##############################################################################
# LASTZ Human Hg38 vs. human GCA_018503255.1
#    (DONE - 2023-03-29 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018503255.1.2023-03-29
    cd /hive/data/genomes/hg38/bed/lastzGCA_018503255.1.2023-03-29

    printf '# human GCA_018503255.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018503255.1_NA18906.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/503/255/GCA_018503255.1/GCA_018503255.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/503/255/GCA_018503255.1/GCA_018503255.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018503255.1.2023-03-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018503255.1_NA18906.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	150m39.450s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018503255.1Link.txt
    # 3048440296 bases of 3299210039 (92.399%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018503255.1Link.txt
    # 3044280661 bases of 3299210039 (92.273%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/503/255/GCA_018503255.1/GCA_018503255.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/503/255/GCA_018503255.1/GCA_018503255.1.chrom.sizes.txt" \
        hg38 GCA_018503255.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m12.500s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018503255.1.txt
    # 2838452762 bases of 3299210039 (86.034%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/503/255/GCA_018503255.1_NA18906.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018503255.1_NA18906.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018503255.1.2023-03-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	120m43.527s

    sed -e 's/^/    # /;' fb.GCA_018503255.1.chainHg38Link.txt
    # 2884269653 bases of 3055692855 (94.390%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018503255.1.chainSynHg38Link.txt
    # 2877890032 bases of 3055692855 (94.181%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/503/255/GCA_018503255.1/GCA_018503255.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/503/255/GCA_018503255.1/GCA_018503255.1.chrom.sizes.txt" \
   GCA_018503255.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m48.978s

    sed -e 's/^/    # /;' fb.GCA_018503255.1.chainRBest.Hg38.txt
    # 2833510609 bases of 3055692855 (92.729%) in intersection

real	420m25.386s
user	0m1.028s
sys	0m1.944s

##############################################################################
# LASTZ Human Hg38 vs. human GCA_021951015.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_021951015.1.2022-03-29
    cd /hive/data/genomes/hg38/bed/lastzGCA_021951015.1.2022-03-29

    printf '# human GCA_021951015.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2022-02-04 GCA_021951015.1_HG002.mat.cur.20211005
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/021/951/015/GCA_021951015.1/GCA_021951015.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/021/951/015/GCA_021951015.1/GCA_021951015.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_021951015.1.2022-03-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_021951015.1_HG002.mat.cur.20211005 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	683m39.622s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_021951015.1Link.txt
    # 3023153297 bases of 3272116950 (92.391%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_021951015.1Link.txt
    # 3019104161 bases of 3272116950 (92.268%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/021/951/015/GCA_021951015.1/GCA_021951015.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/021/951/015/GCA_021951015.1/GCA_021951015.1.chrom.sizes.txt" \
        hg38 GCA_021951015.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	80m40.540s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_021951015.1.txt
    # 2838656141 bases of 3272116950 (86.753%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/021/951/015/GCA_021951015.1_HG002.mat.cur.20211005/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_021951015.1_HG002.mat.cur.20211005 /hive/data/genomes/hg38/bed/lastzGCA_021951015.1.2022-03-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	133m16.011s

    sed -e 's/^/    # /;' fb.GCA_021951015.1.chainHg38Link.txt
    # 2881437844 bases of 3061735012 (94.111%) in intersection
    sed -e 's/^/    # /;' fb.GCA_021951015.1.chainSynHg38Link.txt
    # 2872962839 bases of 3061735012 (93.834%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/021/951/015/GCA_021951015.1/GCA_021951015.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/021/951/015/GCA_021951015.1/GCA_021951015.1.chrom.sizes.txt" \
   GCA_021951015.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	84m40.905s

    sed -e 's/^/    # /;' fb.GCA_021951015.1.chainRBest.Hg38.txt
    # 2836030662 bases of 3061735012 (92.628%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_021950905.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_021950905.1.2022-03-29
    cd /hive/data/genomes/hg38/bed/lastzGCA_021950905.1.2022-03-29

    printf '# human GCA_021950905.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2022-02-04 GCA_021950905.1_HG002.pat.cur.20211005
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/021/950/905/GCA_021950905.1/GCA_021950905.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/021/950/905/GCA_021950905.1/GCA_021950905.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_021950905.1.2022-03-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_021950905.1_HG002.pat.cur.20211005 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	588m18.846s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_021950905.1Link.txt
    # 2895410388 bases of 3272116950 (88.487%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_021950905.1Link.txt
    # 2889961705 bases of 3272116950 (88.321%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/021/950/905/GCA_021950905.1/GCA_021950905.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/021/950/905/GCA_021950905.1/GCA_021950905.1.chrom.sizes.txt" \
        hg38 GCA_021950905.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	77m20.514s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_021950905.1.txt
    # 2709013105 bases of 3272116950 (82.791%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/021/950/905/GCA_021950905.1_HG002.pat.cur.20211005/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_021950905.1_HG002.pat.cur.20211005 /hive/data/genomes/hg38/bed/lastzGCA_021950905.1.2022-03-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	128m39.988s

    sed -e 's/^/    # /;' fb.GCA_021950905.1.chainHg38Link.txt
    # 2752515526 bases of 2959277077 (93.013%) in intersection
    sed -e 's/^/    # /;' fb.GCA_021950905.1.chainSynHg38Link.txt
    # 2743116590 bases of 2959277077 (92.695%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/021/950/905/GCA_021950905.1/GCA_021950905.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/021/950/905/GCA_021950905.1/GCA_021950905.1.chrom.sizes.txt" \
   GCA_021950905.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m56.576s

    sed -e 's/^/    # /;' fb.GCA_021950905.1.chainRBest.Hg38.txt
    # 2708210994 bases of 2959277077 (91.516%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018506975.1
#    (DONE - 2023-04-02 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018506975.1.2023-04-02
    cd /hive/data/genomes/hg38/bed/lastzGCA_018506975.1.2023-04-02

    printf '# human GCA_018506975.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018506975.1_HG00733.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/506/975/GCA_018506975.1/GCA_018506975.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/506/975/GCA_018506975.1/GCA_018506975.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018506975.1.2023-04-02
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018506975.1_HG00733.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	200m27.588s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018506975.1Link.txt
    # 3049128877 bases of 3299210039 (92.420%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018506975.1Link.txt
    # 3044461418 bases of 3299210039 (92.278%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/506/975/GCA_018506975.1/GCA_018506975.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/506/975/GCA_018506975.1/GCA_018506975.1.chrom.sizes.txt" \
        hg38 GCA_018506975.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m37.537s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018506975.1.txt
    # 2836999770 bases of 3299210039 (85.990%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/506/975/GCA_018506975.1_HG00733.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018506975.1_HG00733.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018506975.1.2023-04-02/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	126m45.101s

    sed -e 's/^/    # /;' fb.GCA_018506975.1.chainHg38Link.txt
    # 2873379328 bases of 3026533161 (94.940%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018506975.1.chainSynHg38Link.txt
    # 2868194843 bases of 3026533161 (94.768%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/506/975/GCA_018506975.1/GCA_018506975.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/506/975/GCA_018506975.1/GCA_018506975.1.chrom.sizes.txt" \
   GCA_018506975.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m1.144s

    sed -e 's/^/    # /;' fb.GCA_018506975.1.chainRBest.Hg38.txt
    # 2836972314 bases of 3026533161 (93.737%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472765.1
#    (DONE - 2023-04-02 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472765.1.2023-04-02
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472765.1.2023-04-02

    printf '# human GCA_018472765.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472765.1_HG00735.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/765/GCA_018472765.1/GCA_018472765.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/765/GCA_018472765.1/GCA_018472765.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472765.1.2023-04-02
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472765.1_HG00735.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	209m52.286s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472765.1Link.txt
    # 3048755024 bases of 3299210039 (92.409%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472765.1Link.txt
    # 3044190998 bases of 3299210039 (92.270%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/765/GCA_018472765.1/GCA_018472765.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/765/GCA_018472765.1/GCA_018472765.1.chrom.sizes.txt" \
        hg38 GCA_018472765.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	77m28.446s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472765.1.txt
    # 2838856012 bases of 3299210039 (86.047%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/765/GCA_018472765.1_HG00735.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472765.1_HG00735.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472765.1.2023-04-02/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	126m15.652s

    sed -e 's/^/    # /;' fb.GCA_018472765.1.chainHg38Link.txt
    # 2870973013 bases of 3037795105 (94.508%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472765.1.chainSynHg38Link.txt
    # 2864846067 bases of 3037795105 (94.307%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/765/GCA_018472765.1/GCA_018472765.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/765/GCA_018472765.1/GCA_018472765.1.chrom.sizes.txt" \
   GCA_018472765.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	77m45.108s

    sed -e 's/^/    # /;' fb.GCA_018472765.1.chainRBest.Hg38.txt
    # 2836134995 bases of 3037795105 (93.362%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018506955.1
#    (DONE - 2023-04-02 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018506955.1.2023-04-02
    cd /hive/data/genomes/hg38/bed/lastzGCA_018506955.1.2023-04-02

