##############################################################################
# LASTZ Great Dane canFam5 (DONE - 2020-08-17 - Hiram)
    #	establish a screen to control this job
    mkdir /hive/data/genomes/mm39/bed/lastzCanFam5.2020-08-17
    cd /hive/data/genomes/mm39/bed/lastzCanFam5.2020-08-17

    printf '# German shepard canFam5 vs mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_M=254

# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: German shepard canFam5
SEQ2_DIR=/hive/data/genomes/canFam5/canFam5.2bit
SEQ2_LEN=/hive/data/genomes/canFam5/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/mm39/bed/lastzCanFam5.2020-08-17
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
	-syntenicNet \
	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
	-chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 &
    #	real    200m16.271s

    cat fb.mm39.chainCanFam5Link.txt
    #	778327929 bases of 2654624157 (29.320%) in intersection
    cat fb.mm39.chainSynCanFam5Link.txt
    #   735515331 bases of 2654624157 (27.707%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev mm39 canFam5 \
      -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
    #	real    213m30.572s

    cat fb.mm39.chainRBest.CanFam5.txt
    # 740738480 bases of 2654624157 (27.904%) in intersection

    mkdir /hive/data/genomes/canFam5/bed/blastz.mm39.swap
    cd /hive/data/genomes/canFam5/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/mm39/bed/lastzCanFam5.2020-08-17/DEF \
	-swap -syntenicNet \
	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 &
    #	real    44m12.732s

    cat fb.canFam5.chainMm39Link.txt
    #	762233776 bases of 2337131234 (32.614%) in intersection
    cat fb.canFam5.chainSynMm39Link.txt
    #   731337903 bases of 2337131234 (31.292%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev canFam5 mm39 \
      -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
    # real    174m14.398s

    cat fb.canFam5.chainRBest.Mm39.txt
    # 739648625 bases of 2337131234 (31.648%) in intersection

##############################################################################
# LASTZ mouse mm39 vs marmoset calJac4 (DONE - 2020-09-04 - Hiram)
    #	establish a screen to control this job
    mkdir /hive/data/genomes/mm39/bed/lastzCalJac4.2020-09-04
    cd /hive/data/genomes/mm39/bed/lastzCalJac4.2020-09-04

    printf '# mouse vs marmoset calJac4
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_M=254

# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: marmoset calJac4
SEQ2_DIR=/hive/data/genomes/calJac4/calJac4.2bit
SEQ2_LEN=/hive/data/genomes/calJac4/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/mm39/bed/lastzCalJac4.2020-09-04
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
	-syntenicNet \
	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
	-chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 &
    #	real    269m7.515s

    cat fb.mm39.chainCalJac4Link.txt
    #	878425270 bases of 2654624157 (33.090%) in intersection
    cat fb.mm39.chainSynCalJac4Link.txt
    #   830808798 bases of 2654624157 (31.297%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev mm39 calJac4 \
      -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
    #	real    342m45.296s

    cat fb.mm39.chainRBest.CalJac4.txt
    # 835984408 bases of 2654624157 (31.492%) in intersection

    mkdir /hive/data/genomes/calJac4/bed/blastz.mm39.swap
    cd /hive/data/genomes/calJac4/bed/blastz.mm39.swap

    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/mm39/bed/lastzCalJac4.2020-09-04/DEF \
	-swap -syntenicNet \
	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 &
    #	real    51m44.991s

    cat fb.calJac4.chainMm39Link.txt
    #	885334904 bases of 2859817025 (30.958%) in intersection
    cat fb.calJac4.chainSynMm39Link.txt
    #   831225065 bases of 2859817025 (29.066%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev calJac4 mm39 \
      -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
    # real    298m22.974s

    cat fb.calJac4.chainRBest.Mm39.txt
    # 834211414 bases of 2859817025 (29.170%) in intersection

##############################################################################
# LASTZ Rat rn6 (DONE - 2020-10-20 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzRn6.2020-10-20
    cd /hive/data/genomes/mm39/bed/lastzRn6.2020-10-20

    printf '# rat vs mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Rat Rn6
SEQ2_DIR=/hive/data/genomes/rn6/rn6.2bit
SEQ2_LEN=/hive/data/genomes/rn6/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=500

BASE=/hive/data/genomes/mm39/bed/lastzRn6.2020-10-20
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen -S mm39Rn6
    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
	-syntenicNet \
	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
	-chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 &
    #   real    364m51.738s

    cat fb.mm39.chainRn6Link.txt
    #	1882154751 bases of 2654624157 (70.901%) in intersection
    cat fb.mm39.chainSynRn6Link.txt
    #	1758846483 bases of 2654624157 (66.256%) in intersection


    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	 mm39 rn6) > rbest.log 2>&1 &
    # real    580m33.404s
    cat fb.mm39.chainRBest.Rn6.txt
    #	1738608299 bases of 2654624157 (65.494%) in intersection

    mkdir /hive/data/genomes/rn6/bed/blastz.mm39.swap
    cd /hive/data/genomes/rn6/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/mm39/bed/lastzRn6.2020-10-20/DEF \
	-swap -syntenicNet \
	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
	-chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1
    #	real    129m25.422s

    cat fb.rn6.chainMm39Link.txt
    #   1940254184 bases of 2729860805 (71.075%) in intersection
    cat fb.rn6.chainSynMm39Link.txt
    #	1808524707 bases of 2729860805 (66.250%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	rn6 mm39) > rbest.log 2>&1
    # real    675m42.654s

    cat fb.rn6.chainRBest.Mm39.txt 
    #	1740516499 bases of 2729860805 (63.758%) in intersection

##############################################################################
# LASTZ Rhesus rheMac10 (DONE - 2020-10-20 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzRheMac10.2020-10-20
    cd /hive/data/genomes/mm39/bed/lastzRheMac10.2020-10-20

    printf '# rhesus vs mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Rhesus RheMac10
SEQ2_DIR=/hive/data/genomes/rheMac10/rheMac10.2bit
SEQ2_LEN=/hive/data/genomes/rheMac10/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=500

BASE=/hive/data/genomes/mm39/bed/lastzRheMac10.2020-10-20
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen -S mm39RheMac10
    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
	-syntenicNet \
	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
	-chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 &
    #   real    243m13.015s

    cat fb.mm39.chainRheMac10Link.txt
    #	924807390 bases of 2654624157 (34.838%) in intersection
    cat fb.mm39.chainSynRheMac10Link.txt
    #	878558648 bases of 2654624157 (33.095%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	mm39 rheMac10) > rbest.log 2>&1 &
    # real    309m44.560s

    cat fb.mm39.chainRBest.RheMac10.txt
    #	880466873 bases of 2654624157 (33.167%) in intersection


    mkdir /hive/data/genomes/rheMac10/bed/blastz.mm39.swap
    cd /hive/data/genomes/rheMac10/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/mm39/bed/lastzRheMac10.2020-10-20/DEF \
	-swap -syntenicNet \
	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real    51m43.176s

    cat fb.rheMac10.chainMm39Link.txt
    #   920110067 bases of 2936892733 (31.329%) in intersection
    cat fb.rheMac10.chainSynMm39Link.txt
    #	876443625 bases of 2936892733 (29.843%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	rheMac10 mm39) > rbest.log 2>&1
    # real    255m21.492s

    cat fb.rheMac10.chainRBest.Mm39.txt
    #	879043885 bases of 2936892733 (29.931%) in intersection

##############################################################################
# LASTZ Rat rn7 (DONE - 2021-02-04 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzRn7.2021-02-04
    cd /hive/data/genomes/mm39/bed/lastzRn7.2021-02-04

    printf '# rat vs mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Rat Rn7
SEQ2_DIR=/hive/data/genomes/rn7/rn7.2bit
SEQ2_LEN=/hive/data/genomes/rn7/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=500

BASE=/hive/data/genomes/mm39/bed/lastzRn7.2021-02-04
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen -S mm39Rn7
    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
	-syntenicNet \
	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
	-chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 &
    #   real    364m51.738s

    sed -e 's/^/    # /;' fb.mm39.chainRn7Link.txt
    # 1898735724 bases of 2654624157 (71.526%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynRn7Link.txt
    # 1787593557 bases of 2654624157 (67.339%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	 mm39 rn7) > rbest.log 2>&1 &
    # real    588m38.122s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.Rn7.txt
    # 1754204799 bases of 2654624157 (66.081%) in intersection

    mkdir /hive/data/genomes/rn7/bed/blastz.mm39.swap
    cd /hive/data/genomes/rn7/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/mm39/bed/lastzRn7.2021-02-04/DEF \
	-swap -syntenicNet \
	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
	-chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1
    #	real    116m47.862s

    sed -e 's/^/    # /;' fb.rn7.chainMm39Link.txt
    # 1855165978 bases of 2626580772 (70.630%) in intersection
    sed -e 's/^/    # /;' fb.rn7.chainSynMm39Link.txt
    # 1763550257 bases of 2626580772 (67.142%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	rn7 mm39) > rbest.log 2>&1
    # real    605m42.354s

    sed -e 's/^/    # /;' fb.rn7.chainRBest.Mm39.txt 
    # 1754416686 bases of 2626580772 (66.795%) in intersection

##############################################################################
# LASTZ Chinese hamster criGriChoV2 (DONE - 2020-11-23 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzCriGriChoV2.2020-11-23
    cd /hive/data/genomes/mm39/bed/lastzCriGriChoV2.2020-11-23

    printf '# Chinese hamster vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Chinese hamster CriGriChoV2
SEQ2_DIR=/hive/data/genomes/criGriChoV2/criGriChoV2.2bit
SEQ2_LEN=/hive/data/genomes/criGriChoV2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzCriGriChoV2.2020-11-23
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	458m24.193s

    sed -e 's/^/    #/;' fb.mm39.chainCriGriChoV2Link.txt
    # 1587256983 bases of 2654624157 (59.792%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynCriGriChoV2Link.txt
    # 1476080544 bases of 2654624157 (55.604%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 criGriChoV2) > rbest.log 2>&1
    #	real	593m38.879s

    sed -e's/^/    #/;' fb.mm39.chainRBest.CriGriChoV2.txt
    # 1452642485 bases of 2654624157 (54.721%) in intersection

    mkdir /hive/data/genomes/criGriChoV2/bed/blastz.mm39.swap
    cd /hive/data/genomes/criGriChoV2/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzCriGriChoV2.2020-11-23/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	122m5.549s

    sed -e 's/^/    #/;' fb.criGriChoV2.chainMm39Link.txt
    # 1610424504 bases of 2323924942 (69.298%) in intersection
    sed -e 's/^/    #/;'  fb.criGriChoV2.chainSynMm39Link.txt
    # 1444363698 bases of 2323924942 (62.152%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       criGriChoV2 mm39) > rbest.log 2>&1
    #	real	675m33.754s

    sed -e 's/^/    #/;'  fb.criGriChoV2.chainRBest.Mm39.txt
    # 1454060577 bases of 2323924942 (62.569%) in intersection

##############################################################################
# LASTZ Beaver casCan1 (DONE - 2020-11-23 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzCasCan1.2020-11-23
    cd /hive/data/genomes/mm39/bed/lastzCasCan1.2020-11-23

    printf '# Beaver vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Beaver CasCan1
SEQ2_DIR=/hive/data/genomes/casCan1/casCan1.2bit
SEQ2_LEN=/hive/data/genomes/casCan1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzCasCan1.2020-11-23
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	391m42.423s

    sed -e 's/^/    #/;' fb.mm39.chainCasCan1Link.txt
    # 971598688 bases of 2654624157 (36.600%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynCasCan1Link.txt
    # 860197979 bases of 2654624157 (32.404%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 casCan1) > rbest.log 2>&1
    #	real	309m3.360s

    sed -e's/^/    #/;' fb.mm39.chainRBest.CasCan1.txt
    # 913365652 bases of 2654624157 (34.407%) in intersection

    mkdir /hive/data/genomes/casCan1/bed/blastz.mm39.swap
    cd /hive/data/genomes/casCan1/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzCasCan1.2020-11-23/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	69m39.719s

    sed -e 's/^/    #/;' fb.casCan1.chainMm39Link.txt
    # 1030326326 bases of 2517974654 (40.919%) in intersection
    sed -e 's/^/    #/;'  fb.casCan1.chainSynMm39Link.txt
    # 877942655 bases of 2517974654 (34.867%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       casCan1 mm39) > rbest.log 2>&1
    #	real	342m21.552s

    sed -e 's/^/    #/;'  fb.casCan1.chainRBest.Mm39.txt
    # 912616046 bases of 2517974654 (36.244%) in intersection

##############################################################################
# LASTZ Chinese pangolin manPen1 (DONE - 2020-11-23 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzManPen1.2020-11-23
    cd /hive/data/genomes/mm39/bed/lastzManPen1.2020-11-23

    printf '# Chinese pangolin vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Chinese pangolin ManPen1
SEQ2_DIR=/hive/data/genomes/manPen1/manPen1.2bit
SEQ2_LEN=/hive/data/genomes/manPen1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=500

BASE=/hive/data/genomes/mm39/bed/lastzManPen1.2020-11-23
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	307m16.259s

    sed -e 's/^/    #/;' fb.mm39.chainManPen1Link.txt
    # 725290847 bases of 2654624157 (27.322%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynManPen1Link.txt
    # 600536473 bases of 2654624157 (22.622%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 manPen1) > rbest.log 2>&1
    #	real	254m19.570s

    sed -e's/^/    #/;' fb.mm39.chainRBest.ManPen1.txt
    # 686132793 bases of 2654624157 (25.847%) in intersection

    mkdir /hive/data/genomes/manPen1/bed/blastz.mm39.swap
    cd /hive/data/genomes/manPen1/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzManPen1.2020-11-23/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	57m14.273s

    sed -e 's/^/    #/;' fb.manPen1.chainMm39Link.txt
    # 711536446 bases of 1999066070 (35.593%) in intersection
    sed -e 's/^/    #/;'  fb.manPen1.chainSynMm39Link.txt
    # 600806601 bases of 1999066070 (30.054%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       manPen1 mm39) > rbest.log 2>&1
    #	real	258m8.812s

    sed -e 's/^/    #/;'  fb.manPen1.chainRBest.Mm39.txt
    # 685854051 bases of 1999066070 (34.309%) in intersection

