 (4.293%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` danRer10 \
	lepOcu1) > rbest.log 2>&1 &
    # real    88m25.172s

    cat fb.danRer10.chainRBest.LepOcu1.txt
    #	78985057 bases of 1369683683 (5.767%) in intersection

    mkdir /hive/data/genomes/lepOcu1/bed/blastz.danRer10.swap
    cd /hive/data/genomes/lepOcu1/bed/blastz.danRer10.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/danRer10/bed/lastzLepOcu1.2020-02-25/DEF \
	-chainMinScore=5000 -chainLinearGap=loose \
	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
	-syntenicNet -swap) > swap.log 2>&1
    #	real    7m34.876s

    cat fb.lepOcu1.chainDanRer10Link.txt
    #	98189747 bases of 869414361 (11.294%) in intersection
    cat fb.lepOcu1.chainSynDanRer10Link.txt
    #   47688590 bases of 869414361 (5.485%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
          lepOcu1 danRer10) > rbest.log 2>&1
    # real    83m11.208s

    cat fb.lepOcu1.chainRBest.DanRer10.txt
    #	78000762 bases of 869414361 (8.972%) in intersection

########################################################################
# LASTZ Elephant shark calMil1 (DONE - 2020-02-25 - Hiram)
    mkdir /hive/data/genomes/danRer10/bed/lastzCalMil1.2020-02-25
    cd /hive/data/genomes/danRer10/bed/lastzCalMil1.2020-02-25

    printf '# zebrafish vs. Elephant shark
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_M=254

BLASTZ_H=2000
BLASTZ_Y=9400
BLASTZ_L=3000
BLASTZ_K=3000
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: Zebrafish danRer10
SEQ1_DIR=/hive/data/genomes/danRer10/danRer10.2bit
SEQ1_LEN=/hive/data/genomes/danRer10/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=6

# QUERY: Elephant shark calMil1
SEQ2_DIR=/hive/data/genomes/calMil1/calMil1.2bit
SEQ2_LEN=/hive/data/genomes/calMil1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/danRer10/bed/lastzCalMil1.2020-02-25
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen
    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -chainMinScore=5000 -chainLinearGap=loose \
          -syntenicNet -workhorse=hgwdev -smallClusterHub=ku \
            -bigClusterHub=ku) > do.log 2>&1
    #	real    48m39.821s

    cat fb.danRer10.chainCalMil1Link.txt
    #	76690714 bases of 1369683683 (5.599%) in intersection
    cat fb.danRer10.chainSynCalMil1Link.txt
    #   18240388 bases of 1369683683 (1.332%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` danRer10 \
	calMil1) > rbest.log 2>&1 &
    # real    466m55.498s

    cat fb.danRer10.chainRBest.CalMil1.txt
    # 48435763 bases of 1369683683 (3.536%) in intersection

    mkdir /hive/data/genomes/calMil1/bed/blastz.danRer10.swap
    cd /hive/data/genomes/calMil1/bed/blastz.danRer10.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/danRer10/bed/lastzCalMil1.2020-02-25/DEF \
	-chainMinScore=5000 -chainLinearGap=loose \
	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
	-syntenicNet -swap) > swap.log 2>&1
    #	real    7m34.876s

    cat fb.calMil1.chainDanRer10Link.txt
    #	66411165 bases of 936953458 (7.088%) in intersection
    cat fb.calMil1.chainSynDanRer10Link.txt
    #   15359860 bases of 936953458 (1.639%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
          calMil1 danRer10) > rbest.log 2>&1
    # real    57m38.923s

    cat fb.calMil1.chainRBest.DanRer10.txt
    #   47381650 bases of 936953458 (5.057%) in intersection

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