    printf '# human GCA_018506955.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018506955.1_HG00733.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/506/955/GCA_018506955.1/GCA_018506955.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/506/955/GCA_018506955.1/GCA_018506955.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018506955.1.2023-04-02
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018506955.1_HG00733.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	201m16.524s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018506955.1Link.txt
    # 3049046848 bases of 3299210039 (92.417%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018506955.1Link.txt
    # 3045133832 bases of 3299210039 (92.299%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/506/955/GCA_018506955.1/GCA_018506955.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/506/955/GCA_018506955.1/GCA_018506955.1.chrom.sizes.txt" \
        hg38 GCA_018506955.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m46.689s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018506955.1.txt
    # 2839895561 bases of 3299210039 (86.078%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/506/955/GCA_018506955.1_HG00733.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018506955.1_HG00733.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018506955.1.2023-04-02/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	127m14.540s

    sed -e 's/^/    # /;' fb.GCA_018506955.1.chainHg38Link.txt
    # 2875810655 bases of 3042264782 (94.529%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018506955.1.chainSynHg38Link.txt
    # 2869822512 bases of 3042264782 (94.332%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/506/955/GCA_018506955.1/GCA_018506955.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/506/955/GCA_018506955.1/GCA_018506955.1.chrom.sizes.txt" \
   GCA_018506955.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m3.234s

    sed -e 's/^/    # /;' fb.GCA_018506955.1.chainRBest.Hg38.txt
    # 2839456755 bases of 3042264782 (93.334%) in intersection

real	482m24.334s
user	0m2.606s
sys	0m1.701s
##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472715.1
#    (DONE - 2023-04-02 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472715.1.2023-04-02
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472715.1.2023-04-02

    printf '# human GCA_018472715.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472715.1_HG00735.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/715/GCA_018472715.1/GCA_018472715.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/715/GCA_018472715.1/GCA_018472715.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472715.1.2023-04-02
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472715.1_HG00735.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	204m26.710s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472715.1Link.txt
    # 3049832328 bases of 3299210039 (92.441%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472715.1Link.txt
    # 3045548758 bases of 3299210039 (92.311%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/715/GCA_018472715.1/GCA_018472715.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/715/GCA_018472715.1/GCA_018472715.1.chrom.sizes.txt" \
        hg38 GCA_018472715.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m11.079s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472715.1.txt
    # 2838794506 bases of 3299210039 (86.045%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/715/GCA_018472715.1_HG00735.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472715.1_HG00735.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472715.1.2023-04-02/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	126m58.305s

    sed -e 's/^/    # /;' fb.GCA_018472715.1.chainHg38Link.txt
    # 2870517837 bases of 3033541617 (94.626%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472715.1.chainSynHg38Link.txt
    # 2864517688 bases of 3033541617 (94.428%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/715/GCA_018472715.1/GCA_018472715.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/715/GCA_018472715.1/GCA_018472715.1.chrom.sizes.txt" \
   GCA_018472715.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m29.627s

    sed -e 's/^/    # /;' fb.GCA_018472715.1.chainRBest.Hg38.txt
    # 2835565639 bases of 3033541617 (93.474%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018471095.1
#    (DONE - 2023-04-02 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471095.1.2023-04-02
    cd /hive/data/genomes/hg38/bed/lastzGCA_018471095.1.2023-04-02

    printf '# human GCA_018471095.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018471095.1_HG00741.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/095/GCA_018471095.1/GCA_018471095.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/095/GCA_018471095.1/GCA_018471095.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471095.1.2023-04-02
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018471095.1_HG00741.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	175m18.932s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018471095.1Link.txt
    # 3048859071 bases of 3299210039 (92.412%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018471095.1Link.txt
    # 3044347720 bases of 3299210039 (92.275%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/095/GCA_018471095.1/GCA_018471095.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/471/095/GCA_018471095.1/GCA_018471095.1.chrom.sizes.txt" \
        hg38 GCA_018471095.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	73m55.452s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018471095.1.txt
    # 2837688913 bases of 3299210039 (86.011%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/095/GCA_018471095.1_HG00741.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018471095.1_HG00741.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471095.1.2023-04-02/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	128m25.672s

    sed -e 's/^/    # /;' fb.GCA_018471095.1.chainHg38Link.txt
    # 2872162291 bases of 3036701854 (94.582%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018471095.1.chainSynHg38Link.txt
    # 2865992480 bases of 3036701854 (94.378%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/095/GCA_018471095.1/GCA_018471095.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/095/GCA_018471095.1/GCA_018471095.1.chrom.sizes.txt" \
   GCA_018471095.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	81m7.797s

    sed -e 's/^/    # /;' fb.GCA_018471095.1.chainRBest.Hg38.txt
    # 2835910744 bases of 3036701854 (93.388%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472685.1
#    (DONE - 2023-04-02 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472685.1.2023-04-02
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472685.1.2023-04-02

    printf '# human GCA_018472685.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472685.1_HG01071.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/685/GCA_018472685.1/GCA_018472685.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/685/GCA_018472685.1/GCA_018472685.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472685.1.2023-04-02
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472685.1_HG01071.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	183m14.390s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472685.1Link.txt
    # 3047519463 bases of 3299210039 (92.371%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472685.1Link.txt
    # 3043196829 bases of 3299210039 (92.240%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/685/GCA_018472685.1/GCA_018472685.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/685/GCA_018472685.1/GCA_018472685.1.chrom.sizes.txt" \
        hg38 GCA_018472685.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m34.874s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472685.1.txt
    # 2836768261 bases of 3299210039 (85.983%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/685/GCA_018472685.1_HG01071.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472685.1_HG01071.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472685.1.2023-04-02/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	130m36.307s

    sed -e 's/^/    # /;' fb.GCA_018472685.1.chainHg38Link.txt
    # 2868617976 bases of 3012710110 (95.217%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472685.1.chainSynHg38Link.txt
    # 2862952792 bases of 3012710110 (95.029%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/685/GCA_018472685.1/GCA_018472685.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/685/GCA_018472685.1/GCA_018472685.1.chrom.sizes.txt" \
   GCA_018472685.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	80m25.524s

    sed -e 's/^/    # /;' fb.GCA_018472685.1.chainRBest.Hg38.txt
    # 2833591390 bases of 3012710110 (94.055%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018471105.1
#    (DONE - 2023-04-02 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471105.1.2023-04-02
    cd /hive/data/genomes/hg38/bed/lastzGCA_018471105.1.2023-04-02

    printf '# human GCA_018471105.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018471105.1_HG00741.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/105/GCA_018471105.1/GCA_018471105.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/105/GCA_018471105.1/GCA_018471105.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471105.1.2023-04-02
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018471105.1_HG00741.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	182m2.727s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018471105.1Link.txt
    # 3047619516 bases of 3299210039 (92.374%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018471105.1Link.txt
    # 3043638122 bases of 3299210039 (92.254%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/105/GCA_018471105.1/GCA_018471105.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/471/105/GCA_018471105.1/GCA_018471105.1.chrom.sizes.txt" \
        hg38 GCA_018471105.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m1.197s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018471105.1.txt
    # 2837413728 bases of 3299210039 (86.003%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/105/GCA_018471105.1_HG00741.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018471105.1_HG00741.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471105.1.2023-04-02/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	132m1.463s

    sed -e 's/^/    # /;' fb.GCA_018471105.1.chainHg38Link.txt
    # 2869710420 bases of 3029878036 (94.714%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018471105.1.chainSynHg38Link.txt
    # 2864242851 bases of 3029878036 (94.533%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/105/GCA_018471105.1/GCA_018471105.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/105/GCA_018471105.1/GCA_018471105.1.chrom.sizes.txt" \
   GCA_018471105.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	81m3.458s

    sed -e 's/^/    # /;' fb.GCA_018471105.1.chainRBest.Hg38.txt
    # 2835965394 bases of 3029878036 (93.600%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472725.1
#    (DONE - 2023-04-03 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472725.1.2023-04-03
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472725.1.2023-04-03

    printf '# human GCA_018472725.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472725.1_HG01071.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/725/GCA_018472725.1/GCA_018472725.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/725/GCA_018472725.1/GCA_018472725.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472725.1.2023-04-03
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472725.1_HG01071.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	160m24.666s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472725.1Link.txt
    # 3048680762 bases of 3299210039 (92.406%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472725.1Link.txt
    # 3044321333 bases of 3299210039 (92.274%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/725/GCA_018472725.1/GCA_018472725.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/725/GCA_018472725.1/GCA_018472725.1.chrom.sizes.txt" \
        hg38 GCA_018472725.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	77m30.892s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472725.1.txt
    # 2837612037 bases of 3299210039 (86.009%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/725/GCA_018472725.1_HG01071.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472725.1_HG01071.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472725.1.2023-04-03/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	131m40.602s