##############################################################################
# LASTZ Malayan flying lemur galVar1 (DONE - 2020-11-23 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzGalVar1.2020-11-23
    cd /hive/data/genomes/mm39/bed/lastzGalVar1.2020-11-23

    printf '# Malayan flying lemur vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Malayan flying lemur GalVar1
SEQ2_DIR=/hive/data/genomes/galVar1/galVar1.2bit
SEQ2_LEN=/hive/data/genomes/galVar1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=500

BASE=/hive/data/genomes/mm39/bed/lastzGalVar1.2020-11-23
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	409m27.010s

    sed -e 's/^/    #/;' fb.mm39.chainGalVar1Link.txt
    # 948074394 bases of 2654624157 (35.714%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynGalVar1Link.txt
    # 833172992 bases of 2654624157 (31.386%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 galVar1) > rbest.log 2>&1
    #	real	355m41.194s

    sed -e's/^/    #/;' fb.mm39.chainRBest.GalVar1.txt
    # 895962299 bases of 2654624157 (33.751%) in intersection

    mkdir /hive/data/genomes/galVar1/bed/blastz.mm39.swap
    cd /hive/data/genomes/galVar1/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzGalVar1.2020-11-23/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	113m39.933s

    sed -e 's/^/    #/;' fb.galVar1.chainMm39Link.txt
    # 1013311093 bases of 2802917674 (36.152%) in intersection
    sed -e 's/^/    #/;'  fb.galVar1.chainSynMm39Link.txt
    # 857584853 bases of 2802917674 (30.596%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       galVar1 mm39) > rbest.log 2>&1
    #	real	412m23.326s

    sed -e 's/^/    #/;'  fb.galVar1.chainRBest.Mm39.txt
    # 894445877 bases of 2802917674 (31.911%) in intersection

##############################################################################
# LASTZ Gorilla gorGor6 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzGorGor6.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzGorGor6.2020-11-24

    printf '# Gorilla vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Gorilla GorGor6
SEQ2_DIR=/hive/data/genomes/gorGor6/gorGor6.2bit
SEQ2_LEN=/hive/data/genomes/gorGor6/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGorGor6.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	298m31.850s

    sed -e 's/^/    #/;' fb.mm39.chainGorGor6Link.txt
    # 930815279 bases of 2654624157 (35.064%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynGorGor6Link.txt
    # 882010048 bases of 2654624157 (33.225%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 gorGor6) > rbest.log 2>&1
    #	real	302m25.603s

    sed -e's/^/    #/;' fb.mm39.chainRBest.GorGor6.txt
    # 885577700 bases of 2654624157 (33.360%) in intersection

    mkdir /hive/data/genomes/gorGor6/bed/blastz.mm39.swap
    cd /hive/data/genomes/gorGor6/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzGorGor6.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	56m58.641s

    sed -e 's/^/    #/;' fb.gorGor6.chainMm39Link.txt
    # 1021664774 bases of 2999027915 (34.067%) in intersection
    sed -e 's/^/    #/;'  fb.gorGor6.chainSynMm39Link.txt
    # 881068629 bases of 2999027915 (29.378%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       gorGor6 mm39) > rbest.log 2>&1
    #	real	263m46.802s

    sed -e 's/^/    #/;'  fb.gorGor6.chainRBest.Mm39.txt
    # 884060521 bases of 2999027915 (29.478%) in intersection

# ERROR: can not find hg38 vs. mm39 /DEF
##############################################################################
# LASTZ Bonobo panPan3 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzPanPan3.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzPanPan3.2020-11-24

    printf '# Bonobo vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Bonobo PanPan3
SEQ2_DIR=/hive/data/genomes/panPan3/panPan3.2bit
SEQ2_LEN=/hive/data/genomes/panPan3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzPanPan3.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	314m48.787s

    sed -e 's/^/    #/;' fb.mm39.chainPanPan3Link.txt
    # 936595620 bases of 2654624157 (35.282%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynPanPan3Link.txt
    # 889095516 bases of 2654624157 (33.492%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 panPan3) > rbest.log 2>&1
    #	real	315m43.802s

    sed -e's/^/    #/;' fb.mm39.chainRBest.PanPan3.txt
    # 891388431 bases of 2654624157 (33.579%) in intersection

    mkdir /hive/data/genomes/panPan3/bed/blastz.mm39.swap
    cd /hive/data/genomes/panPan3/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzPanPan3.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	55m37.718s

    sed -e 's/^/    #/;' fb.panPan3.chainMm39Link.txt
    # 1022366328 bases of 3015350297 (33.905%) in intersection
    sed -e 's/^/    #/;'  fb.panPan3.chainSynMm39Link.txt
    # 888141375 bases of 3015350297 (29.454%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       panPan3 mm39) > rbest.log 2>&1
    #	real	275m25.911s

    sed -e 's/^/    #/;'  fb.panPan3.chainRBest.Mm39.txt
    # 889786782 bases of 3015350297 (29.509%) in intersection

##############################################################################
# LASTZ Chimp panTro6 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzPanTro6.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzPanTro6.2020-11-24

    printf '# Chimp vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Chimp PanTro6
SEQ2_DIR=/hive/data/genomes/panTro6/panTro6.2bit
SEQ2_LEN=/hive/data/genomes/panTro6/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzPanTro6.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	292m55.308s

    sed -e 's/^/    #/;' fb.mm39.chainPanTro6Link.txt
    # 936842603 bases of 2654624157 (35.291%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynPanTro6Link.txt
    # 889591386 bases of 2654624157 (33.511%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 panTro6) > rbest.log 2>&1
    #	real	318m39.695s

    sed -e's/^/    #/;' fb.mm39.chainRBest.PanTro6.txt
    # 892161322 bases of 2654624157 (33.608%) in intersection

    mkdir /hive/data/genomes/panTro6/bed/blastz.mm39.swap
    cd /hive/data/genomes/panTro6/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzPanTro6.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	54m39.744s

    sed -e 's/^/    #/;' fb.panTro6.chainMm39Link.txt
    # 936830473 bases of 3018592990 (31.035%) in intersection
    sed -e 's/^/    #/;'  fb.panTro6.chainSynMm39Link.txt
    # 890135394 bases of 3018592990 (29.488%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       panTro6 mm39) > rbest.log 2>&1
    #	real	272m44.051s

    sed -e 's/^/    #/;'  fb.panTro6.chainRBest.Mm39.txt
    # 890578770 bases of 3018592990 (29.503%) in intersection

##############################################################################
# LASTZ Tarsier tarSyr2 (DONE - 2020-11-23 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzTarSyr2.2020-11-23
    cd /hive/data/genomes/mm39/bed/lastzTarSyr2.2020-11-23

    printf '# Tarsier vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
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_LAP=0
SEQ2_LIMIT=500

BASE=/hive/data/genomes/mm39/bed/lastzTarSyr2.2020-11-23
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	209m1.579s
real	235m21.878s

    sed -e 's/^/    #/;' fb.mm39.chainTarSyr2Link.txt
    # 856869221 bases of 2654624157 (32.278%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynTarSyr2Link.txt
    # 767407640 bases of 2654624157 (28.908%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 tarSyr2) > rbest.log 2>&1
    #	real	235m21.816s

    sed -e's/^/    #/;' fb.mm39.chainRBest.TarSyr2.txt
    # 813072686 bases of 2654624157 (30.629%) in intersection

    mkdir /hive/data/genomes/tarSyr2/bed/blastz.mm39.swap
    cd /hive/data/genomes/tarSyr2/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzTarSyr2.2020-11-23/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	138m17.406s

    sed -e 's/^/    #/;' fb.tarSyr2.chainMm39Link.txt
    # 901691832 bases of 3405755564 (26.476%) in intersection
    sed -e 's/^/    #/;'  fb.tarSyr2.chainSynMm39Link.txt
    # 771115772 bases of 3405755564 (22.642%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       tarSyr2 mm39) > rbest.log 2>&1
    #	

    sed -e 's/^/    #/;'  fb.tarSyr2.chainRBest.Mm39.txt
##############################################################################
# LASTZ Bushbaby otoGar3 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzOtoGar3.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzOtoGar3.2020-11-24

    printf '# Bushbaby vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Bushbaby OtoGar3
SEQ2_DIR=/hive/data/genomes/otoGar3/otoGar3.2bit
SEQ2_LEN=/hive/data/genomes/otoGar3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzOtoGar3.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	397m59.255s

    sed -e 's/^/    #/;' fb.mm39.chainOtoGar3Link.txt
    # 789200353 bases of 2654624157 (29.729%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynOtoGar3Link.txt
    # 740066864 bases of 2654624157 (27.878%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 otoGar3) > rbest.log 2>&1
    #	real	188m39.612s

    sed -e's/^/    #/;' fb.mm39.chainRBest.OtoGar3.txt
    # 750275917 bases of 2654624157 (28.263%) in intersection

    mkdir /hive/data/genomes/otoGar3/bed/blastz.mm39.swap
    cd /hive/data/genomes/otoGar3/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzOtoGar3.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	45m14.239s

    sed -e 's/^/    #/;' fb.otoGar3.chainMm39Link.txt
    # 776190961 bases of 2359530453 (32.896%) in intersection
    sed -e 's/^/    #/;'  fb.otoGar3.chainSynMm39Link.txt
    # 734606528 bases of 2359530453 (31.134%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       otoGar3 mm39) > rbest.log 2>&1
    #	real	166m37.534s

    sed -e 's/^/    #/;'  fb.otoGar3.chainRBest.Mm39.txt
    # 749239900 bases of 2359530453 (31.754%) in intersection

##############################################################################
# LASTZ Horse equCab3 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzEquCab3.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzEquCab3.2020-11-24

    printf '# Horse vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Horse EquCab3
SEQ2_DIR=/hive/data/genomes/equCab3/equCab3.2bit
SEQ2_LEN=/hive/data/genomes/equCab3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzEquCab3.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	406m37.315s

    sed -e 's/^/    #/;' fb.mm39.chainEquCab3Link.txt
    # 924631395 bases of 2654624157 (34.831%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynEquCab3Link.txt
    # 877123772 bases of 2654624157 (33.041%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 equCab3) > rbest.log 2>&1
    #	real	247m56.186s

    sed -e's/^/    #/;' fb.mm39.chainRBest.EquCab3.txt
    # 878079495 bases of 2654624157 (33.077%) in intersection

    mkdir /hive/data/genomes/equCab3/bed/blastz.mm39.swap
    cd /hive/data/genomes/equCab3/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzEquCab3.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	60m58.831s

    sed -e 's/^/    #/;' fb.equCab3.chainMm39Link.txt
    # 933513515 bases of 2497530654 (37.377%) in intersection
    sed -e 's/^/    #/;'  fb.equCab3.chainSynMm39Link.txt
    # 897517908 bases of 2497530654 (35.936%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       equCab3 mm39) > rbest.log 2>&1
    #	real	185m17.962s

    sed -e 's/^/    #/;'  fb.equCab3.chainRBest.Mm39.txt
    # 876632896 bases of 2497530654 (35.100%) in intersection

##############################################################################
# LASTZ Dolphin turTru2 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzTurTru2.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzTurTru2.2020-11-24

    printf '# Dolphin vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Dolphin TurTru2
SEQ2_DIR=/hive/data/genomes/turTru2/turTru2.2bit
SEQ2_LEN=/hive/data/genomes/turTru2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=500

BASE=/hive/data/genomes/mm39/bed/lastzTurTru2.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	391m42.619s

    sed -e 's/^/    #/;' fb.mm39.chainTurTru2Link.txt
    # 801389023 bases of 2654624157 (30.188%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynTurTru2Link.txt
    # 661029305 bases of 2654624157 (24.901%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 turTru2) > rbest.log 2>&1
    #	real	315m15.793s

    sed -e's/^/    #/;' fb.mm39.chainRBest.TurTru2.txt
    # 763697442 bases of 2654624157 (28.769%) in intersection

    mkdir /hive/data/genomes/turTru2/bed/blastz.mm39.swap
    cd /hive/data/genomes/turTru2/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzTurTru2.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	86m10.671s

    sed -e 's/^/    #/;' fb.turTru2.chainMm39Link.txt
    # 780128552 bases of 2332402443 (33.447%) in intersection
    sed -e 's/^/    #/;'  fb.turTru2.chainSynMm39Link.txt
    # 660604333 bases of 2332402443 (28.323%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       turTru2 mm39) > rbest.log 2>&1
    #	real	344m38.287s

    sed -e 's/^/    #/;'  fb.turTru2.chainRBest.Mm39.txt
    # 763173700 bases of 2332402443 (32.720%) in intersection

##############################################################################
# LASTZ Dog canFam4 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzCanFam4.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzCanFam4.2020-11-24

    printf '# Dog vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Dog CanFam4
SEQ2_DIR=/hive/data/genomes/canFam4/canFam4.2bit
SEQ2_LEN=/hive/data/genomes/canFam4/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzCanFam4.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	394m53.229s

    sed -e 's/^/    #/;' fb.mm39.chainCanFam4Link.txt
    # 779819643 bases of 2654624157 (29.376%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynCanFam4Link.txt
    # 736821453 bases of 2654624157 (27.756%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 canFam4) > rbest.log 2>&1
    #	real	220m48.500s

    sed -e's/^/    #/;' fb.mm39.chainRBest.CanFam4.txt
    # 742006400 bases of 2654624157 (27.951%) in intersection

    mkdir /hive/data/genomes/canFam4/bed/blastz.mm39.swap
    cd /hive/data/genomes/canFam4/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzCanFam4.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	50m2.866s

    sed -e 's/^/    #/;' fb.canFam4.chainMm39Link.txt
    # 775644736 bases of 2481941580 (31.252%) in intersection
    sed -e 's/^/    #/;'  fb.canFam4.chainSynMm39Link.txt
    # 738180386 bases of 2481941580 (29.742%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       canFam4 mm39) > rbest.log 2>&1
    #	real	184m49.168s

    sed -e 's/^/    #/;'  fb.canFam4.chainRBest.Mm39.txt
    # 740879439 bases of 2481941580 (29.851%) in intersection

##############################################################################
# LASTZ Pig susScr3 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzSusScr3.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzSusScr3.2020-11-24

    printf '# Pig vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Pig SusScr3
SEQ2_DIR=/hive/data/genomes/susScr3/susScr3.2bit
SEQ2_LEN=/hive/data/genomes/susScr3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzSusScr3.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	392m59.025s

    sed -e 's/^/    #/;' fb.mm39.chainSusScr3Link.txt
    # 679873302 bases of 2654624157 (25.611%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynSusScr3Link.txt
    # 617246479 bases of 2654624157 (23.252%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 susScr3) > rbest.log 2>&1
    #	real	354m58.989s

    sed -e's/^/    #/;' fb.mm39.chainRBest.SusScr3.txt
    # 644866009 bases of 2654624157 (24.292%) in intersection

    mkdir /hive/data/genomes/susScr3/bed/blastz.mm39.swap
    cd /hive/data/genomes/susScr3/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzSusScr3.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	42m7.986s

    sed -e 's/^/    #/;' fb.susScr3.chainMm39Link.txt
    # 742566440 bases of 2525294057 (29.405%) in intersection
    sed -e 's/^/    #/;'  fb.susScr3.chainSynMm39Link.txt
    # 695214883 bases of 2525294057 (27.530%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       susScr3 mm39) > rbest.log 2>&1
    #	real	317m19.244s

    sed -e 's/^/    #/;'  fb.susScr3.chainRBest.Mm39.txt
    # 644557808 bases of 2525294057 (25.524%) in intersection

##############################################################################
# LASTZ Elephant loxAfr3 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzLoxAfr3.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzLoxAfr3.2020-11-24

    printf '# Elephant vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Elephant LoxAfr3
SEQ2_DIR=/hive/data/genomes/loxAfr3/loxAfr3.2bit
SEQ2_LEN=/hive/data/genomes/loxAfr3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzLoxAfr3.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	644m59.241s

    sed -e 's/^/    #/;' fb.mm39.chainLoxAfr3Link.txt
    # 683720656 bases of 2654624157 (25.756%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynLoxAfr3Link.txt
    # 632517819 bases of 2654624157 (23.827%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 loxAfr3) > rbest.log 2>&1
    #	real	212m39.008s

    sed -e's/^/    #/;' fb.mm39.chainRBest.LoxAfr3.txt
    # 648164944 bases of 2654624157 (24.416%) in intersection

    mkdir /hive/data/genomes/loxAfr3/bed/blastz.mm39.swap
    cd /hive/data/genomes/loxAfr3/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzLoxAfr3.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	48m31.606s

    sed -e 's/^/    #/;' fb.loxAfr3.chainMm39Link.txt
    # 673050238 bases of 3118565340 (21.582%) in intersection
    sed -e 's/^/    #/;'  fb.loxAfr3.chainSynMm39Link.txt
    # 630456477 bases of 3118565340 (20.216%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       loxAfr3 mm39) > rbest.log 2>&1
    #	real	181m46.370s

    sed -e 's/^/    #/;'  fb.loxAfr3.chainRBest.Mm39.txt
    # 647633378 bases of 3118565340 (20.767%) in intersection

##############################################################################
# LASTZ Rabbit oryCun2 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzOryCun2.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzOryCun2.2020-11-24

    printf '# Rabbit vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Rabbit OryCun2
SEQ2_DIR=/hive/data/genomes/oryCun2/oryCun2.2bit
SEQ2_LEN=/hive/data/genomes/oryCun2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzOryCun2.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	549m40.618s

    sed -e 's/^/    #/;' fb.mm39.chainOryCun2Link.txt
    # 668479596 bases of 2654624157 (25.182%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynOryCun2Link.txt
    # 612665047 bases of 2654624157 (23.079%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 oryCun2) > rbest.log 2>&1
    #	real	315m53.451s

    sed -e's/^/    #/;' fb.mm39.chainRBest.OryCun2.txt
    # 631190305 bases of 2654624157 (23.777%) in intersection

    mkdir /hive/data/genomes/oryCun2/bed/blastz.mm39.swap
    cd /hive/data/genomes/oryCun2/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzOryCun2.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	40m58.805s

    sed -e 's/^/    #/;' fb.oryCun2.chainMm39Link.txt
    # 668039169 bases of 2604023284 (25.654%) in intersection
    sed -e 's/^/    #/;'  fb.oryCun2.chainSynMm39Link.txt
    # 610356040 bases of 2604023284 (23.439%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       oryCun2 mm39) > rbest.log 2>&1
    #	real	308m22.599s

    sed -e 's/^/    #/;'  fb.oryCun2.chainRBest.Mm39.txt
    # 630726758 bases of 2604023284 (24.221%) in intersection

##############################################################################
# LASTZ Sheep oviAri4 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzOviAri4.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzOviAri4.2020-11-24

    printf '# Sheep vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Sheep OviAri4
SEQ2_DIR=/hive/data/genomes/oviAri4/oviAri4.2bit
SEQ2_LEN=/hive/data/genomes/oviAri4/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzOviAri4.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	558m13.976s

    sed -e 's/^/    #/;' fb.mm39.chainOviAri4Link.txt
    # 695514891 bases of 2654624157 (26.200%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynOviAri4Link.txt
    # 646653235 bases of 2654624157 (24.360%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 oviAri4) > rbest.log 2>&1
    #	real	285m33.374s

    sed -e's/^/    #/;' fb.mm39.chainRBest.OviAri4.txt
    # 657902325 bases of 2654624157 (24.783%) in intersection

    mkdir /hive/data/genomes/oviAri4/bed/blastz.mm39.swap
    cd /hive/data/genomes/oviAri4/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzOviAri4.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	40m40.419s

    sed -e 's/^/    #/;' fb.oviAri4.chainMm39Link.txt
    # 681813597 bases of 2587515673 (26.350%) in intersection
    sed -e 's/^/    #/;'  fb.oviAri4.chainSynMm39Link.txt
    # 643966161 bases of 2587515673 (24.887%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       oviAri4 mm39) > rbest.log 2>&1
    #	real	244m54.731s

    sed -e 's/^/    #/;'  fb.oviAri4.chainRBest.Mm39.txt
    # 657036323 bases of 2587515673 (25.393%) in intersection

##############################################################################
# LASTZ Hawaiian monk seal neoSch1 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzNeoSch1.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzNeoSch1.2020-11-24

    printf '# Hawaiian monk seal vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Hawaiian monk seal NeoSch1
SEQ2_DIR=/hive/data/genomes/neoSch1/neoSch1.2bit
SEQ2_LEN=/hive/data/genomes/neoSch1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzNeoSch1.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	528m58.199s

    sed -e 's/^/    #/;' fb.mm39.chainNeoSch1Link.txt
    # 829753178 bases of 2654624157 (31.257%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynNeoSch1Link.txt
    # 782537839 bases of 2654624157 (29.478%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 neoSch1) > rbest.log 2>&1
    #	real	188m16.478s

    sed -e's/^/    #/;' fb.mm39.chainRBest.NeoSch1.txt
    # 789218206 bases of 2654624157 (29.730%) in intersection

    mkdir /hive/data/genomes/neoSch1/bed/blastz.mm39.swap
    cd /hive/data/genomes/neoSch1/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzNeoSch1.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	48m21.632s

    sed -e 's/^/    #/;' fb.neoSch1.chainMm39Link.txt
    # 806278963 bases of 2347122535 (34.352%) in intersection
    sed -e 's/^/    #/;'  fb.neoSch1.chainSynMm39Link.txt
    # 776403929 bases of 2347122535 (33.079%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       neoSch1 mm39) > rbest.log 2>&1
    #	real	148m0.700s

    sed -e 's/^/    #/;'  fb.neoSch1.chainRBest.Mm39.txt
    # 788121681 bases of 2347122535 (33.578%) in intersection

##############################################################################
# LASTZ Cow bosTau9 (DONE - 2020-11-23 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzBosTau9.2020-11-23
    cd /hive/data/genomes/mm39/bed/lastzBosTau9.2020-11-23

    printf '# Cow vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Cow BosTau9
SEQ2_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit
SEQ2_LEN=/hive/data/genomes/bosTau9/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzBosTau9.2020-11-23
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	174m47.736s

    sed -e 's/^/    #/;' fb.mm39.chainBosTau9Link.txt
    # 705812203 bases of 2654624157 (26.588%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynBosTau9Link.txt
    # 659578523 bases of 2654624157 (24.846%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 bosTau9) > rbest.log 2>&1
    #	real	229m35.741s

    sed -e's/^/    #/;' fb.mm39.chainRBest.BosTau9.txt
    # 668635567 bases of 2654624157 (25.188%) in intersection

    mkdir /hive/data/genomes/bosTau9/bed/blastz.mm39.swap
    cd /hive/data/genomes/bosTau9/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzBosTau9.2020-11-23/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	40m50.213s

    sed -e 's/^/    #/;' fb.bosTau9.chainMm39Link.txt
    # 697118681 bases of 2715853792 (25.668%) in intersection
    sed -e 's/^/    #/;'  fb.bosTau9.chainSynMm39Link.txt
    # 661108066 bases of 2715853792 (24.343%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       bosTau9 mm39) > rbest.log 2>&1
    #	real	194m20.003s

    sed -e 's/^/    #/;'  fb.bosTau9.chainRBest.Mm39.txt
    # 667741402 bases of 2715853792 (24.587%) in intersection

##############################################################################
# LASTZ Hedgehog eriEur2 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzEriEur2.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzEriEur2.2020-11-24

    printf '# Hedgehog vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Hedgehog EriEur2
SEQ2_DIR=/hive/data/genomes/eriEur2/eriEur2.2bit
SEQ2_LEN=/hive/data/genomes/eriEur2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzEriEur2.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	494m20.449s

    sed -e 's/^/    #/;' fb.mm39.chainEriEur2Link.txt
    # 357042649 bases of 2654624157 (13.450%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynEriEur2Link.txt
    # 252215223 bases of 2654624157 (9.501%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 eriEur2) > rbest.log 2>&1
    #	real	289m12.956s

    sed -e's/^/    #/;' fb.mm39.chainRBest.EriEur2.txt
    # 327119175 bases of 2654624157 (12.323%) in intersection

    mkdir /hive/data/genomes/eriEur2/bed/blastz.mm39.swap
    cd /hive/data/genomes/eriEur2/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzEriEur2.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	24m29.084s

    sed -e 's/^/    #/;' fb.eriEur2.chainMm39Link.txt
    # 345274697 bases of 2333073535 (14.799%) in intersection
    sed -e 's/^/    #/;'  fb.eriEur2.chainSynMm39Link.txt
    # 251961733 bases of 2333073535 (10.800%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       eriEur2 mm39) > rbest.log 2>&1
    #	real	275m16.464s

    sed -e 's/^/    #/;'  fb.eriEur2.chainRBest.Mm39.txt
    # 327058246 bases of 2333073535 (14.018%) in intersection

##############################################################################
# LASTZ Tenrec echTel2 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzEchTel2.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzEchTel2.2020-11-24

    printf '# Tenrec vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Tenrec EchTel2
SEQ2_DIR=/hive/data/genomes/echTel2/echTel2.2bit
SEQ2_LEN=/hive/data/genomes/echTel2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzEchTel2.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    #	real	652m56.936s

    sed -e 's/^/    #/;' fb.mm39.chainEchTel2Link.txt
    # 383749102 bases of 2654624157 (14.456%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynEchTel2Link.txt
    # 296272244 bases of 2654624157 (11.161%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 echTel2) > rbest.log 2>&1
    #	real	308m56.712s

    sed -e's/^/    #/;' fb.mm39.chainRBest.EchTel2.txt
    # 353828423 bases of 2654624157 (13.329%) in intersection

    mkdir /hive/data/genomes/echTel2/bed/blastz.mm39.swap
    cd /hive/data/genomes/echTel2/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzEchTel2.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real	26m3.037s

    sed -e 's/^/    #/;' fb.echTel2.chainMm39Link.txt
    # 380081282 bases of 2605196361 (14.589%) in intersection
    sed -e 's/^/    #/;'  fb.echTel2.chainSynMm39Link.txt
    # 295227610 bases of 2605196361 (11.332%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       echTel2 mm39) > rbest.log 2>&1
    #	real	289m38.161s

    sed -e 's/^/    #/;'  fb.echTel2.chainRBest.Mm39.txt
    # 353819264 bases of 2605196361 (13.581%) in intersection