    sed -e 's/^/    # /;' fb.GCA_018472725.1.chainHg38Link.txt
    # 2872704373 bases of 3057222025 (93.965%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472725.1.chainSynHg38Link.txt
    # 2866971315 bases of 3057222025 (93.777%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/725/GCA_018472725.1/GCA_018472725.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/725/GCA_018472725.1/GCA_018472725.1.chrom.sizes.txt" \
   GCA_018472725.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	81m9.750s

    sed -e 's/^/    # /;' fb.GCA_018472725.1.chainRBest.Hg38.txt
    # 2835295801 bases of 3057222025 (92.741%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018471345.1
#    (DONE - 2023-04-03 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471345.1.2023-04-03
    cd /hive/data/genomes/hg38/bed/lastzGCA_018471345.1.2023-04-03

    printf '# human GCA_018471345.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018471345.1_HG01106.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/345/GCA_018471345.1/GCA_018471345.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/345/GCA_018471345.1/GCA_018471345.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471345.1.2023-04-03
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018471345.1_HG01106.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	163m27.915s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018471345.1Link.txt
    # 3052479767 bases of 3299210039 (92.522%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018471345.1Link.txt
    # 3047870251 bases of 3299210039 (92.382%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/345/GCA_018471345.1/GCA_018471345.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/471/345/GCA_018471345.1/GCA_018471345.1.chrom.sizes.txt" \
        hg38 GCA_018471345.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m56.306s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018471345.1.txt
    # 2839586059 bases of 3299210039 (86.069%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/345/GCA_018471345.1_HG01106.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018471345.1_HG01106.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471345.1.2023-04-03/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	136m8.430s

    sed -e 's/^/    # /;' fb.GCA_018471345.1.chainHg38Link.txt
    # 2870939240 bases of 3035845582 (94.568%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018471345.1.chainSynHg38Link.txt
    # 2864604476 bases of 3035845582 (94.359%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/345/GCA_018471345.1/GCA_018471345.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/345/GCA_018471345.1/GCA_018471345.1.chrom.sizes.txt" \
   GCA_018471345.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	81m1.908s

    sed -e 's/^/    # /;' fb.GCA_018471345.1.chainRBest.Hg38.txt
    # 2838573475 bases of 3035845582 (93.502%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472605.1
#    (DONE - 2023-04-03 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472605.1.2023-04-03
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472605.1.2023-04-03

    printf '# human GCA_018472605.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472605.1_HG00621.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/605/GCA_018472605.1/GCA_018472605.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/605/GCA_018472605.1/GCA_018472605.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472605.1.2023-04-03
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472605.1_HG00621.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	189m7.217s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472605.1Link.txt
    # 3048862121 bases of 3299210039 (92.412%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472605.1Link.txt
    # 3044640548 bases of 3299210039 (92.284%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/605/GCA_018472605.1/GCA_018472605.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/605/GCA_018472605.1/GCA_018472605.1.chrom.sizes.txt" \
        hg38 GCA_018472605.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m0.667s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472605.1.txt
    # 2836238209 bases of 3299210039 (85.967%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/605/GCA_018472605.1_HG00621.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472605.1_HG00621.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472605.1.2023-04-03/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	136m8.411s

    sed -e 's/^/    # /;' fb.GCA_018472605.1.chainHg38Link.txt
    # 2864962762 bases of 3023026071 (94.771%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472605.1.chainSynHg38Link.txt
    # 2859512924 bases of 3023026071 (94.591%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/605/GCA_018472605.1/GCA_018472605.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/605/GCA_018472605.1/GCA_018472605.1.chrom.sizes.txt" \
   GCA_018472605.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	82m40.326s

    sed -e 's/^/    # /;' fb.GCA_018472605.1.chainRBest.Hg38.txt
    # 2834151666 bases of 3023026071 (93.752%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018471515.1
#    (DONE - 2023-04-03 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471515.1.2023-04-03
    cd /hive/data/genomes/hg38/bed/lastzGCA_018471515.1.2023-04-03

    printf '# human GCA_018471515.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018471515.1_HG00438.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/515/GCA_018471515.1/GCA_018471515.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/515/GCA_018471515.1/GCA_018471515.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471515.1.2023-04-03
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018471515.1_HG00438.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	197m39.931s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018471515.1Link.txt
    # 3048509903 bases of 3299210039 (92.401%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018471515.1Link.txt
    # 3044275459 bases of 3299210039 (92.273%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/515/GCA_018471515.1/GCA_018471515.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/471/515/GCA_018471515.1/GCA_018471515.1.chrom.sizes.txt" \
        hg38 GCA_018471515.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m24.518s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018471515.1.txt
    # 2837640885 bases of 3299210039 (86.010%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/515/GCA_018471515.1_HG00438.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018471515.1_HG00438.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471515.1.2023-04-03/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	136m4.523s

    sed -e 's/^/    # /;' fb.GCA_018471515.1.chainHg38Link.txt
    # 2870944460 bases of 3035735720 (94.572%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018471515.1.chainSynHg38Link.txt
    # 2865099920 bases of 3035735720 (94.379%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/515/GCA_018471515.1/GCA_018471515.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/515/GCA_018471515.1/GCA_018471515.1.chrom.sizes.txt" \
   GCA_018471515.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	82m16.558s

    sed -e 's/^/    # /;' fb.GCA_018471515.1.chainRBest.Hg38.txt
    # 2835732395 bases of 3035735720 (93.412%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472595.1
#    (DONE - 2023-04-03 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472595.1.2023-04-03
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472595.1.2023-04-03

    printf '# human GCA_018472595.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472595.1_HG00438.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/595/GCA_018472595.1/GCA_018472595.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/595/GCA_018472595.1/GCA_018472595.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472595.1.2023-04-03
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472595.1_HG00438.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	196m7.811s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472595.1Link.txt
    # 3048581733 bases of 3299210039 (92.403%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472595.1Link.txt
    # 3044528695 bases of 3299210039 (92.281%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/595/GCA_018472595.1/GCA_018472595.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/595/GCA_018472595.1/GCA_018472595.1.chrom.sizes.txt" \
        hg38 GCA_018472595.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m33.317s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472595.1.txt
    # 2840594342 bases of 3299210039 (86.099%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/595/GCA_018472595.1_HG00438.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472595.1_HG00438.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472595.1.2023-04-03/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	137m31.327s

    sed -e 's/^/    # /;' fb.GCA_018472595.1.chainHg38Link.txt
    # 2871502587 bases of 3025118465 (94.922%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472595.1.chainSynHg38Link.txt
    # 2865278629 bases of 3025118465 (94.716%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/595/GCA_018472595.1/GCA_018472595.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/595/GCA_018472595.1/GCA_018472595.1.chrom.sizes.txt" \
   GCA_018472595.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	82m56.603s

    sed -e 's/^/    # /;' fb.GCA_018472595.1.chainRBest.Hg38.txt
    # 2836658931 bases of 3025118465 (93.770%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472575.1
#    (DONE - 2023-04-03 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472575.1.2023-04-03
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472575.1.2023-04-03

    printf '# human GCA_018472575.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472575.1_HG00621.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/575/GCA_018472575.1/GCA_018472575.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/575/GCA_018472575.1/GCA_018472575.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472575.1.2023-04-03
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472575.1_HG00621.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	176m47.456s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472575.1Link.txt
    # 2920833052 bases of 3299210039 (88.531%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472575.1Link.txt
    # 2916328121 bases of 3299210039 (88.395%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/575/GCA_018472575.1/GCA_018472575.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/575/GCA_018472575.1/GCA_018472575.1.chrom.sizes.txt" \
        hg38 GCA_018472575.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m25.435s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472575.1.txt
    # 2710256427 bases of 3299210039 (82.149%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/575/GCA_018472575.1_HG00621.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472575.1_HG00621.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472575.1.2023-04-03/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	125m33.570s

    sed -e 's/^/    # /;' fb.GCA_018472575.1.chainHg38Link.txt
    # 2739127249 bases of 2905948993 (94.259%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472575.1.chainSynHg38Link.txt
    # 2733323310 bases of 2905948993 (94.060%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/575/GCA_018472575.1/GCA_018472575.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/575/GCA_018472575.1/GCA_018472575.1.chrom.sizes.txt" \
   GCA_018472575.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m16.094s

    sed -e 's/^/    # /;' fb.GCA_018472575.1.chainRBest.Hg38.txt
    # 2709554231 bases of 2905948993 (93.242%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472585.1
#    (DONE - 2023-04-03 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472585.1.2023-04-03
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472585.1.2023-04-03