##############################################################################
# LASTZ Opossum monDom5 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzMonDom5.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzMonDom5.2020-11-24

    printf '# Opossum vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Opossum MonDom5
SEQ2_DIR=/hive/data/genomes/monDom5/monDom5.2bit
SEQ2_LEN=/hive/data/genomes/monDom5/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzMonDom5.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    #	real	393m28.801s

    sed -e 's/^/    #/;' fb.mm39.chainMonDom5Link.txt
    # 142865188 bases of 2654624157 (5.382%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynMonDom5Link.txt
    # 116528842 bases of 2654624157 (4.390%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 monDom5) > rbest.log 2>&1
    #	real	317m52.699s

    sed -e's/^/    #/;' fb.mm39.chainRBest.MonDom5.txt
    # 122836952 bases of 2654624157 (4.627%) in intersection

    mkdir /hive/data/genomes/monDom5/bed/blastz.mm39.swap
    cd /hive/data/genomes/monDom5/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzMonDom5.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1
    #	real	14m50.171s

    sed -e 's/^/    #/;' fb.monDom5.chainMm39Link.txt
    # 141605466 bases of 3501660299 (4.044%) in intersection
    sed -e 's/^/    #/;'  fb.monDom5.chainSynMm39Link.txt
    # 117256524 bases of 3501660299 (3.349%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       monDom5 mm39) > rbest.log 2>&1
    #	real	293m57.633s

    sed -e 's/^/    #/;'  fb.monDom5.chainRBest.Mm39.txt
    # 123101776 bases of 3501660299 (3.516%) in intersection

##############################################################################
# LASTZ X. tropicalis xenTro9 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzXenTro9.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzXenTro9.2020-11-24

    printf '# X. tropicalis vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: X. tropicalis XenTro9
SEQ2_DIR=/hive/data/genomes/xenTro9/xenTro9.2bit
SEQ2_LEN=/hive/data/genomes/xenTro9/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzXenTro9.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    #	real	331m42.313s

    sed -e 's/^/    #/;' fb.mm39.chainXenTro9Link.txt
    # 51383904 bases of 2654624157 (1.936%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynXenTro9Link.txt
    # 20789787 bases of 2654624157 (0.783%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 xenTro9) > rbest.log 2>&1
    #	real	140m2.922s

    sed -e's/^/    #/;' fb.mm39.chainRBest.XenTro9.txt
    # 35952894 bases of 2654624157 (1.354%) in intersection

    mkdir /hive/data/genomes/xenTro9/bed/blastz.mm39.swap
    cd /hive/data/genomes/xenTro9/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzXenTro9.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1
    #	real	8m9.270s

    sed -e 's/^/    #/;' fb.xenTro9.chainMm39Link.txt
    # 53364345 bases of 1369865365 (3.896%) in intersection
    sed -e 's/^/    #/;'  fb.xenTro9.chainSynMm39Link.txt
    # 21157884 bases of 1369865365 (1.545%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       xenTro9 mm39) > rbest.log 2>&1
    #	real	130m14.139s

    sed -e 's/^/    #/;'  fb.xenTro9.chainRBest.Mm39.txt
    # 35757239 bases of 1369865365 (2.610%) in intersection

##############################################################################
# LASTZ Chicken galGal6 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzGalGal6.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzGalGal6.2020-11-24

    printf '# Chicken vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Chicken GalGal6
SEQ2_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ2_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGalGal6.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    #	real	266m7.103s

    sed -e 's/^/    #/;' fb.mm39.chainGalGal6Link.txt
    # 67356693 bases of 2654624157 (2.537%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynGalGal6Link.txt
    # 48715227 bases of 2654624157 (1.835%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 galGal6) > rbest.log 2>&1
    #	real	66m59.502s

    sed -e's/^/    #/;' fb.mm39.chainRBest.GalGal6.txt
    # 53500116 bases of 2654624157 (2.015%) in intersection

    mkdir /hive/data/genomes/galGal6/bed/blastz.mm39.swap
    cd /hive/data/genomes/galGal6/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzGalGal6.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1
    #	real	4m26.280s

    sed -e 's/^/    #/;' fb.galGal6.chainMm39Link.txt
    # 56760804 bases of 1055588482 (5.377%) in intersection
    sed -e 's/^/    #/;'  fb.galGal6.chainSynMm39Link.txt
    # 48093000 bases of 1055588482 (4.556%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       galGal6 mm39) > rbest.log 2>&1
    #	real	45m18.947s

    sed -e 's/^/    #/;'  fb.galGal6.chainRBest.Mm39.txt
    # 53410494 bases of 1055588482 (5.060%) in intersection

##############################################################################
# LASTZ Lamprey petMar3 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzPetMar3.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzPetMar3.2020-11-24

    printf '# Lamprey vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Lamprey PetMar3
SEQ2_DIR=/hive/data/genomes/petMar3/petMar3.2bit
SEQ2_LEN=/hive/data/genomes/petMar3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzPetMar3.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    #	real	194m56.315s

    sed -e 's/^/    #/;' fb.mm39.chainPetMar3Link.txt
    # 24028824 bases of 2654624157 (0.905%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynPetMar3Link.txt
    # 726866 bases of 2654624157 (0.027%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 petMar3) > rbest.log 2>&1
    #	real	82m40.621s

    sed -e's/^/    #/;' fb.mm39.chainRBest.PetMar3.txt
    # 13736315 bases of 2654624157 (0.517%) in intersection

    mkdir /hive/data/genomes/petMar3/bed/blastz.mm39.swap
    cd /hive/data/genomes/petMar3/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzPetMar3.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1
    #	real	3m0.468s

    sed -e 's/^/    #/;' fb.petMar3.chainMm39Link.txt
    # 22633976 bases of 1043181598 (2.170%) in intersection
    sed -e 's/^/    #/;'  fb.petMar3.chainSynMm39Link.txt
    # 729652 bases of 1043181598 (0.070%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       petMar3 mm39) > rbest.log 2>&1
    #	real	75m38.286s

    sed -e 's/^/    #/;'  fb.petMar3.chainRBest.Mm39.txt
    # 13597551 bases of 1043181598 (1.303%) in intersection

##############################################################################
# LASTZ Zebrafish danRer11 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzDanRer11.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzDanRer11.2020-11-24

    printf '# Zebrafish vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Zebrafish DanRer11
SEQ2_DIR=/hive/data/genomes/danRer11/danRer11.2bit
SEQ2_LEN=/hive/data/genomes/danRer11/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzDanRer11.2020-11-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    #	real	311m5.559s

    sed -e 's/^/    #/;' fb.mm39.chainDanRer11Link.txt
    # 37601772 bases of 2654624157 (1.416%) in intersection
    sed -e 's/^/    #/;' fb.mm39.chainSynDanRer11Link.txt
    # 4901291 bases of 2654624157 (0.185%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 danRer11) > rbest.log 2>&1
    #	real	105m41.096s

    sed -e's/^/    #/;' fb.mm39.chainRBest.DanRer11.txt
    # 25140390 bases of 2654624157 (0.947%) in intersection

    mkdir /hive/data/genomes/danRer11/bed/blastz.mm39.swap
    cd /hive/data/genomes/danRer11/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzDanRer11.2020-11-24/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1
    #	real	4m19.907s

    sed -e 's/^/    #/;' fb.danRer11.chainMm39Link.txt
    # 46907638 bases of 1674677181 (2.801%) in intersection
    sed -e 's/^/    #/;'  fb.danRer11.chainSynMm39Link.txt
    # 6476709 bases of 1674677181 (0.387%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       danRer11 mm39) > rbest.log 2>&1
    #	real	96m59.148s

    sed -e 's/^/    #/;'  fb.danRer11.chainRBest.Mm39.txt
    # 25019759 bases of 1674677181 (1.494%) in intersection

##############################################################################
# LASTZ American beaver GCF_001984765.1 (DONE - 2021-01-22 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzGCF_001984765.1.2021-01-22
    cd /hive/data/genomes/mm39/bed/lastzGCF_001984765.1.2021-01-22

    printf '# GCF_001984765.1 vs mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: American beaver GCF_001984765.1
# GCF/001/984/765/GCF_001984765.1_C.can_genome_v1.0
# should be the same as casCan1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/001/984/765/GCF_001984765.1/GCF_001984765.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/001/984/765/GCF_001984765.1/GCF_001984765.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCF_001984765.1.2021-01-22
TMPDIR=/dev/shm
' > DEF

export targetDb="mm39"
export asmId="GCF_001984765.1"
export accessionId="${asmId}_C.can_genome_v1.0"
export gcPath="GCF/001/984/765"
cd /hive/data/genomes/${targetDb}/bed/lastz${asmId}.2021-01-22
time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
grep -w real do.log | sed -e 's/^/    # /;'
    # real      159m54.416s


sed -e 's/^/    # /;' fb.$targetDb.chain.${asmId}Link.txt
    # 965922133 bases of 2728222451 (35.405%) in intersection
sed -e 's/^/    # /;' fb.$targetDb.chainSyn.${asmId}Link.txt
    # 861770999 bases of 2728222451 (31.587%) in intersection

time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
-query2Bit="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.2bit" \
-querySizes="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.chrom.sizes.txt" \
$targetDb ${asmId}) >> rbest.log 2>&1
grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      308m15.730s

sed -e 's/^/    # /;' fb.$targetDb.chainRBest.$asmId.txt
    # 913563482 bases of 2728222451 (33.486%) in intersection

# real    468m10.166s total time all of above


export target="mm39"
export Target="Mm39"
export query="GCF_001984765.1"
export asmId="GCF_001984765.1_C.can_genome_v1.0"
export gcPath="GCF/001/984/765"

mkdir /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap
cd /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap

time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 -swapDir=`pwd` \
    /hive/data/genomes/${target}/bed/lastz.${query}/DEF -syntenicNet \
  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -swap -chainMinScore=3000 -chainLinearGap=medium) >> swap.log 2>&1
grep -w real swap.log | sed -e 's/^/    # /;'
    # real      70m57.610s

sed -e 's/^/    # /;' fb.${query}.chain.${Target}Link.txt
    # 1021869459 bases of 2518306565 (40.578%) in intersection
sed -e 's/^/    # /;' fb.${query}.chainSyn.${Target}Link.txt
    # 879061651 bases of 2518306565 (34.907%) in intersection

time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
-target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \
$query $target) >> rbest.log 2>&1
grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      294m45.010s

sed -e 's/^/    # /;' fb.${query}.chainRBest.${Target}.txt
    # 913513030 bases of 2518306565 (36.275%) in intersection

##############################################################################
# LASTZ lance-tailed manakin GCF_009829145.1 (DONE - 2020-11-24 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzGCF_009829145.1.2020-11-24
    cd /hive/data/genomes/mm39/bed/lastzGCF_009829145.1.2020-11-24

    printf '# GCF_009829145.1 vs mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: lance-tailed manakin GCF_009829145.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/009/829/145/GCF_009829145.1/GCF_009829145.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/009/829/145/GCF_009829145.1/GCF_009829145.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCF_009829145.1.2020-11-24
TMPDIR=/dev/shm
' > DEF

export targetDb="mm39"
export asmId="GCF_009829145.1"
export accessionId="${asmId}_bChiLan1.pri"
export gcPath="GCF/009/829/145"
cd /hive/data/genomes/${targetDb}/bed/lastz${asmId}.2020-11-24
time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
grep -w real do.log | sed -e 's/^/    # /;'
    # real      159m54.416s  missed this measurement

sed -e 's/^/    # /;' fb.$targetDb.chain.${asmId}Link.txt
    # 67418947 bases of 2728222451 (2.471%) in intersection
sed -e 's/^/    # /;' fb.$targetDb.chainSyn.${asmId}Link.txt
    # 12681011 bases of 2728222451 (0.465%) in intersection

time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
-query2Bit="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.2bit" \
-querySizes="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.chrom.sizes.txt" \
$targetDb ${asmId}) >> rbest.log 2>&1
grep -w real rbest.log | sed -e 's/^/    # /;'
    # real    323m14.591s

sed -e 's/^/    # /;' fb.$targetDb.chainRBest.$asmId.txt
    # 52282223 bases of 2728222451 (1.916%) in intersection

export target="mm39"
export Target="Mm39"
export query="GCF_009829145.1"
export asmId="GCF_009829145.1_bChiLan1.pri"
export gcPath="GCF/009/829/145"

mkdir /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap
cd /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap

time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 -swapDir=`pwd` \
    /hive/data/genomes/${target}/bed/lastz.${query}/DEF -syntenicNet \
  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -swap -chainMinScore=3000 -chainLinearGap=medium) >> swap.log 2>&1
grep -w real swap.log | sed -e 's/^/    # /;'
    # real      5m33.993s

sed -e 's/^/    # /;' fb.${query}.chain.${Target}Link.txt
    # 56730326 bases of 1089631598 (5.206%) in intersection
sed -e 's/^/    # /;' fb.${query}.chainSyn.${Target}Link.txt
    # 12678262 bases of 1089631598 (1.164%) in intersection

time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
-target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \
$query $target) >> rbest.log 2>&1
grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      288m55.058s

sed -e 's/^/    # /;' fb.${query}.chainRBest.${Target}.txt
    # 51851922 bases of 1089631598 (4.759%) in intersection

    # overall time for all swap
    # real    294m29.066s

##############################################################################
# LASTZ  Chinese hamster CHO GCF_003668045.3 (DONE - 2020-12-08 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzGCF_003668045.3.2020-12-08
    cd /hive/data/genomes/mm39/bed/lastzGCF_003668045.3.2020-12-08

    printf '# GCF_003668045.3 vs mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Chinese hamster GCF_003668045.3
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/003/668/045/GCF_003668045.3/GCF_003668045.3.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/003/668/045/GCF_003668045.3/GCF_003668045.3.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCF_003668045.3.2020-12-08
TMPDIR=/dev/shm
' > DEF

export targetDb="mm39"
export asmId="GCF_003668045.3"
export accessionId="${asmId}_CriGri-PICRH-1.0"
export gcPath="GCF/003/668/045"
cd /hive/data/genomes/${targetDb}/bed/lastz${asmId}.2020-12-08
time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
grep -w real do.log | sed -e 's/^/    # /;'
    # real      291m46.571s

sed -e 's/^/    # /;' fb.$targetDb.chain.${asmId}Link.txt
    # 1582370207 bases of 2728222451 (58.000%) in intersection

sed -e 's/^/    # /;' fb.$targetDb.chainSyn.${asmId}Link.txt
    # 1484311234 bases of 2728222451 (54.406%) in intersection

time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
-query2Bit="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.2bit" \
-querySizes="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.chrom.sizes.txt" \
$targetDb ${asmId}) >> rbest.log 2>&1
grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      821m47.400s

sed -e 's/^/    # /;' fb.$targetDb.chainRBest.$asmId.txt
    # 1455588785 bases of 2728222451 (53.353%) in intersection