    printf '# human GCA_018472585.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472585.1_HG00673.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/585/GCA_018472585.1/GCA_018472585.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/585/GCA_018472585.1/GCA_018472585.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472585.1.2023-04-03
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472585.1_HG00673.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	181m4.915s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472585.1Link.txt
    # 2919592068 bases of 3299210039 (88.494%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472585.1Link.txt
    # 2914421362 bases of 3299210039 (88.337%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/585/GCA_018472585.1/GCA_018472585.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/585/GCA_018472585.1/GCA_018472585.1.chrom.sizes.txt" \
        hg38 GCA_018472585.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	74m31.767s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472585.1.txt
    # 2707836905 bases of 3299210039 (82.075%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/585/GCA_018472585.1_HG00673.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472585.1_HG00673.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472585.1.2023-04-03/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	126m45.526s

    sed -e 's/^/    # /;' fb.GCA_018472585.1.chainHg38Link.txt
    # 2741986527 bases of 2925716157 (93.720%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472585.1.chainSynHg38Link.txt
    # 2736302463 bases of 2925716157 (93.526%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/585/GCA_018472585.1/GCA_018472585.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/585/GCA_018472585.1/GCA_018472585.1.chrom.sizes.txt" \
   GCA_018472585.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	73m6.616s

    sed -e 's/^/    # /;' fb.GCA_018472585.1.chainRBest.Hg38.txt
    # 2707556807 bases of 2925716157 (92.543%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472565.1
#    (DONE - 2023-04-03 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472565.1.2023-04-03
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472565.1.2023-04-03

    printf '# human GCA_018472565.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472565.1_HG00673.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/565/GCA_018472565.1/GCA_018472565.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/565/GCA_018472565.1/GCA_018472565.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472565.1.2023-04-03
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472565.1_HG00673.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	193m23.535s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472565.1Link.txt
    # 3048046135 bases of 3299210039 (92.387%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472565.1Link.txt
    # 3043672595 bases of 3299210039 (92.255%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/565/GCA_018472565.1/GCA_018472565.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/565/GCA_018472565.1/GCA_018472565.1.chrom.sizes.txt" \
        hg38 GCA_018472565.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	77m57.561s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472565.1.txt
    # 2839459324 bases of 3299210039 (86.065%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/565/GCA_018472565.1_HG00673.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472565.1_HG00673.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472565.1.2023-04-03/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	135m7.995s

    sed -e 's/^/    # /;' fb.GCA_018472565.1.chainHg38Link.txt
    # 2875683503 bases of 3053585067 (94.174%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472565.1.chainSynHg38Link.txt
    # 2869784047 bases of 3053585067 (93.981%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/565/GCA_018472565.1/GCA_018472565.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/565/GCA_018472565.1/GCA_018472565.1.chrom.sizes.txt" \
   GCA_018472565.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m55.124s

    sed -e 's/^/    # /;' fb.GCA_018472565.1.chainRBest.Hg38.txt
    # 2835964470 bases of 3053585067 (92.873%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018504645.1
#    (DONE - 2023-04-04 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018504645.1.2023-04-04
    cd /hive/data/genomes/hg38/bed/lastzGCA_018504645.1.2023-04-04

    printf '# human GCA_018504645.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018504645.1_HG01109.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/504/645/GCA_018504645.1/GCA_018504645.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/504/645/GCA_018504645.1/GCA_018504645.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018504645.1.2023-04-04
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018504645.1_HG01109.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	203m4.556s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018504645.1Link.txt
    # 2920217350 bases of 3299210039 (88.513%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018504645.1Link.txt
    # 2915634332 bases of 3299210039 (88.374%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/504/645/GCA_018504645.1/GCA_018504645.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/504/645/GCA_018504645.1/GCA_018504645.1.chrom.sizes.txt" \
        hg38 GCA_018504645.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	81m18.405s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018504645.1.txt
    # 2712395314 bases of 3299210039 (82.213%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/504/645/GCA_018504645.1_HG01109.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018504645.1_HG01109.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018504645.1.2023-04-04/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	130m58.222s

    sed -e 's/^/    # /;' fb.GCA_018504645.1.chainHg38Link.txt
    # 2747539796 bases of 2921876128 (94.033%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018504645.1.chainSynHg38Link.txt
    # 2742166983 bases of 2921876128 (93.850%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/504/645/GCA_018504645.1/GCA_018504645.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/504/645/GCA_018504645.1/GCA_018504645.1.chrom.sizes.txt" \
   GCA_018504645.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m24.687s

    sed -e 's/^/    # /;' fb.GCA_018504645.1.chainRBest.Hg38.txt
    # 2711590537 bases of 2921876128 (92.803%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018471075.1
#    (DONE - 2023-04-04 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471075.1.2023-04-04
    cd /hive/data/genomes/hg38/bed/lastzGCA_018471075.1.2023-04-04

    printf '# human GCA_018471075.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018471075.1_HG01106.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/075/GCA_018471075.1/GCA_018471075.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/075/GCA_018471075.1/GCA_018471075.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471075.1.2023-04-04
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018471075.1_HG01106.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	209m12.834s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018471075.1Link.txt
    # 2920665557 bases of 3299210039 (88.526%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018471075.1Link.txt
    # 2915808493 bases of 3299210039 (88.379%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/075/GCA_018471075.1/GCA_018471075.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/471/075/GCA_018471075.1/GCA_018471075.1.chrom.sizes.txt" \
        hg38 GCA_018471075.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m53.525s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018471075.1.txt
    # 2711607125 bases of 3299210039 (82.190%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/075/GCA_018471075.1_HG01106.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018471075.1_HG01106.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471075.1.2023-04-04/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	132m43.054s

    sed -e 's/^/    # /;' fb.GCA_018471075.1.chainHg38Link.txt
    # 2744444887 bases of 2927007346 (93.763%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018471075.1.chainSynHg38Link.txt
    # 2738739772 bases of 2927007346 (93.568%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/075/GCA_018471075.1/GCA_018471075.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/075/GCA_018471075.1/GCA_018471075.1.chrom.sizes.txt" \
   GCA_018471075.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m15.192s

    sed -e 's/^/    # /;' fb.GCA_018471075.1.chainRBest.Hg38.txt
    # 2710147089 bases of 2927007346 (92.591%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018471065.1
#    (DONE - 2023-04-04 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471065.1.2023-04-04
    cd /hive/data/genomes/hg38/bed/lastzGCA_018471065.1.2023-04-04

    printf '# human GCA_018471065.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018471065.1_HG01175.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/065/GCA_018471065.1/GCA_018471065.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/065/GCA_018471065.1/GCA_018471065.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471065.1.2023-04-04
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018471065.1_HG01175.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	166m0.387s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018471065.1Link.txt
    # 3047883175 bases of 3299210039 (92.382%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018471065.1Link.txt
    # 3043689722 bases of 3299210039 (92.255%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/065/GCA_018471065.1/GCA_018471065.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/471/065/GCA_018471065.1/GCA_018471065.1.chrom.sizes.txt" \
        hg38 GCA_018471065.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m45.945s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018471065.1.txt
    # 2837540130 bases of 3299210039 (86.007%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/065/GCA_018471065.1_HG01175.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018471065.1_HG01175.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471065.1.2023-04-04/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	115m9.563s

    sed -e 's/^/    # /;' fb.GCA_018471065.1.chainHg38Link.txt
    # 2867069552 bases of 3030026811 (94.622%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018471065.1.chainSynHg38Link.txt
    # 2861422546 bases of 3030026811 (94.436%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/065/GCA_018471065.1/GCA_018471065.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/065/GCA_018471065.1/GCA_018471065.1.chrom.sizes.txt" \
   GCA_018471065.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m34.161s

    sed -e 's/^/    # /;' fb.GCA_018471065.1.chainRBest.Hg38.txt
    # 2835565461 bases of 3030026811 (93.582%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018504045.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018504045.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018504045.1.2023-04-05

    printf '# human GCA_018504045.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018504045.1_HG01243.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/504/045/GCA_018504045.1/GCA_018504045.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/504/045/GCA_018504045.1/GCA_018504045.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018504045.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018504045.1_HG01243.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	150m59.122s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018504045.1Link.txt
    # 2919254671 bases of 3299210039 (88.483%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018504045.1Link.txt
    # 2913695572 bases of 3299210039 (88.315%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/504/045/GCA_018504045.1/GCA_018504045.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/504/045/GCA_018504045.1/GCA_018504045.1.chrom.sizes.txt" \
        hg38 GCA_018504045.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	72m53.423s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018504045.1.txt
    # 2709479193 bases of 3299210039 (82.125%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/504/045/GCA_018504045.1_HG01243.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018504045.1_HG01243.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018504045.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	119m46.883s

    sed -e 's/^/    # /;' fb.GCA_018504045.1.chainHg38Link.txt
    # 2743073817 bases of 2908728425 (94.305%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018504045.1.chainSynHg38Link.txt
    # 2737254676 bases of 2908728425 (94.105%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/504/045/GCA_018504045.1/GCA_018504045.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/504/045/GCA_018504045.1/GCA_018504045.1.chrom.sizes.txt" \
   GCA_018504045.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	72m42.690s