### XXX haven't done this yet
export target="mm39"
export Target="Mm39"
export query="GCF_003668045.3"
export asmId="GCF_003668045.3_CriGri-PICRH-1.0"
export gcPath="GCF/003/668/045"

mkdir /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap
cd /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap

time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 -swapDir=`pwd` \
    /hive/data/genomes/${target}/bed/lastz.${query}/DEF -syntenicNet \
  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -swap -chainMinScore=3000 -chainLinearGap=medium) >> swap.log 2>&1
grep -w real swap.log | sed -e 's/^/    # /;'
    # real      70m57.610s  missed this measurement

sed -e 's/^/    # /;' fb.${query}.chain.${Target}Link.txt
    # 1557925479 bases of 2366634374 (65.829%) in intersection
sed -e 's/^/    # /;' fb.${query}.chainSyn.${Target}Link.txt
    # 1455333889 bases of 2366634374 (61.494%) in intersection

time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
-target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \
$query $target) >> rbest.log 2>&1
grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      798m57.398s

sed -e 's/^/    # /;' fb.${query}.chainRBest.${Target}.txt
    # 1456469555 bases of 2366634374 (61.542%) in intersection

##############################################################################
# LASTZ X. tropicalis xenTro10 (DONE - 2021-02-22 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzXenTro10.2021-02-22
    cd /hive/data/genomes/mm39/bed/lastzXenTro10.2021-02-22

    printf '# X. tropicalis vs Mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: X. tropicalis XenTro10
SEQ2_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit
SEQ2_LEN=/hive/data/genomes/xenTro10/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzXenTro10.2021-02-22
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    #	real    231m18.929s

    sed -e 's/^/    # /;' fb.mm39.chainXenTro10Link.txt
    # 53459877 bases of 2654624157 (2.014%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynXenTro10Link.txt
    # 22503702 bases of 2654624157 (0.848%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
           mm39 xenTro10) > rbest.log 2>&1
    #	real    188m44.842s

    sed -e's/^/    # /;' fb.mm39.chainRBest.XenTro10.txt
    # 38090013 bases of 2654624157 (1.435%) in intersection

    mkdir /hive/data/genomes/xenTro10/bed/blastz.mm39.swap
    cd /hive/data/genomes/xenTro10/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzXenTro10.2021-02-22/DEF \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1
    #	real    11m51.841s

    sed -e 's/^/    # /;' fb.xenTro10.chainMm39Link.txt
    # 69880088 bases of 1448461978 (4.824%) in intersection
    sed -e 's/^/    # /;'  fb.xenTro10.chainSynMm39Link.txt
    # 22992776 bases of 1448461978 (1.587%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       xenTro10 mm39) > rbest.log 2>&1
    #	real    189m59.538s

    sed -e 's/^/    # /;'  fb.xenTro10.chainRBest.Mm39.txt

    # 37509757 bases of 1448461978 (2.590%) in intersection

##############################################################################
# LASTZ boxer Tasha canFam6 (DONE - 2021-05-18 - Hiram)
    #	establish a screen to control this job
    mkdir /hive/data/genomes/mm39/bed/lastzCanFam6.2021-05-18
    cd /hive/data/genomes/mm39/bed/lastzCanFam6.2021-05-18

    printf '# boxer Tasha canFam6 vs mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_M=254

# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: boxer Tasha canFam6
SEQ2_DIR=/hive/data/genomes/canFam6/canFam6.2bit
SEQ2_LEN=/hive/data/genomes/canFam6/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/mm39/bed/lastzCanFam6.2021-05-18
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
	-syntenicNet \
	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
	-chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 &
    #  real    218m56.391s

    sed -e 's/^/    # /;' fb.mm39.chainCanFam6Link.txt
    # 769381640 bases of 2654624157 (28.983%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynCanFam6Link.txt
    # 727357801 bases of 2654624157 (27.400%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev mm39 canFam6 \
      -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
    #	real    227m46.230s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.CanFam6.txt
    # 732010764 bases of 2654624157 (27.575%) in intersection

    mkdir /hive/data/genomes/canFam6/bed/blastz.mm39.swap
    cd /hive/data/genomes/canFam6/bed/blastz.mm39.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/mm39/bed/lastzCanFam6.2021-05-18/DEF \
	-swap -syntenicNet \
	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 &
    #	real    45m15.626s

    sed -e 's/^/    # /;' fb.canFam6.chainMm39Link.txt
    # 749339105 bases of 2312743346 (32.400%) in intersection
    sed -e 's/^/    # /;' fb.canFam6.chainSynMm39Link.txt
    # 721148735 bases of 2312743346 (31.182%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev canFam6 mm39 \
      -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
    # real    204m49.212s

    sed -e 's/^/    # /;' fb.canFam6.chainRBest.Mm39.txt
    # 730973192 bases of 2312743346 (31.606%) in intersection

##############################################################################
# LASTZ human hg19 (DONE - 2021-09-30 - Hiram)

# should be able to run this from anywhere, this time it was run from:
    cd /hive/data/genomes/mm39/bed

  time (~/kent/src/hg/utils/automation/pairLastz.sh mm39 hg19 mammal primate) \
      > mm39.hg19.log 2>&1

    grep -w real mm39.hg19.log | tail -1 | sed -e 's/^/    # /;'
    # real    1200m57.924s

    # this command outputs this makeDoc text:

    cat lastz.hg19/makeDoc.txt

##############################################################################
# LASTZ Mouse Mm39 vs. Human Hg19 (DONE - 2021-09-30 - Hiram)
    mkdir /hive/data/genomes/mm39/bed/lastzHg19.2021-09-30
    cd /hive/data/genomes/mm39/bed/lastzHg19.2021-09-30

    printf '# Human Hg19 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse Mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: Human Hg19
SEQ2_DIR=/hive/data/genomes/hg19/hg19.2bit
SEQ2_LEN=/hive/data/genomes/hg19/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzHg19.2021-09-30
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -verbose=2 `pwd`/DEF -syntenicNet \
        -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real      474m8.118s
    #     # real        474m8.118s
    #     # real        370m29.622s
    # real      844m37.788s

    sed -e 's/^/    # /;' fb.mm39.chainHg19Link.txt
    # 938444606 bases of 2654624157 (35.351%) in intersection

    ### and for the swap

    cd /hive/data/genomes/hg19/bed/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl   -swap -verbose=2 \
      /hive/data/genomes/mm39/bed/lastzHg19.2021-09-30/DEF -swapDir=`pwd` \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
         -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real      57m17.328s

    sed -e 's/^/    # /;' fb.hg19.chainMm39Link.txt
    # 969322683 bases of 2991710746 (32.400%) in intersection
    sed -e 's/^/    # /;' fb.hg19.chainSynMm39Link.txt
    # 921405754 bases of 2991710746 (30.799%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
       hg19 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      299m2.449s

    sed -e 's/^/    # /;' fb.hg19.chainRBest.Mm39.txt
    # 892863094 bases of 2991710746 (29.845%) in intersection

##############################################################################
# LASTZ Mouse Mm39 vs. Seba's short-tailed bat GCA_004027735.1 (DONE - 2022-10-10 - Gerardo)

# should be able to run this from anywhere, this time it was run from:
    cd kent/src/hg/utils/automation

  time (~/kent/src/hg/utils/automation/pairLastz.sh \
	mm39 GCA_004027735.1_CarPer_v1_BIUU mammal mammal) \
	   > mm39.GCA_004027735.1_20221010.log 2>&1 &
  # check the total time
grep -w real  mm39.GCA_004027735.1_20221010.log  | tail -1 | sed -e 's/^/    # /;'
    # real      4941m5.588s

    # this command outputs this makeDoc text:

    cat /hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10/makeDoc.txt
##############################################################################
# LASTZ Mouse Mm39 vs. Seba's short-tailed bat GCA_004027735.1
#    (DONE - 2022-10-10 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10
    cd /hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10

    printf '# Seba's short-tailed bat GCA_004027735.1 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: Seba's short-tailed bat 2019-01-16 GCA_004027735.1_CarPer_v1_BIUU
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=500

BASE=/hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_004027735.1_CarPer_v1_BIUU -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	682m7.456s

    sed -e 's/^/    # /;' fb.mm39.chainGCA_004027735.1Link.txt
    # 646007750 bases of 2728222451 (23.679%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCA_004027735.1Link.txt
    # 266104069 bases of 2728222451 (9.754%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.chrom.sizes.txt" \
        mm39 GCA_004027735.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	514m58.090s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCA_004027735.1.txt
    # 613273332 bases of 2728222451 (22.479%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/004/027/735/GCA_004027735.1_CarPer_v1_BIUU/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_004027735.1_CarPer_v1_BIUU /hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	1925m11.716s

    sed -e 's/^/    # /;' fb.GCA_004027735.1.chainMm39Link.txt
    # 687442098 bases of 2689411905 (25.561%) in intersection
    sed -e 's/^/    # /;' fb.GCA_004027735.1.chainSynMm39Link.txt
    # 261303649 bases of 2689411905 (9.716%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.chrom.sizes.txt" \
   GCA_004027735.1 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	1818m46.969s

    sed -e 's/^/    # /;' fb.GCA_004027735.1.chainRBest.Mm39.txt
    # 614276787 bases of 2689411905 (22.841%) in intersection
##############################################################################
#  Mm39 vs. eastern European house mouse GCA_001624775.1 (DONE - 2022-10-29 - Gerardo)

  time (~/kent/src/hg/utils/automation/pairLastz.sh \
	mm39 GCA_001624775.1_PWK_PhJ_v1 mammal mammal) \
	   > mm39.GCA_001624775.1_20221029.log 2>&1 &
  # check the total time
grep -w real mm39.GCA_001624775.1_20221029.log | tail -1 | sed -e 's/^/    # /;'
    # real     1337m18.429s

    # this command outputs this makeDoc text:

    cat /hive/data/genomes/mm39/bed/lastzGCA_001624775.1.2022-10-29/makeDoc.txt
##############################################################################
# LASTZ Mouse Mm39 vs. eastern European house mouse GCA_001624775.1
#    (DONE - 2022-10-29 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCA_001624775.1.2022-10-29
    cd /hive/data/genomes/mm39/bed/lastzGCA_001624775.1.2022-10-29

    printf '# eastern European house mouse GCA_001624775.1 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: eastern European house mouse 2016-04-26 GCA_001624775.1_PWK_PhJ_v1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/001/624/775/GCA_001624775.1/GCA_001624775.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/001/624/775/GCA_001624775.1/GCA_001624775.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCA_001624775.1.2022-10-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_001624775.1_PWK_PhJ_v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	796m20.050s

    sed -e 's/^/    # /;' fb.mm39.chainGCA_001624775.1Link.txt
    # 2352701230 bases of 2728222451 (86.236%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCA_001624775.1Link.txt
    # 2250688932 bases of 2728222451 (82.497%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/001/624/775/GCA_001624775.1/GCA_001624775.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/001/624/775/GCA_001624775.1/GCA_001624775.1.chrom.sizes.txt" \
        mm39 GCA_001624775.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	140m24.553s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCA_001624775.1.txt
    # 2217435105 bases of 2728222451 (81.278%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/001/624/775/GCA_001624775.1_PWK_PhJ_v1/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_001624775.1_PWK_PhJ_v1 /hive/data/genomes/mm39/bed/lastzGCA_001624775.1.2022-10-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	272m39.311s

    sed -e 's/^/    # /;' fb.GCA_001624775.1.chainMm39Link.txt
    # 2243083403 bases of 2559987392 (87.621%) in intersection
    sed -e 's/^/    # /;' fb.GCA_001624775.1.chainSynMm39Link.txt
    # 2222161260 bases of 2559987392 (86.804%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/001/624/775/GCA_001624775.1/GCA_001624775.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/001/624/775/GCA_001624775.1/GCA_001624775.1.chrom.sizes.txt" \
   GCA_001624775.1 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	127m54.093s

    sed -e 's/^/    # /;' fb.GCA_001624775.1.chainRBest.Mm39.txt
    # 2221859352 bases of 2559987392 (86.792%) in intersection
##############################################################################
# LASTZ Mouse Mm39 vs. western European house mouse GCA_001624835.1 (DONE - 2022-10-29 - Gerardo)

  time (~/kent/src/hg/utils/automation/pairLastz.sh \
	mm39 GCA_001624835.1_WSB_EiJ_v1 mammal mammal) \
	   > mm39.GCA_001624835.1_20221029.log 2>&1 &
  # check the total time
grep -w real  mm39.GCA_001624835.1_20221029.log  | tail -1 | sed -e 's/^/    # /;'
    # real      1435m16.301s

    # this command outputs this makeDoc text:

    cat /hive/data/genomes/mm39/bed/lastzGCA_001624835.1.2022-10-29/makeDoc.txt
##############################################################################
# LASTZ Mouse Mm39 vs. western European house mouse GCA_001624835.1
#    (DONE - 2022-10-29 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCA_001624835.1.2022-10-29
    cd /hive/data/genomes/mm39/bed/lastzGCA_001624835.1.2022-10-29

    printf '# western European house mouse GCA_001624835.1 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: western European house mouse 2016-04-26 GCA_001624835.1_WSB_EiJ_v1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCA_001624835.1.2022-10-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_001624835.1_WSB_EiJ_v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	1043m35.512s

    sed -e 's/^/    # /;' fb.mm39.chainGCA_001624835.1Link.txt
    # 2340951592 bases of 2728222451 (85.805%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCA_001624835.1Link.txt
    # 2248126645 bases of 2728222451 (82.403%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.chrom.sizes.txt" \
        mm39 GCA_001624835.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	83m41.863s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCA_001624835.1.txt
    # 2216500165 bases of 2728222451 (81.243%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/001/624/835/GCA_001624835.1_WSB_EiJ_v1/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_001624835.1_WSB_EiJ_v1 /hive/data/genomes/mm39/bed/lastzGCA_001624835.1.2022-10-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	245m21.222s

    sed -e 's/^/    # /;' fb.GCA_001624835.1.chainMm39Link.txt
    # 2231272516 bases of 2689657557 (82.957%) in intersection
    sed -e 's/^/    # /;' fb.GCA_001624835.1.chainSynMm39Link.txt
    # 2222181450 bases of 2689657557 (82.619%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.chrom.sizes.txt" \
   GCA_001624835.1 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	62m37.202s

    sed -e 's/^/    # /;' fb.GCA_001624835.1.chainRBest.Mm39.txt
    # 2218790179 bases of 2689657557 (82.493%) in intersection
##############################################################################
# LASTZ Mouse Mm39 vs. southeastern Asian house mouse GCA_001624445.1
#    (DONE - 2023-04-07 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCA_001624445.1.2023-04-07
    cd /hive/data/genomes/mm39/bed/lastzGCA_001624445.1.2023-04-07

    printf '# southeastern Asian house mouse GCA_001624445.1 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: southeastern Asian house mouse 2016-04-26 GCA_001624445.1_CAST_EiJ_v1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCA_001624445.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_001624445.1_CAST_EiJ_v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	1058m44.662s

    sed -e 's/^/    # /;' fb.mm39.chainGCA_001624445.1Link.txt
    # 2329782432 bases of 2728222451 (85.396%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCA_001624445.1Link.txt
    # 2229270653 bases of 2728222451 (81.711%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.chrom.sizes.txt" \
        mm39 GCA_001624445.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	127m51.046s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCA_001624445.1.txt
    # 2199319876 bases of 2728222451 (80.614%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/001/624/445/GCA_001624445.1_CAST_EiJ_v1/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_001624445.1_CAST_EiJ_v1 /hive/data/genomes/mm39/bed/lastzGCA_001624445.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	106m53.512s

    sed -e 's/^/    # /;' fb.GCA_001624445.1.chainMm39Link.txt
    # 2223373125 bases of 2653990650 (83.775%) in intersection
    sed -e 's/^/    # /;' fb.GCA_001624445.1.chainSynMm39Link.txt
    # 2205392126 bases of 2653990650 (83.097%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.chrom.sizes.txt" \
   GCA_001624445.1 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	99m38.174s

    sed -e 's/^/    # /;' fb.GCA_001624445.1.chainRBest.Mm39.txt
    # 2202774272 bases of 2653990650 (82.999%) in intersection

real	1393m12.216s
user	0m2.744s
sys	0m1.859s
##############################################################################
# LASTZ Mouse Mm39 vs. house mouse GCA_921998555.2
#    (DONE - 2023-04-11 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCA_921998555.2.2023-04-11
    cd /hive/data/genomes/mm39/bed/lastzGCA_921998555.2.2023-04-11

    printf '# house mouse GCA_921998555.2 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: house mouse 2022-07-01 GCA_921998555.2_129S1_SvImJ_v3
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/921/998/555/GCA_921998555.2/GCA_921998555.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/921/998/555/GCA_921998555.2/GCA_921998555.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCA_921998555.2.2023-04-11
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_921998555.2_129S1_SvImJ_v3 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	1387m17.732s

    sed -e 's/^/    # /;' fb.mm39.chainGCA_921998555.2Link.txt
    # 2580206535 bases of 2728222451 (94.575%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCA_921998555.2Link.txt
    # 2517300763 bases of 2728222451 (92.269%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/921/998/555/GCA_921998555.2/GCA_921998555.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/921/998/555/GCA_921998555.2/GCA_921998555.2.chrom.sizes.txt" \
        mm39 GCA_921998555.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	80m53.604s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCA_921998555.2.txt
    # 2448910113 bases of 2728222451 (89.762%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/921/998/555/GCA_921998555.2_129S1_SvImJ_v3/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_921998555.2_129S1_SvImJ_v3 /hive/data/genomes/mm39/bed/lastzGCA_921998555.2.2023-04-11/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	140m34.982s

    sed -e 's/^/    # /;' fb.GCA_921998555.2.chainMm39Link.txt
    # 2462764705 bases of 2516264171 (97.874%) in intersection
    sed -e 's/^/    # /;' fb.GCA_921998555.2.chainSynMm39Link.txt
    # 2454637999 bases of 2516264171 (97.551%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/921/998/555/GCA_921998555.2/GCA_921998555.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/921/998/555/GCA_921998555.2/GCA_921998555.2.chrom.sizes.txt" \
   GCA_921998555.2 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	61m37.296s

    sed -e 's/^/    # /;' fb.GCA_921998555.2.chainRBest.Mm39.txt
    # 2449674283 bases of 2516264171 (97.354%) in intersection

real	1670m26.743s
user	0m2.054s
sys	0m1.924s
##############################################################################
# LASTZ Mouse Mm39 vs. chicken GCF_016699485.2
#    (DONE - 2023-05-29 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCF_016699485.2.2023-05-29
    cd /hive/data/genomes/mm39/bed/lastzGCF_016699485.2.2023-05-29

    printf '# chicken GCF_016699485.2 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: chicken 2021-01-19 GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCF_016699485.2.2023-05-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	435m53.262s

    sed -e 's/^/    # /;' fb.mm39.chainGCF_016699485.2Link.txt
    # 67189810 bases of 2728222451 (2.463%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_016699485.2Link.txt
    # 48811233 bases of 2728222451 (1.789%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt" \
        mm39 GCF_016699485.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	51m5.222s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_016699485.2.txt
    # 53298237 bases of 2728222451 (1.954%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b /hive/data/genomes/mm39/bed/lastzGCF_016699485.2.2023-05-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	4m5.058s

    sed -e 's/^/    # /;' fb.GCF_016699485.2.chainMm39Link.txt
    # 56503060 bases of 1053332251 (5.364%) in intersection
    sed -e 's/^/    # /;' fb.GCF_016699485.2.chainSynMm39Link.txt
    # 48074471 bases of 1053332251 (4.564%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt" \
   GCF_016699485.2 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	34m39.964s

    sed -e 's/^/    # /;' fb.GCF_016699485.2.chainRBest.Mm39.txt
    # 53178672 bases of 1053332251 (5.049%) in intersection

real	525m50.616s
user	0m1.738s
sys	0m2.087s
##############################################################################
# LASTZ Mouse Mm39 vs. domestic ferret GCF_011764305.1
#    (DONE - 2023-05-29 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCF_011764305.1.2023-05-29
    cd /hive/data/genomes/mm39/bed/lastzGCF_011764305.1.2023-05-29

    printf '# domestic ferret GCF_011764305.1 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: domestic ferret 2020-03-27 GCF_011764305.1_ASM1176430v1.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/011/764/305/GCF_011764305.1/GCF_011764305.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/011/764/305/GCF_011764305.1/GCF_011764305.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCF_011764305.1.2023-05-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_011764305.1_ASM1176430v1.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	852m25.289s

    sed -e 's/^/    # /;' fb.mm39.chainGCF_011764305.1Link.txt
    # 763807668 bases of 2728222451 (27.997%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_011764305.1Link.txt
    # 716560841 bases of 2728222451 (26.265%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/011/764/305/GCF_011764305.1/GCF_011764305.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/011/764/305/GCF_011764305.1/GCF_011764305.1.chrom.sizes.txt" \
        mm39 GCF_011764305.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	154m41.629s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_011764305.1.txt
    # 725906862 bases of 2728222451 (26.607%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/011/764/305/GCF_011764305.1_ASM1176430v1.1/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_011764305.1_ASM1176430v1.1 /hive/data/genomes/mm39/bed/lastzGCF_011764305.1.2023-05-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	44m36.988s

    sed -e 's/^/    # /;' fb.GCF_011764305.1.chainMm39Link.txt
    # 761141027 bases of 2577107489 (29.535%) in intersection
    sed -e 's/^/    # /;' fb.GCF_011764305.1.chainSynMm39Link.txt
    # 716305280 bases of 2577107489 (27.795%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/011/764/305/GCF_011764305.1/GCF_011764305.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/011/764/305/GCF_011764305.1/GCF_011764305.1.chrom.sizes.txt" \
   GCF_011764305.1 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	121m45.274s

    sed -e 's/^/    # /;' fb.GCF_011764305.1.chainRBest.Mm39.txt
    # 725361939 bases of 2577107489 (28.146%) in intersection

real	1173m34.419s
user	0m2.095s
sys	0m2.301s
##############################################################################
# LASTZ Mouse Mm39 vs. Sumatran orangutan GCF_028885655.1
#    (DONE - 2023-05-29 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCF_028885655.1.2023-05-29
    cd /hive/data/genomes/mm39/bed/lastzGCF_028885655.1.2023-05-29

    printf '# Sumatran orangutan GCF_028885655.1 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: Sumatran orangutan 2023-02-28 GCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_pri
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/028/885/655/GCF_028885655.1/GCF_028885655.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/028/885/655/GCF_028885655.1/GCF_028885655.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCF_028885655.1.2023-05-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_pri -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	940m23.193s

    sed -e 's/^/    # /;' fb.mm39.chainGCF_028885655.1Link.txt
    # 941283209 bases of 2728222451 (34.502%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_028885655.1Link.txt
    # 893464035 bases of 2728222451 (32.749%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/028/885/655/GCF_028885655.1/GCF_028885655.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/028/885/655/GCF_028885655.1/GCF_028885655.1.chrom.sizes.txt" \
        mm39 GCF_028885655.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	275m37.724s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_028885655.1.txt
    # 895752761 bases of 2728222451 (32.833%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/028/885/655/GCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_pri/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_pri /hive/data/genomes/mm39/bed/lastzGCF_028885655.1.2023-05-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	53m46.711s

    sed -e 's/^/    # /;' fb.GCF_028885655.1.chainMm39Link.txt
    # 970824025 bases of 3365490689 (28.846%) in intersection
    sed -e 's/^/    # /;' fb.GCF_028885655.1.chainSynMm39Link.txt
    # 905819364 bases of 3365490689 (26.915%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/028/885/655/GCF_028885655.1/GCF_028885655.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/028/885/655/GCF_028885655.1/GCF_028885655.1.chrom.sizes.txt" \
   GCF_028885655.1 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	237m40.734s

    sed -e 's/^/    # /;' fb.GCF_028885655.1.chainRBest.Mm39.txt
    # 894076603 bases of 3365490689 (26.566%) in intersection

real	1507m34.121s
user	0m2.845s
sys	0m2.181s
##############################################################################
# LASTZ chimpanzee GCF_028858775.1 vs. Mouse Mm39
#    (DONE - 2023-05-29 - Gerardo)

    mkdir /hive/data/genomes/asmHubs/allBuild/GCF/028/858/775/GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri/trackData/lastzMm39.2023-05-29
    cd /hive/data/genomes/asmHubs/allBuild/GCF/028/858/775/GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri/trackData/lastzMm39.2023-05-29

    printf '# Mouse Mm39 vs. chimpanzee GCF_028858775.1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: chimpanzee 2023-02-27 GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri
SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/028/858/775/GCF_028858775.1/GCF_028858775.1.2bit
SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/028/858/775/GCF_028858775.1/GCF_028858775.1.chrom.sizes.txt
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: Mouse  mm39
SEQ2_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ2_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/asmHubs/allBuild/GCF/028/858/775/GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri/trackData/lastzMm39.2023-05-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -tAsmId GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	960m42.867s

    sed -e 's/^/    # /;' fb.GCF_028858775.1.chainMm39Link.txt
    # 1056035654 bases of 3225356997 (32.742%) in intersection
    sed -e 's/^/    # /;' fb.GCF_028858775.1.chainSynMm39Link.txt
    # 903788000 bases of 3225356997 (28.021%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
      -target2Bit="/hive/data/genomes/asmHubs/GCF/028/858/775/GCF_028858775.1/GCF_028858775.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/028/858/775/GCF_028858775.1/GCF_028858775.1.chrom.sizes.txt" \
       \
        GCF_028858775.1 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	237m54.207s

    sed -e 's/^/    # /;' fb.GCF_028858775.1.chainRBest.Mm39.txt
    # 893978029 bases of 3225356997 (27.717%) in intersection

    ### and for the swap

    cd /hive/data/genomes/mm39/bed/blastz.GCF_028858775.1.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
  -tAsmId GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri  /hive/data/genomes/asmHubs/allBuild/GCF/028/858/775/GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri/trackData/lastzMm39.2023-05-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	60m41.085s

    sed -e 's/^/    # /;' fb.mm39.chainGCF_028858775.1Link.txt
    # 940808438 bases of 2728222451 (34.484%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_028858775.1Link.txt
    # 893120131 bases of 2728222451 (32.736%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
   -query2bit="/hive/data/genomes/asmHubs/GCF/028/858/775/GCF_028858775.1/GCF_028858775.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/028/858/775/GCF_028858775.1/GCF_028858775.1.chrom.sizes.txt" \
    \
   mm39 GCF_028858775.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	275m57.758s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_028858775.1.txt
    # 895679835 bases of 2728222451 (32.830%) in intersection

real	1535m22.222s
user	0m3.257s
sys	0m2.265s
##############################################################################
# LASTZ western lowland gorilla GCF_029281585.1 vs. Mouse Mm39
#    (DONE - 2023-05-29 - Gerardo)

    mkdir /hive/data/genomes/asmHubs/allBuild/GCF/029/281/585/GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri/trackData/lastzMm39.2023-05-29
    cd /hive/data/genomes/asmHubs/allBuild/GCF/029/281/585/GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri/trackData/lastzMm39.2023-05-29

    printf '# Mouse Mm39 vs. western lowland gorilla GCF_029281585.1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: western lowland gorilla 2023-03-20 GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri
SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.2bit
SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.chrom.sizes.txt
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: Mouse  mm39
SEQ2_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ2_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/asmHubs/allBuild/GCF/029/281/585/GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri/trackData/lastzMm39.2023-05-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -tAsmId GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	984m39.047s

    sed -e 's/^/    # /;' fb.GCF_029281585.1.chainMm39Link.txt
    # 1170286145 bases of 3600562452 (32.503%) in intersection
    sed -e 's/^/    # /;' fb.GCF_029281585.1.chainSynMm39Link.txt
    # 902054620 bases of 3600562452 (25.053%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
      -target2Bit="/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.chrom.sizes.txt" \
       \
        GCF_029281585.1 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	274m15.491s

    sed -e 's/^/    # /;' fb.GCF_029281585.1.chainRBest.Mm39.txt
    # 894069759 bases of 3600562452 (24.831%) in intersection