    sed -e 's/^/    # /;' fb.GCA_018504045.1.chainRBest.Hg38.txt
    # 2706781589 bases of 2908728425 (93.057%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469405.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469405.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469405.1.2023-04-05

    printf '# human GCA_018469405.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469405.1_HG01258.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/405/GCA_018469405.1/GCA_018469405.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/405/GCA_018469405.1/GCA_018469405.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469405.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469405.1_HG01258.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	156m49.282s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469405.1Link.txt
    # 3049729340 bases of 3299210039 (92.438%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469405.1Link.txt
    # 3045207974 bases of 3299210039 (92.301%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/405/GCA_018469405.1/GCA_018469405.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/405/GCA_018469405.1/GCA_018469405.1.chrom.sizes.txt" \
        hg38 GCA_018469405.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m50.802s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469405.1.txt
    # 2836720842 bases of 3299210039 (85.982%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/405/GCA_018469405.1_HG01258.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469405.1_HG01258.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469405.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	126m38.759s

    sed -e 's/^/    # /;' fb.GCA_018469405.1.chainHg38Link.txt
    # 2873269175 bases of 3032420282 (94.752%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469405.1.chainSynHg38Link.txt
    # 2867398349 bases of 3032420282 (94.558%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/405/GCA_018469405.1/GCA_018469405.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/405/GCA_018469405.1/GCA_018469405.1.chrom.sizes.txt" \
   GCA_018469405.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m41.856s

    sed -e 's/^/    # /;' fb.GCA_018469405.1.chainRBest.Hg38.txt
    # 2835173854 bases of 3032420282 (93.495%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469675.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469675.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469675.1.2023-04-05

    printf '# human GCA_018469675.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469675.1_HG01258.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/675/GCA_018469675.1/GCA_018469675.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/675/GCA_018469675.1/GCA_018469675.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469675.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469675.1_HG01258.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	162m37.126s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469675.1Link.txt
    # 2920623841 bases of 3299210039 (88.525%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469675.1Link.txt
    # 2915334531 bases of 3299210039 (88.365%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/675/GCA_018469675.1/GCA_018469675.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/675/GCA_018469675.1/GCA_018469675.1.chrom.sizes.txt" \
        hg38 GCA_018469675.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m17.382s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469675.1.txt
    # 2711692640 bases of 3299210039 (82.192%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/675/GCA_018469675.1_HG01258.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469675.1_HG01258.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469675.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	119m29.520s

    sed -e 's/^/    # /;' fb.GCA_018469675.1.chainHg38Link.txt
    # 2742067216 bases of 2915178237 (94.062%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469675.1.chainSynHg38Link.txt
    # 2736192130 bases of 2915178237 (93.860%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/675/GCA_018469675.1/GCA_018469675.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/675/GCA_018469675.1/GCA_018469675.1.chrom.sizes.txt" \
   GCA_018469675.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	72m13.307s

    sed -e 's/^/    # /;' fb.GCA_018469675.1.chainRBest.Hg38.txt
    # 2708251212 bases of 2915178237 (92.902%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469685.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469685.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469685.1.2023-04-05

    printf '# human GCA_018469685.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469685.1_HG01361.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/685/GCA_018469685.1/GCA_018469685.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/685/GCA_018469685.1/GCA_018469685.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469685.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469685.1_HG01361.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	171m14.537s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469685.1Link.txt
    # 3048195466 bases of 3299210039 (92.392%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469685.1Link.txt
    # 3043159939 bases of 3299210039 (92.239%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/685/GCA_018469685.1/GCA_018469685.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/685/GCA_018469685.1/GCA_018469685.1.chrom.sizes.txt" \
        hg38 GCA_018469685.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	73m22.770s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469685.1.txt
    # 2833943818 bases of 3299210039 (85.898%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/685/GCA_018469685.1_HG01361.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469685.1_HG01361.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469685.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	123m21.537s

    sed -e 's/^/    # /;' fb.GCA_018469685.1.chainHg38Link.txt
    # 2863544355 bases of 3025313608 (94.653%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469685.1.chainSynHg38Link.txt
    # 2858105884 bases of 3025313608 (94.473%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/685/GCA_018469685.1/GCA_018469685.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/685/GCA_018469685.1/GCA_018469685.1.chrom.sizes.txt" \
   GCA_018469685.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m30.190s

    sed -e 's/^/    # /;' fb.GCA_018469685.1.chainRBest.Hg38.txt
    # 2830977232 bases of 3025313608 (93.576%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469665.1
#    (DONE - 2023-04-04 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469665.1.2023-04-04
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469665.1.2023-04-04

    printf '# human GCA_018469665.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469665.1_HG01123.pri.mat.f1_v2.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/665/GCA_018469665.1/GCA_018469665.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/665/GCA_018469665.1/GCA_018469665.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469665.1.2023-04-04
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469665.1_HG01123.pri.mat.f1_v2.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	213m6.351s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469665.1Link.txt
    # 3048844569 bases of 3299210039 (92.411%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469665.1Link.txt
    # 3044500979 bases of 3299210039 (92.280%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/665/GCA_018469665.1/GCA_018469665.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/665/GCA_018469665.1/GCA_018469665.1.chrom.sizes.txt" \
        hg38 GCA_018469665.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	85m45.377s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469665.1.txt
    # 2836682774 bases of 3299210039 (85.981%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/665/GCA_018469665.1_HG01123.pri.mat.f1_v2.1/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469665.1_HG01123.pri.mat.f1_v2.1 /hive/data/genomes/hg38/bed/lastzGCA_018469665.1.2023-04-04/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	133m41.257s

    sed -e 's/^/    # /;' fb.GCA_018469665.1.chainHg38Link.txt
    # 2865875487 bases of 3012822948 (95.123%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469665.1.chainSynHg38Link.txt
    # 2860544697 bases of 3012822948 (94.946%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/665/GCA_018469665.1/GCA_018469665.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/665/GCA_018469665.1/GCA_018469665.1.chrom.sizes.txt" \
   GCA_018469665.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	80m1.738s

    sed -e 's/^/    # /;' fb.GCA_018469665.1.chainRBest.Hg38.txt
    # 2834465468 bases of 3012822948 (94.080%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469865.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469865.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469865.1.2023-04-05

    printf '# human GCA_018469865.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469865.1_HG01358.pri.mat.f1_v2.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/865/GCA_018469865.1/GCA_018469865.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/865/GCA_018469865.1/GCA_018469865.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469865.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469865.1_HG01358.pri.mat.f1_v2.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	168m13.600s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469865.1Link.txt
    # 3047657353 bases of 3299210039 (92.375%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469865.1Link.txt
    # 3043194543 bases of 3299210039 (92.240%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/865/GCA_018469865.1/GCA_018469865.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/865/GCA_018469865.1/GCA_018469865.1.chrom.sizes.txt" \
        hg38 GCA_018469865.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	77m3.311s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469865.1.txt
    # 2838079272 bases of 3299210039 (86.023%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/865/GCA_018469865.1_HG01358.pri.mat.f1_v2.1/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469865.1_HG01358.pri.mat.f1_v2.1 /hive/data/genomes/hg38/bed/lastzGCA_018469865.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	123m12.696s

    sed -e 's/^/    # /;' fb.GCA_018469865.1.chainHg38Link.txt
    # 2865143593 bases of 3029587694 (94.572%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469865.1.chainSynHg38Link.txt
    # 2859636823 bases of 3029587694 (94.390%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/865/GCA_018469865.1/GCA_018469865.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/865/GCA_018469865.1/GCA_018469865.1.chrom.sizes.txt" \
   GCA_018469865.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	74m43.717s

    sed -e 's/^/    # /;' fb.GCA_018469865.1.chainRBest.Hg38.txt
    # 2834353735 bases of 3029587694 (93.556%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469965.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469965.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469965.1.2023-04-05

    printf '# human GCA_018469965.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469965.1_HG01358.alt.pat.f1_v2.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/965/GCA_018469965.1/GCA_018469965.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/965/GCA_018469965.1/GCA_018469965.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469965.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469965.1_HG01358.alt.pat.f1_v2.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	143m44.220s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469965.1Link.txt
    # 2920305964 bases of 3299210039 (88.515%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469965.1Link.txt
    # 2915298077 bases of 3299210039 (88.364%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/965/GCA_018469965.1/GCA_018469965.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/965/GCA_018469965.1/GCA_018469965.1.chrom.sizes.txt" \
        hg38 GCA_018469965.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m41.070s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469965.1.txt
    # 2712668877 bases of 3299210039 (82.222%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/965/GCA_018469965.1_HG01358.alt.pat.f1_v2.1/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469965.1_HG01358.alt.pat.f1_v2.1 /hive/data/genomes/hg38/bed/lastzGCA_018469965.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	112m18.392s