    ### and for the swap

    cd /hive/data/genomes/mm39/bed/blastz.GCF_029281585.1.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
  -tAsmId GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri  /hive/data/genomes/asmHubs/allBuild/GCF/029/281/585/GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri/trackData/lastzMm39.2023-05-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	62m35.300s

    sed -e 's/^/    # /;' fb.mm39.chainGCF_029281585.1Link.txt
    # 941358541 bases of 2728222451 (34.504%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_029281585.1Link.txt
    # 893311044 bases of 2728222451 (32.743%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
   -query2bit="/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.chrom.sizes.txt" \
    \
   mm39 GCF_029281585.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	285m21.078s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_029281585.1.txt
    # 895609380 bases of 2728222451 (32.828%) in intersection

real	1606m58.270s
user	0m4.597s
sys	0m2.305s
##############################################################################
# LASTZ Mouse Mm39 vs. water buffalo GCF_019923935.1
#    (DONE - 2024-01-10 - hiram)

    mkdir /hive/data/genomes/mm39/bed/lastzGCF_019923935.1.2024-01-04
    cd /hive/data/genomes/mm39/bed/lastzGCF_019923935.1.2024-01-04

    printf '# water buffalo GCF_019923935.1 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCF_019923935.1.2024-01-04
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_019923935.1_NDDB_SH_1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	53m59.287s

    sed -e 's/^/    # /;' fb.mm39.chainGCF_019923935.1Link.txt
    # 705799341 bases of 2728222451 (25.870%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_019923935.1Link.txt
    # 658049513 bases of 2728222451 (24.120%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \
        mm39 GCF_019923935.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	2m50.155s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_019923935.1.txt
    # 667871734 bases of 2728222451 (24.480%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/mm39/bed/lastzGCF_019923935.1.2024-01-04/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	48m50.148s

    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainMm39Link.txt
    # 692990771 bases of 2622460639 (26.425%) in intersection
    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainSynMm39Link.txt
    # 657252141 bases of 2622460639 (25.062%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \
   GCF_019923935.1 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	189m53.630s

    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainRBest.Mm39.txt
    # 666929206 bases of 2622460639 (25.431%) in intersection

##############################################################################
# LASTZ Mouse Mm39 vs. southeastern Asian house mouse GCA_921999005.2
#    (DONE - 2024-01-19 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCA_921999005.2.2024-01-17
    cd /hive/data/genomes/mm39/bed/lastzGCA_921999005.2.2024-01-17

    printf '# southeastern Asian house mouse GCA_921999005.2 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: southeastern Asian house mouse 2022-07-01 GCA_921999005.2_CAST_EiJ_v3
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/921/999/005/GCA_921999005.2/GCA_921999005.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/921/999/005/GCA_921999005.2/GCA_921999005.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCA_921999005.2.2024-01-17
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_921999005.2_CAST_EiJ_v3 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	1359m58.695s

    sed -e 's/^/    # /;' fb.mm39.chainGCA_921999005.2Link.txt
    # 2501251357 bases of 2728222451 (91.681%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCA_921999005.2Link.txt
    # 2431341452 bases of 2728222451 (89.118%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/921/999/005/GCA_921999005.2/GCA_921999005.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/921/999/005/GCA_921999005.2/GCA_921999005.2.chrom.sizes.txt" \
        mm39 GCA_921999005.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCA_921999005.2.txt

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/921/999/005/GCA_921999005.2_CAST_EiJ_v3/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_921999005.2_CAST_EiJ_v3 /hive/data/genomes/mm39/bed/lastzGCA_921999005.2.2024-01-17/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	140m46.400s

    sed -e 's/^/    # /;' fb.GCA_921999005.2.chainMm39Link.txt
    # 2390038015 bases of 2519863764 (94.848%) in intersection
    sed -e 's/^/    # /;' fb.GCA_921999005.2.chainSynMm39Link.txt
    # 2373697524 bases of 2519863764 (94.199%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/921/999/005/GCA_921999005.2/GCA_921999005.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/921/999/005/GCA_921999005.2/GCA_921999005.2.chrom.sizes.txt" \
   GCA_921999005.2 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m41.067s

    sed -e 's/^/    # /;' fb.GCA_921999005.2.chainRBest.Mm39.txt
    # 2365131997 bases of 2519863764 (93.860%) in intersection

real	216m31.324s
user	0m2.037s
sys	0m1.892s
##############################################################################
# LASTZ Mouse Mm39 vs. house mouse GCA_921997125.2
#    (DONE - 2024-01-19 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCA_921997125.2.2024-01-19
    cd /hive/data/genomes/mm39/bed/lastzGCA_921997125.2.2024-01-19

    printf '# house mouse GCA_921997125.2 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: house mouse 2022-07-01 GCA_921997125.2_C3H_HeJ_v3
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCA_921997125.2.2024-01-19
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_921997125.2_C3H_HeJ_v3 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	2979m32.120s

    sed -e 's/^/    # /;' fb.mm39.chainGCA_921997125.2Link.txt
    # 2579672710 bases of 2728222451 (94.555%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCA_921997125.2Link.txt
    # 2517293978 bases of 2728222451 (92.269%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.chrom.sizes.txt" \
        mm39 GCA_921997125.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m31.586s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCA_921997125.2.txt
    # 2453630589 bases of 2728222451 (89.935%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/921/997/125/GCA_921997125.2_C3H_HeJ_v3/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_921997125.2_C3H_HeJ_v3 /hive/data/genomes/mm39/bed/lastzGCA_921997125.2.2024-01-19/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	148m7.378s

    sed -e 's/^/    # /;' fb.GCA_921997125.2.chainMm39Link.txt
    # 2466008293 bases of 2532437445 (97.377%) in intersection
    sed -e 's/^/    # /;' fb.GCA_921997125.2.chainSynMm39Link.txt
    # 2459127633 bases of 2532437445 (97.105%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.chrom.sizes.txt" \
   GCA_921997125.2 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	59m10.825s

    sed -e 's/^/    # /;' fb.GCA_921997125.2.chainRBest.Mm39.txt
    # 2454104373 bases of 2532437445 (96.907%) in intersection

real	3266m26.008s
user	0m3.015s
sys	0m3.143s
##############################################################################
# LASTZ Mouse Mm39 vs. house mouse GCA_921997145.2
#    (DONE - 2024-03-26 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCA_921997145.2.2024-03-26
    cd /hive/data/genomes/mm39/bed/lastzGCA_921997145.2.2024-03-26

    printf '# house mouse GCA_921997145.2 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: house mouse 2022-07-01 GCA_921997145.2_BALB_cJ_v3
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCA_921997145.2.2024-03-26
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_921997145.2_BALB_cJ_v3 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	2547m29.086s

    sed -e 's/^/    # /;' fb.mm39.chainGCA_921997145.2Link.txt
    # 2585656877 bases of 2728222451 (94.774%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCA_921997145.2Link.txt
    # 2527529181 bases of 2728222451 (92.644%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.chrom.sizes.txt" \
        mm39 GCA_921997145.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	82m9.988s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCA_921997145.2.txt
    # 2460723628 bases of 2728222451 (90.195%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/921/997/145/GCA_921997145.2_BALB_cJ_v3/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_921997145.2_BALB_cJ_v3 /hive/data/genomes/mm39/bed/lastzGCA_921997145.2.2024-03-26/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	159m4.651s

    sed -e 's/^/    # /;' fb.GCA_921997145.2.chainMm39Link.txt
    # 2474241874 bases of 2519913072 (98.188%) in intersection
    sed -e 's/^/    # /;' fb.GCA_921997145.2.chainSynMm39Link.txt
    # 2467271087 bases of 2519913072 (97.911%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.chrom.sizes.txt" \
   GCA_921997145.2 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	63m16.206s

    sed -e 's/^/    # /;' fb.GCA_921997145.2.chainRBest.Mm39.txt
    # 2461542910 bases of 2519913072 (97.684%) in intersection

real	2852m3.826s
user	0m2.832s
sys	0m2.990s
##############################################################################

# LASTZ Mouse Mm39 vs. house mouse GCA_921999865.2
#    (DONE - 2024-06-24 - mspeir)

    mkdir /hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24
    cd /hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24

    printf '# house mouse GCA_921999865.2 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: house mouse 2022-07-01 GCA_921999865.2_C57BL_6NJ_v3
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_921999865.2_C57BL_6NJ_v3 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	836m4.496s

    sed -e 's/^/    # /;' fb.mm39.chainGCA_921999865.2Link.txt
    # 2617230462 bases of 2728222451 (95.932%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCA_921999865.2Link.txt
    # 2559197304 bases of 2728222451 (93.805%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.chrom.sizes.txt" \
        mm39 GCA_921999865.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	94m40.087s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCA_921999865.2.txt
    # 2496889698 bases of 2728222451 (91.521%) in intersection