    sed -e 's/^/    # /;' fb.GCA_018469965.1.chainHg38Link.txt
    # 2748397653 bases of 2932540871 (93.721%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469965.1.chainSynHg38Link.txt
    # 2742649822 bases of 2932540871 (93.525%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/965/GCA_018469965.1/GCA_018469965.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/965/GCA_018469965.1/GCA_018469965.1.chrom.sizes.txt" \
   GCA_018469965.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m24.412s

    sed -e 's/^/    # /;' fb.GCA_018469965.1.chainRBest.Hg38.txt
    # 2710789449 bases of 2932540871 (92.438%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018467155.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018467155.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018467155.1.2023-04-05

    printf '# human GCA_018467155.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018467155.1_HG01891.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/467/155/GCA_018467155.1/GCA_018467155.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/467/155/GCA_018467155.1/GCA_018467155.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018467155.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018467155.1_HG01891.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	167m43.516s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018467155.1Link.txt
    # 3047773145 bases of 3299210039 (92.379%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018467155.1Link.txt
    # 3042967052 bases of 3299210039 (92.233%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/467/155/GCA_018467155.1/GCA_018467155.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/467/155/GCA_018467155.1/GCA_018467155.1.chrom.sizes.txt" \
        hg38 GCA_018467155.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m46.717s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018467155.1.txt
    # 2834653179 bases of 3299210039 (85.919%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/467/155/GCA_018467155.1_HG01891.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018467155.1_HG01891.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018467155.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	125m58.945s

    sed -e 's/^/    # /;' fb.GCA_018467155.1.chainHg38Link.txt
    # 2866986413 bases of 3022952778 (94.841%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018467155.1.chainSynHg38Link.txt
    # 2861260988 bases of 3022952778 (94.651%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/467/155/GCA_018467155.1/GCA_018467155.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/467/155/GCA_018467155.1/GCA_018467155.1.chrom.sizes.txt" \
   GCA_018467155.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	77m35.492s

    sed -e 's/^/    # /;' fb.GCA_018467155.1.chainRBest.Hg38.txt
    # 2832748344 bases of 3022952778 (93.708%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469705.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469705.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469705.1.2023-04-05

    printf '# human GCA_018469705.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469705.1_HG01361.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/705/GCA_018469705.1/GCA_018469705.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/705/GCA_018469705.1/GCA_018469705.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469705.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469705.1_HG01361.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	181m59.456s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469705.1Link.txt
    # 3048539612 bases of 3299210039 (92.402%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469705.1Link.txt
    # 3044490947 bases of 3299210039 (92.279%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/705/GCA_018469705.1/GCA_018469705.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/705/GCA_018469705.1/GCA_018469705.1.chrom.sizes.txt" \
        hg38 GCA_018469705.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m20.100s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469705.1.txt
    # 2837562648 bases of 3299210039 (86.007%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/705/GCA_018469705.1_HG01361.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469705.1_HG01361.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469705.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	127m44.548s

    sed -e 's/^/    # /;' fb.GCA_018469705.1.chainHg38Link.txt
    # 2865148414 bases of 3010067136 (95.186%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469705.1.chainSynHg38Link.txt
    # 2859768016 bases of 3010067136 (95.007%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/705/GCA_018469705.1/GCA_018469705.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/705/GCA_018469705.1/GCA_018469705.1.chrom.sizes.txt" \
   GCA_018469705.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m30.039s

    sed -e 's/^/    # /;' fb.GCA_018469705.1.chainRBest.Hg38.txt
    # 2835320194 bases of 3010067136 (94.195%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018467165.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018467165.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018467165.1.2023-04-05

    printf '# human GCA_018467165.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018467165.1_HG01891.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/467/165/GCA_018467165.1/GCA_018467165.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/467/165/GCA_018467165.1/GCA_018467165.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018467165.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018467165.1_HG01891.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	159m31.347s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018467165.1Link.txt
    # 3049116083 bases of 3299210039 (92.420%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018467165.1Link.txt
    # 3044731829 bases of 3299210039 (92.287%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/467/165/GCA_018467165.1/GCA_018467165.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/467/165/GCA_018467165.1/GCA_018467165.1.chrom.sizes.txt" \
        hg38 GCA_018467165.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m38.348s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018467165.1.txt
    # 2838013120 bases of 3299210039 (86.021%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/467/165/GCA_018467165.1_HG01891.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018467165.1_HG01891.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018467165.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	125m4.249s

    sed -e 's/^/    # /;' fb.GCA_018467165.1.chainHg38Link.txt
    # 2874312102 bases of 3043232268 (94.449%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018467165.1.chainSynHg38Link.txt
    # 2868483040 bases of 3043232268 (94.258%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/467/165/GCA_018467165.1/GCA_018467165.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/467/165/GCA_018467165.1/GCA_018467165.1.chrom.sizes.txt" \
   GCA_018467165.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m4.728s

    sed -e 's/^/    # /;' fb.GCA_018467165.1.chainRBest.Hg38.txt
    # 2836904281 bases of 3043232268 (93.220%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018505825.1
#    (DONE - 2023-04-06 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018505825.1.2023-04-06
    cd /hive/data/genomes/hg38/bed/lastzGCA_018505825.1.2023-04-06

    printf '# human GCA_018505825.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018505825.1_HG02109.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/505/825/GCA_018505825.1/GCA_018505825.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/505/825/GCA_018505825.1/GCA_018505825.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018505825.1.2023-04-06
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018505825.1_HG02109.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	159m28.473s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018505825.1Link.txt
    # 3048266987 bases of 3299210039 (92.394%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018505825.1Link.txt
    # 3044144120 bases of 3299210039 (92.269%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/505/825/GCA_018505825.1/GCA_018505825.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/505/825/GCA_018505825.1/GCA_018505825.1.chrom.sizes.txt" \
        hg38 GCA_018505825.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m14.803s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018505825.1.txt
    # 2837240177 bases of 3299210039 (85.998%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/505/825/GCA_018505825.1_HG02109.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018505825.1_HG02109.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018505825.1.2023-04-06/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	130m6.019s

    sed -e 's/^/    # /;' fb.GCA_018505825.1.chainHg38Link.txt
    # 2870938986 bases of 3026115826 (94.872%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018505825.1.chainSynHg38Link.txt
    # 2865131757 bases of 3026115826 (94.680%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/505/825/GCA_018505825.1/GCA_018505825.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/505/825/GCA_018505825.1/GCA_018505825.1.chrom.sizes.txt" \
   GCA_018505825.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	80m15.495s

    sed -e 's/^/    # /;' fb.GCA_018505825.1.chainRBest.Hg38.txt
    # 2835084887 bases of 3026115826 (93.687%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472705.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472705.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472705.1.2023-04-05

    printf '# human GCA_018472705.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472705.1_HG01928.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/705/GCA_018472705.1/GCA_018472705.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/705/GCA_018472705.1/GCA_018472705.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472705.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472705.1_HG01928.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	163m14.294s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472705.1Link.txt
    # 2920759025 bases of 3299210039 (88.529%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472705.1Link.txt
    # 2915870383 bases of 3299210039 (88.381%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/705/GCA_018472705.1/GCA_018472705.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/705/GCA_018472705.1/GCA_018472705.1.chrom.sizes.txt" \
        hg38 GCA_018472705.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	73m53.132s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472705.1.txt
    # 2710751652 bases of 3299210039 (82.164%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/705/GCA_018472705.1_HG01928.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472705.1_HG01928.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472705.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	117m32.936s

    sed -e 's/^/    # /;' fb.GCA_018472705.1.chainHg38Link.txt
    # 2743643391 bases of 2923053911 (93.862%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472705.1.chainSynHg38Link.txt
    # 2737701220 bases of 2923053911 (93.659%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/705/GCA_018472705.1/GCA_018472705.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/705/GCA_018472705.1/GCA_018472705.1.chrom.sizes.txt" \
   GCA_018472705.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m3.576s

    sed -e 's/^/    # /;' fb.GCA_018472705.1.chainRBest.Hg38.txt
    # 2708545372 bases of 2923053911 (92.661%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018471545.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471545.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018471545.1.2023-04-05

    printf '# human GCA_018471545.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018471545.1_HG01952.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/545/GCA_018471545.1/GCA_018471545.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/545/GCA_018471545.1/GCA_018471545.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471545.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018471545.1_HG01952.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	168m9.773s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018471545.1Link.txt
    # 3048619956 bases of 3299210039 (92.405%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018471545.1Link.txt
    # 3044170738 bases of 3299210039 (92.270%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/545/GCA_018471545.1/GCA_018471545.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/471/545/GCA_018471545.1/GCA_018471545.1.chrom.sizes.txt" \
        hg38 GCA_018471545.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m53.550s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018471545.1.txt
    # 2838487930 bases of 3299210039 (86.035%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/545/GCA_018471545.1_HG01952.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018471545.1_HG01952.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471545.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	122m47.581s

    sed -e 's/^/    # /;' fb.GCA_018471545.1.chainHg38Link.txt
    # 2872293644 bases of 3020563005 (95.091%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018471545.1.chainSynHg38Link.txt
    # 2866375735 bases of 3020563005 (94.895%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/545/GCA_018471545.1/GCA_018471545.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/545/GCA_018471545.1/GCA_018471545.1.chrom.sizes.txt" \
   GCA_018471545.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m19.571s

    sed -e 's/^/    # /;' fb.GCA_018471545.1.chainRBest.Hg38.txt
    # 2836401226 bases of 3020563005 (93.903%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018471555.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471555.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018471555.1.2023-04-05

    printf '# human GCA_018471555.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018471555.1_HG01952.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/555/GCA_018471555.1/GCA_018471555.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/555/GCA_018471555.1/GCA_018471555.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471555.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018471555.1_HG01952.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	140m13.734s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018471555.1Link.txt
    # 2918848968 bases of 3299210039 (88.471%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018471555.1Link.txt
    # 2913549109 bases of 3299210039 (88.311%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/555/GCA_018471555.1/GCA_018471555.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/471/555/GCA_018471555.1/GCA_018471555.1.chrom.sizes.txt" \
        hg38 GCA_018471555.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	73m22.011s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018471555.1.txt
    # 2707032716 bases of 3299210039 (82.051%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/555/GCA_018471555.1_HG01952.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018471555.1_HG01952.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471555.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	118m59.134s

    sed -e 's/^/    # /;' fb.GCA_018471555.1.chainHg38Link.txt
    # 2738500264 bases of 2913263982 (94.001%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018471555.1.chainSynHg38Link.txt
    # 2732826954 bases of 2913263982 (93.806%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/555/GCA_018471555.1/GCA_018471555.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/555/GCA_018471555.1/GCA_018471555.1.chrom.sizes.txt" \
   GCA_018471555.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	77m18.124s

    sed -e 's/^/    # /;' fb.GCA_018471555.1.chainRBest.Hg38.txt
    # 2706500715 bases of 2913263982 (92.903%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472865.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472865.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472865.1.2023-04-05

    printf '# human GCA_018472865.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472865.1_HG01978.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/865/GCA_018472865.1/GCA_018472865.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/865/GCA_018472865.1/GCA_018472865.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472865.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472865.1_HG01978.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	171m14.446s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472865.1Link.txt
    # 3047365592 bases of 3299210039 (92.367%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472865.1Link.txt
    # 3043049700 bases of 3299210039 (92.236%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/865/GCA_018472865.1/GCA_018472865.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/865/GCA_018472865.1/GCA_018472865.1.chrom.sizes.txt" \
        hg38 GCA_018472865.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m46.282s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472865.1.txt
    # 2835747386 bases of 3299210039 (85.952%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/865/GCA_018472865.1_HG01978.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472865.1_HG01978.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472865.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	132m37.621s

    sed -e 's/^/    # /;' fb.GCA_018472865.1.chainHg38Link.txt
    # 2867278593 bases of 3051869401 (93.952%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472865.1.chainSynHg38Link.txt
    # 2861527125 bases of 3051869401 (93.763%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/865/GCA_018472865.1/GCA_018472865.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/865/GCA_018472865.1/GCA_018472865.1.chrom.sizes.txt" \
   GCA_018472865.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m37.229s

    sed -e 's/^/    # /;' fb.GCA_018472865.1.chainRBest.Hg38.txt
    # 2834379833 bases of 3051869401 (92.874%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472845.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472845.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472845.1.2023-04-05

    printf '# human GCA_018472845.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472845.1_HG01978.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/845/GCA_018472845.1/GCA_018472845.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/845/GCA_018472845.1/GCA_018472845.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472845.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472845.1_HG01978.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	161m59.381s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472845.1Link.txt
    # 3048225496 bases of 3299210039 (92.393%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472845.1Link.txt
    # 3043723937 bases of 3299210039 (92.256%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/845/GCA_018472845.1/GCA_018472845.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/845/GCA_018472845.1/GCA_018472845.1.chrom.sizes.txt" \
        hg38 GCA_018472845.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m7.625s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472845.1.txt
    # 2836404970 bases of 3299210039 (85.972%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/845/GCA_018472845.1_HG01978.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472845.1_HG01978.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472845.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	133m43.664s

    sed -e 's/^/    # /;' fb.GCA_018472845.1.chainHg38Link.txt
    # 2874258628 bases of 3055071491 (94.082%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472845.1.chainSynHg38Link.txt
    # 2868180892 bases of 3055071491 (93.883%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/845/GCA_018472845.1/GCA_018472845.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/845/GCA_018472845.1/GCA_018472845.1.chrom.sizes.txt" \
   GCA_018472845.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	77m2.491s

    sed -e 's/^/    # /;' fb.GCA_018472845.1.chainRBest.Hg38.txt
    # 2834756457 bases of 3055071491 (92.789%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018506125.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018506125.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018506125.1.2023-04-05

    printf '# human GCA_018506125.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018506125.1_HG02055.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/506/125/GCA_018506125.1/GCA_018506125.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/506/125/GCA_018506125.1/GCA_018506125.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018506125.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018506125.1_HG02055.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	159m9.601s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018506125.1Link.txt
    # 3049130531 bases of 3299210039 (92.420%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018506125.1Link.txt
    # 3044658662 bases of 3299210039 (92.284%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/506/125/GCA_018506125.1/GCA_018506125.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/506/125/GCA_018506125.1/GCA_018506125.1.chrom.sizes.txt" \
        hg38 GCA_018506125.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m34.779s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018506125.1.txt
    # 2837132708 bases of 3299210039 (85.994%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/506/125/GCA_018506125.1_HG02055.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018506125.1_HG02055.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018506125.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	134m43.050s

    sed -e 's/^/    # /;' fb.GCA_018506125.1.chainHg38Link.txt
    # 2866177825 bases of 3019590183 (94.919%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018506125.1.chainSynHg38Link.txt
    # 2860016612 bases of 3019590183 (94.715%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/506/125/GCA_018506125.1/GCA_018506125.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/506/125/GCA_018506125.1/GCA_018506125.1.chrom.sizes.txt" \
   GCA_018506125.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	80m18.027s

    sed -e 's/^/    # /;' fb.GCA_018506125.1.chainRBest.Hg38.txt
    # 2834560427 bases of 3019590183 (93.872%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018505855.1
#    (DONE - 2023-04-06 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018505855.1.2023-04-06
    cd /hive/data/genomes/hg38/bed/lastzGCA_018505855.1.2023-04-06

    printf '# human GCA_018505855.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018505855.1_HG02055.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018505855.1.2023-04-06
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018505855.1_HG02055.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	160m27.006s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018505855.1Link.txt
    # 2920085105 bases of 3299210039 (88.509%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018505855.1Link.txt
    # 2915187308 bases of 3299210039 (88.360%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.chrom.sizes.txt" \
        hg38 GCA_018505855.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m52.496s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018505855.1.txt
    # 2712237293 bases of 3299210039 (82.209%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/505/855/GCA_018505855.1_HG02055.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018505855.1_HG02055.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018505855.1.2023-04-06/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	122m39.734s

    sed -e 's/^/    # /;' fb.GCA_018505855.1.chainHg38Link.txt
    # 2749378239 bases of 2950246117 (93.191%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018505855.1.chainSynHg38Link.txt
    # 2742930636 bases of 2950246117 (92.973%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.chrom.sizes.txt" \
   GCA_018505855.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	84m36.497s

    sed -e 's/^/    # /;' fb.GCA_018505855.1.chainRBest.Hg38.txt
    # 2707923188 bases of 2950246117 (91.786%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018504055.1
#    (DONE - 2023-04-06 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018504055.1.2023-04-06
    cd /hive/data/genomes/hg38/bed/lastzGCA_018504055.1.2023-04-06

    printf '# human GCA_018504055.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018504055.1_HG02080.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/504/055/GCA_018504055.1/GCA_018504055.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/504/055/GCA_018504055.1/GCA_018504055.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018504055.1.2023-04-06
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018504055.1_HG02080.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	172m6.313s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018504055.1Link.txt
    # 3048389081 bases of 3299210039 (92.398%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018504055.1Link.txt
    # 3043986538 bases of 3299210039 (92.264%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/504/055/GCA_018504055.1/GCA_018504055.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/504/055/GCA_018504055.1/GCA_018504055.1.chrom.sizes.txt" \
        hg38 GCA_018504055.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	80m21.855s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018504055.1.txt
    # 2836952811 bases of 3299210039 (85.989%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/504/055/GCA_018504055.1_HG02080.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018504055.1_HG02080.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018504055.1.2023-04-06/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	124m22.855s

    sed -e 's/^/    # /;' fb.GCA_018504055.1.chainHg38Link.txt
    # 2869987747 bases of 3024505444 (94.891%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018504055.1.chainSynHg38Link.txt
    # 2864430996 bases of 3024505444 (94.707%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/504/055/GCA_018504055.1/GCA_018504055.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/504/055/GCA_018504055.1/GCA_018504055.1.chrom.sizes.txt" \
   GCA_018504055.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	77m53.994s