    ### and for the swap
# swap into: /hive/data/genomes/asmHubs/allBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/blastz.mm39.swap
# running /hive/data/genomes/asmHubs/allBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/blastz.mm39.swap/runSwap.sh
+ cd /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3
+ export defaultName=GCA_921999865.2_C57BL_6NJ_v3
+ defaultName=GCA_921999865.2_C57BL_6NJ_v3
+ export asmId=GCA_921999865.2_C57BL_6NJ_v3
+ asmId=GCA_921999865.2_C57BL_6NJ_v3
+ export buildDir=/hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3
+ buildDir=/hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3
+ rm -f GCA_921999865.2_C57BL_6NJ_v3.chromAlias.txt
+ ln -s trackData/chromAlias/GCA_921999865.2_C57BL_6NJ_v3.chromAlias.txt .
+ '[' -s trackData/chromAlias/GCA_921999865.2_C57BL_6NJ_v3.chromAlias.bb ']'
+ rm -f GCA_921999865.2_C57BL_6NJ_v3.chromAlias.bb
+ ln -s trackData/chromAlias/GCA_921999865.2_C57BL_6NJ_v3.chromAlias.bb .
+ /cluster/home/mspeir/kent/src/hg/utils/automation/asmHubTrackDb.sh GCA_921999865.2_C57BL_6NJ_v3 GCA_921999865.2_C57BL_6NJ_v3 /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3
# no ensGene found
single chainNet
+ '[' 2 -ne 2 ']'
+ export asmId=GCA_921999865.2_C57BL_6NJ_v3
+ asmId=GCA_921999865.2_C57BL_6NJ_v3
+ export buildDir=/hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3
+ buildDir=/hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3
+ export hubLinks=/hive/data/genomes/asmHubs/hubLinks
+ hubLinks=/hive/data/genomes/asmHubs/hubLinks
+ export accessionId=GCA_921999865.2_C57BL_6NJ_v3
+ accessionId=GCA_921999865.2_C57BL_6NJ_v3
+ case ${asmId} in
++ echo GCA_921999865.2_C57BL_6NJ_v3
++ awk -F_ '{printf "%s_%s", $1, $2}'
+ accessionId=GCA_921999865.2
+ export scriptDir=/cluster/home/mspeir/kent/src/hg/utils/automation
+ scriptDir=/cluster/home/mspeir/kent/src/hg/utils/automation
+ mkdir -p /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi
+ mkdir -p /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/liftOver
+ export chainNetPriority=1
+ chainNetPriority=1
+ printf '# asmHubChainNetTrackDb.pl GCA_921999865.2_C57BL_6NJ_v3 /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3\n'
# asmHubChainNetTrackDb.pl GCA_921999865.2_C57BL_6NJ_v3 /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3
+ for D in '${buildDir}/trackData/lastz.*'
+ targetDb=GCA_921999865.2
++ basename /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39
+ lastzDir=lastz.mm39
++ echo lastz.mm39
++ sed -e 's/lastz.//;'
+ otherDb=mm39
+ OtherDb=Mm39
++ ls -d /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/download/GCA_921999865.2_C57BL_6NJ_v3_assembly_report.txt
+ asmReport=/hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/download/GCA_921999865.2_C57BL_6NJ_v3_assembly_report.txt
+ overChain=GCA_921999865.2.mm39.over.chain.gz
+ overToChain=GCA_921999865.2ToMm39.over.chain.gz
+ printf 'asmReport: %s\n' /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/download/GCA_921999865.2_C57BL_6NJ_v3_assembly_report.txt
asmReport: /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/download/GCA_921999865.2_C57BL_6NJ_v3_assembly_report.txt
+ '[' '!' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/download/GCA_921999865.2_C57BL_6NJ_v3_assembly_report.txt ']'
+ '[' '!' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/axtChain/chainMm39.bb ']'
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainMm39.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainMm39Link.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39Link.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39Link.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39Link.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.net.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.net.summary.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.summary.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.summary.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.liftOverNet.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.liftOverNet.summary.bb
+ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/liftOver/GCA_921999865.2ToMm39.over.chain.gz
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/axtChain/GCA_921999865.2.mm39.over.chain.gz ']'
+ ln -s ../trackData/lastz.mm39/axtChain/GCA_921999865.2.mm39.over.chain.gz /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/liftOver/GCA_921999865.2ToMm39.over.chain.gz
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/axtChain/chainMm39.bb ']'
+ ln -s ../trackData/lastz.mm39/axtChain/chainMm39.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainMm39.bb
+ ln -s ../trackData/lastz.mm39/axtChain/chainMm39Link.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainMm39Link.bb
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.net.bb ']'
+ ln -s ../trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.net.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.net.bb
+ ln -s ../trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.net.summary.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.net.summary.bb
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/axtChain/chainSynMm39.bb ']'
+ ln -s ../trackData/lastz.mm39/axtChain/chainSynMm39.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39.bb
+ ln -s ../trackData/lastz.mm39/axtChain/chainSynMm39Link.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39Link.bb
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.synNet.bb ']'
+ ln -s ../trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.synNet.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.bb
+ ln -s ../trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.synNet.summary.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.summary.bb
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/axtChain/chainRBestMm39.bb ']'
+ ln -s ../trackData/lastz.mm39/axtChain/chainRBestMm39.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39.bb
+ ln -s ../trackData/lastz.mm39/axtChain/chainRBestMm39Link.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39Link.bb
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.rbestNet.bb ']'
+ ln -s ../trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.rbestNet.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.bb
+ ln -s ../trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.rbestNet.summary.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.summary.bb
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/axtChain/chainLiftOverMm39.bb ']'
+ printf '# making chainLiftOverMm39.bb\n'
# making chainLiftOverMm39.bb
+ ln -s ../trackData/lastz.mm39/axtChain/chainLiftOverMm39.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39.bb
+ ln -s ../trackData/lastz.mm39/axtChain/chainLiftOverMm39Link.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39Link.bb
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.liftOverNet.bb ']'
++ echo mm39
++ cut -c1-2
+ otherPrefix=mm
+ '[' mm = GC ']'
++ hgsql -N -e 'select organism from dbDb where name="mm39"' hgcentraltest
+ organism=Mouse
++ hgsql -N -e 'select scientificName from dbDb where name="mm39"' hgcentraltest
+ sciName='Mus musculus'
++ hgsql -N -e 'select taxId from dbDb where name="mm39"' hgcentraltest
+ taxId=10090
++ hgsql -N -e 'select description from dbDb where name="mm39"' hgcentraltest
+ o_date='Jun. 2020 (GRCm39/mm39)'
++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl mm39 GCA_921999865.2
++ grep matrix
+ matrix='matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91'
++ echo mm39
++ cut -c1-2
+ otherPrefix=mm
+ '[' mm = GC ']'
++ hgsql -N -e 'select organism from dbDb where name="mm39"' hgcentraltest
+ organism=Mouse
++ hgsql -N -e 'select scientificName from dbDb where name="mm39"' hgcentraltest
+ sciName='Mus musculus'
++ hgsql -N -e 'select taxId from dbDb where name="mm39"' hgcentraltest
+ taxId=10090
++ hgsql -N -e 'select description from dbDb where name="mm39"' hgcentraltest
+ o_date='Jun. 2020 (GRCm39/mm39)'
++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl mm39 GCA_921999865.2
++ grep matrix
+ matrix='matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91'
++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl mm39 GCA_921999865.2
++ grep MinScore
+ minScore='chainMinScore 3000'
++ grep LinearGap
++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl mm39 GCA_921999865.2
+ linGap='chainLinearGap medium'
+ printf '##############################################################################
# mm39 - Mouse - Mus musculus - taxId: 10090
##############################################################################
'
+ printf 'track chainNetMm39
compositeTrack on
shortLabel Mouse Chain/Net
longLabel Mouse (Jun. 2020 (GRCm39/mm39)), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
group compGeno
'
+ printf 'priority 100.1
color 0,0,0
altColor 100,50,0
type bed 3
sortOrder view=+
'
+ '[' 'xmatrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91y' = xy ']'
+ printf 'matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
chainMinScore 3000
chainLinearGap medium
matrixHeader A, C, G, T
otherDb mm39
html html/GCA_921999865.2_C57BL_6NJ_v3.chainNet

'
+ printf '    track chainNetMm39Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetMm39
    spectrum on

        track chainMm39
        parent chainNetMm39Viewchain
        subGroups view=chain
        shortLabel Mouse Chain
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainMm39.bb
        linkDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainMm39Link.bb
        priority %d

' 1
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39.bb ']'
+ printf '        track chainSynMm39
        parent chainNetMm39Viewchain
        subGroups view=chain
        shortLabel Mouse synChain
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Syntenic Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39.bb
        linkDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39Link.bb
        priority %d

' 2
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39.bb ']'
+ printf '        track chainRBestMm39
        parent chainNetMm39Viewchain
        subGroups view=chain
        shortLabel Mouse rbChain
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Reciprocal Best Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39.bb
        linkDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39Link.bb
        priority %d

' 3
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39.bb ']'
+ printf '        track chainLiftOverMm39
        parent chainNetMm39Viewchain
        subGroups view=chain
        shortLabel Mouse loChain
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Lift Over Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39.bb
        linkDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39Link.bb
        priority %d

' 4
+ printf '    track mafNetMm39Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetMm39

        track netMm39
        parent mafNetMm39Viewnet
        subGroups view=net
        shortLabel Mouse net
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.net.bb
        summary bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.net.summary.bb
        speciesOrder mm39
        priority %d

' 5
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.summary.bb ']'
+ printf '        track synNetMm39
        parent mafNetMm39Viewnet
        subGroups view=net
        shortLabel Mouse synNet
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.bb
        summary bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.summary.bb
        speciesOrder mm39
        priority %d

' 6
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.summary.bb ']'
+ printf '        track rbestNetMm39
        parent mafNetMm39Viewnet
        subGroups view=net
        shortLabel Mouse rbestNet
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.bb
        summary bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.summary.bb
        speciesOrder mm39
        priority %d

' 7
+ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.liftOverNet.summary.bb ']'

##############################################################################
# LASTZ Mouse Mm39 vs. house mouse GCA_921999865.2
#    (DONE - 2024-06-24 - mspeir)

    mkdir /hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24
    cd /hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24

    printf '# house mouse GCA_921999865.2 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: house mouse 2022-07-01 GCA_921999865.2_C57BL_6NJ_v3
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_921999865.2_C57BL_6NJ_v3 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	836m4.496s

    sed -e 's/^/    # /;' fb.mm39.chainGCA_921999865.2Link.txt
    # 2617230462 bases of 2728222451 (95.932%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCA_921999865.2Link.txt
    # 2559197304 bases of 2728222451 (93.805%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.chrom.sizes.txt" \
        mm39 GCA_921999865.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	94m40.087s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCA_921999865.2.txt
    # 2496889698 bases of 2728222451 (91.521%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_921999865.2_C57BL_6NJ_v3 /hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	320m49.857s

    sed -e 's/^/    # /;' fb.GCA_921999865.2.chainMm39Link.txt
    # 2503336620 bases of 2514593528 (99.552%) in intersection
    sed -e 's/^/    # /;' fb.GCA_921999865.2.chainSynMm39Link.txt
    # 2500544042 bases of 2514593528 (99.441%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.chrom.sizes.txt" \
   GCA_921999865.2 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m13.662s

    sed -e 's/^/    # /;' fb.GCA_921999865.2.chainRBest.Mm39.txt
    # 2497498017 bases of 2514593528 (99.320%) in intersection

real	1318m52.288s
user	0m2.240s
sys	0m2.560s

##############################################################################
# LASTZ Mouse Mm39 vs. rabbit GCF_009806435.1
#    (DONE - 2024-06-28 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCF_009806435.1.2024-06-28
    cd /hive/data/genomes/mm39/bed/lastzGCF_009806435.1.2024-06-28

    printf '# rabbit GCF_009806435.1 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: rabbit 2021-02-04 GCF_009806435.1_UM_NZW_1.0
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCF_009806435.1.2024-06-28
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_009806435.1_UM_NZW_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	354m26.805s

    sed -e 's/^/    # /;' fb.mm39.chainGCF_009806435.1Link.txt
    # 668346839 bases of 2728222451 (24.498%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_009806435.1Link.txt
    # 614245411 bases of 2728222451 (22.514%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.chrom.sizes.txt" \
        mm39 GCF_009806435.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	270m13.288s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_009806435.1.txt
    # 632080850 bases of 2728222451 (23.168%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/009/806/435/GCF_009806435.1_UM_NZW_1.0/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_009806435.1_UM_NZW_1.0 /hive/data/genomes/mm39/bed/lastzGCF_009806435.1.2024-06-28/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	44m16.282s

    sed -e 's/^/    # /;' fb.GCF_009806435.1.chainMm39Link.txt
    # 700149744 bases of 2841507030 (24.640%) in intersection
    sed -e 's/^/    # /;' fb.GCF_009806435.1.chainSynMm39Link.txt
    # 622621309 bases of 2841507030 (21.912%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.chrom.sizes.txt" \
   GCF_009806435.1 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	288m41.391s

    sed -e 's/^/    # /;' fb.GCF_009806435.1.chainRBest.Mm39.txt
    # 632186963 bases of 2841507030 (22.248%) in intersection

real	957m44.686s
user	0m3.153s
sys	0m3.273s
##############################################################################

# LASTZ Mouse Mm39 vs. Ryukyu mouse GCF_900094665.2
#    (DONE - 2025-02-26 - mspeir)

    mkdir /hive/data/genomes/mm39/bed/lastzGCF_900094665.2.2025-02-26
    cd /hive/data/genomes/mm39/bed/lastzGCF_900094665.2.2025-02-26

    printf '# Ryukyu mouse GCF_900094665.2 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: Ryukyu mouse 2017-04-28 GCF_900094665.2_CAROLI_EIJ_v1.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/900/094/665/GCF_900094665.2/GCF_900094665.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/900/094/665/GCF_900094665.2/GCF_900094665.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCF_900094665.2.2025-02-26
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_900094665.2_CAROLI_EIJ_v1.1 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	2335m45.275s

    sed -e 's/^/    # /;' fb.mm39.chainGCF_900094665.2Link.txt
    # 2237789751 bases of 2728222451 (82.024%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_900094665.2Link.txt
    # 2122444979 bases of 2728222451 (77.796%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/900/094/665/GCF_900094665.2/GCF_900094665.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/900/094/665/GCF_900094665.2/GCF_900094665.2.chrom.sizes.txt" \
        mm39 GCF_900094665.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	167m27.678s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_900094665.2.txt
    # 2076006651 bases of 2728222451 (76.094%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/900/094/665/GCF_900094665.2_CAROLI_EIJ_v1.1/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_900094665.2_CAROLI_EIJ_v1.1 /hive/data/genomes/mm39/bed/lastzGCF_900094665.2.2025-02-26/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	222m31.825s

    sed -e 's/^/    # /;' fb.GCF_900094665.2.chainMm39Link.txt
    # 2110458120 bases of 2552825103 (82.671%) in intersection
    sed -e 's/^/    # /;' fb.GCF_900094665.2.chainSynMm39Link.txt
    # 2082567540 bases of 2552825103 (81.579%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/900/094/665/GCF_900094665.2/GCF_900094665.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/900/094/665/GCF_900094665.2/GCF_900094665.2.chrom.sizes.txt" \
   GCF_900094665.2 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	119m42.469s

    sed -e 's/^/    # /;' fb.GCF_900094665.2.chainRBest.Mm39.txt
    # 2078634547 bases of 2552825103 (81.425%) in intersection

real	2845m30.827s
user	0m2.303s
sys	0m1.599s
##############################################################################
# LASTZ Mouse Mm39 vs. platypus GCF_004115215.2
#    (DONE - 2025-03-29 - Gerardo)

    mkdir /hive/data/genomes/mm39/bed/lastzGCF_004115215.2.2025-03-29
    cd /hive/data/genomes/mm39/bed/lastzGCF_004115215.2.2025-03-29

    printf '# platypus GCF_004115215.2 vs. Mouse Mm39
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Mouse  mm39
SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: platypus 2020-11-06 GCF_004115215.2_mOrnAna1.pri.v4
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/mm39/bed/lastzGCF_004115215.2.2025-03-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_004115215.2_mOrnAna1.pri.v4 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	308m17.060s

    sed -e 's/^/    # /;' fb.mm39.chainGCF_004115215.2Link.txt
    # 101989173 bases of 2728222451 (3.738%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_004115215.2Link.txt
    # 24293541 bases of 2728222451 (0.890%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.chrom.sizes.txt" \
        mm39 GCF_004115215.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	389m20.997s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_004115215.2.txt
    # 83872608 bases of 2728222451 (3.074%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/004/115/215/GCF_004115215.2_mOrnAna1.pri.v4/trackData/blastz.mm39.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_004115215.2_mOrnAna1.pri.v4 /hive/data/genomes/mm39/bed/lastzGCF_004115215.2.2025-03-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	6m56.680s

    sed -e 's/^/    # /;' fb.GCF_004115215.2.chainMm39Link.txt
    # 95207479 bases of 1859281927 (5.121%) in intersection
    sed -e 's/^/    # /;' fb.GCF_004115215.2.chainSynMm39Link.txt
    # 24305943 bases of 1859281927 (1.307%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.chrom.sizes.txt" \
   GCF_004115215.2 mm39) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	323m29.354s

    sed -e 's/^/    # /;' fb.GCF_004115215.2.chainRBest.Mm39.txt
    # 83311268 bases of 1859281927 (4.481%) in intersection


real	1028m8.414s
user	0m2.230s
sys	0m1.480s
##############################################################################