    sed -e 's/^/    # /;' fb.GCA_018504055.1.chainRBest.Hg38.txt
    # 2835545942 bases of 3024505444 (93.752%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472695.1
#    (DONE - 2023-04-05 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472695.1.2023-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472695.1.2023-04-05

    printf '# human GCA_018472695.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472695.1_HG01928.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/695/GCA_018472695.1/GCA_018472695.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/695/GCA_018472695.1/GCA_018472695.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472695.1.2023-04-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472695.1_HG01928.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	159m39.178s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472695.1Link.txt
    # 3048263455 bases of 3299210039 (92.394%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472695.1Link.txt
    # 3043984227 bases of 3299210039 (92.264%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/695/GCA_018472695.1/GCA_018472695.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/695/GCA_018472695.1/GCA_018472695.1.chrom.sizes.txt" \
        hg38 GCA_018472695.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m32.710s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472695.1.txt
    # 2836761152 bases of 3299210039 (85.983%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/695/GCA_018472695.1_HG01928.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472695.1_HG01928.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472695.1.2023-04-05/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	124m6.184s

    sed -e 's/^/    # /;' fb.GCA_018472695.1.chainHg38Link.txt
    # 2861018135 bases of 3025961049 (94.549%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472695.1.chainSynHg38Link.txt
    # 2855644289 bases of 3025961049 (94.371%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/695/GCA_018472695.1/GCA_018472695.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/695/GCA_018472695.1/GCA_018472695.1.chrom.sizes.txt" \
   GCA_018472695.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m26.475s

    sed -e 's/^/    # /;' fb.GCA_018472695.1.chainRBest.Hg38.txt
    # 2834035035 bases of 3025961049 (93.657%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018505865.1
#    (DONE - 2023-04-06 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018505865.1.2023-04-06
    cd /hive/data/genomes/hg38/bed/lastzGCA_018505865.1.2023-04-06

    printf '# human GCA_018505865.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018505865.1_HG02109.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/505/865/GCA_018505865.1/GCA_018505865.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/505/865/GCA_018505865.1/GCA_018505865.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018505865.1.2023-04-06
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018505865.1_HG02109.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	160m3.516s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018505865.1Link.txt
    # 3047625196 bases of 3299210039 (92.374%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018505865.1Link.txt
    # 3042874733 bases of 3299210039 (92.230%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/505/865/GCA_018505865.1/GCA_018505865.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/505/865/GCA_018505865.1/GCA_018505865.1.chrom.sizes.txt" \
        hg38 GCA_018505865.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m43.610s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018505865.1.txt
    # 2833687168 bases of 3299210039 (85.890%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/505/865/GCA_018505865.1_HG02109.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018505865.1_HG02109.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018505865.1.2023-04-06/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	126m35.567s

    sed -e 's/^/    # /;' fb.GCA_018505865.1.chainHg38Link.txt
    # 2876560953 bases of 3037645976 (94.697%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018505865.1.chainSynHg38Link.txt
    # 2870540804 bases of 3037645976 (94.499%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/505/865/GCA_018505865.1/GCA_018505865.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/505/865/GCA_018505865.1/GCA_018505865.1.chrom.sizes.txt" \
   GCA_018505865.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m48.823s

    sed -e 's/^/    # /;' fb.GCA_018505865.1.chainRBest.Hg38.txt
    # 2831355849 bases of 3037645976 (93.209%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018852595.1
#    (DONE - 2023-04-06 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018852595.1.2023-04-06
    cd /hive/data/genomes/hg38/bed/lastzGCA_018852595.1.2023-04-06

    printf '# human GCA_018852595.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-06-11 GCA_018852595.1_HG02145.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/852/595/GCA_018852595.1/GCA_018852595.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/852/595/GCA_018852595.1/GCA_018852595.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018852595.1.2023-04-06
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018852595.1_HG02145.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	161m31.383s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018852595.1Link.txt
    # 2919103331 bases of 3299210039 (88.479%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018852595.1Link.txt
    # 2913933347 bases of 3299210039 (88.322%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/852/595/GCA_018852595.1/GCA_018852595.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/852/595/GCA_018852595.1/GCA_018852595.1.chrom.sizes.txt" \
        hg38 GCA_018852595.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	73m49.405s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018852595.1.txt
    # 2710039024 bases of 3299210039 (82.142%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/852/595/GCA_018852595.1_HG02145.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018852595.1_HG02145.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018852595.1.2023-04-06/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	120m50.547s

    sed -e 's/^/    # /;' fb.GCA_018852595.1.chainHg38Link.txt
    # 2742888946 bases of 2937649060 (93.370%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018852595.1.chainSynHg38Link.txt
    # 2737171352 bases of 2937649060 (93.176%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/852/595/GCA_018852595.1/GCA_018852595.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/852/595/GCA_018852595.1/GCA_018852595.1.chrom.sizes.txt" \
   GCA_018852595.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	73m45.520s

    sed -e 's/^/    # /;' fb.GCA_018852595.1.chainRBest.Hg38.txt
    # 2707347565 bases of 2937649060 (92.160%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018852585.1
#    (DONE - 2023-04-06 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018852585.1.2023-04-06
    cd /hive/data/genomes/hg38/bed/lastzGCA_018852585.1.2023-04-06

    printf '# human GCA_018852585.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-06-11 GCA_018852585.1_HG02145.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/852/585/GCA_018852585.1/GCA_018852585.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/852/585/GCA_018852585.1/GCA_018852585.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018852585.1.2023-04-06
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018852585.1_HG02145.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	167m43.691s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018852585.1Link.txt
    # 3047411553 bases of 3299210039 (92.368%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018852585.1Link.txt
    # 3042640686 bases of 3299210039 (92.223%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/852/585/GCA_018852585.1/GCA_018852585.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/852/585/GCA_018852585.1/GCA_018852585.1.chrom.sizes.txt" \
        hg38 GCA_018852585.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	77m41.802s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018852585.1.txt
    # 2836739477 bases of 3299210039 (85.982%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/852/585/GCA_018852585.1_HG02145.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018852585.1_HG02145.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018852585.1.2023-04-06/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	127m13.975s

    sed -e 's/^/    # /;' fb.GCA_018852585.1.chainHg38Link.txt
    # 2869643668 bases of 3030589160 (94.689%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018852585.1.chainSynHg38Link.txt
    # 2863267731 bases of 3030589160 (94.479%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/852/585/GCA_018852585.1/GCA_018852585.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/852/585/GCA_018852585.1/GCA_018852585.1.chrom.sizes.txt" \
   GCA_018852585.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m51.106s

    sed -e 's/^/    # /;' fb.GCA_018852585.1.chainRBest.Hg38.txt
    # 2834665080 bases of 3030589160 (93.535%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018471535.1
#    (DONE - 2023-04-06 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471535.1.2023-04-06
    cd /hive/data/genomes/hg38/bed/lastzGCA_018471535.1.2023-04-06

    printf '# human GCA_018471535.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018471535.1_HG02148.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/535/GCA_018471535.1/GCA_018471535.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/535/GCA_018471535.1/GCA_018471535.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471535.1.2023-04-06
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018471535.1_HG02148.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	162m53.749s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018471535.1Link.txt
    # 3048175937 bases of 3299210039 (92.391%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018471535.1Link.txt
    # 3043661652 bases of 3299210039 (92.254%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/535/GCA_018471535.1/GCA_018471535.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/471/535/GCA_018471535.1/GCA_018471535.1.chrom.sizes.txt" \
        hg38 GCA_018471535.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m54.110s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018471535.1.txt
    # 2836277742 bases of 3299210039 (85.968%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/535/GCA_018471535.1_HG02148.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018471535.1_HG02148.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471535.1.2023-04-06/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	125m10.441s

    sed -e 's/^/    # /;' fb.GCA_018471535.1.chainHg38Link.txt
    # 2865718393 bases of 3036136215 (94.387%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018471535.1.chainSynHg38Link.txt
    # 2860195079 bases of 3036136215 (94.205%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/535/GCA_018471535.1/GCA_018471535.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/535/GCA_018471535.1/GCA_018471535.1.chrom.sizes.txt" \
   GCA_018471535.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m59.478s

    sed -e 's/^/    # /;' fb.GCA_018471535.1.chainRBest.Hg38.txt
    # 2834274274 bases of 3036136215 (93.351%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018471525.1
#    (DONE - 2023-04-06 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471525.1.2023-04-06
    cd /hive/data/genomes/hg38/bed/lastzGCA_018471525.1.2023-04-06

    printf '# human GCA_018471525.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018471525.1_HG02148.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/525/GCA_018471525.1/GCA_018471525.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/525/GCA_018471525.1/GCA_018471525.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471525.1.2023-04-06
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018471525.1_HG02148.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	156m46.785s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018471525.1Link.txt
    # 3047938250 bases of 3299210039 (92.384%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018471525.1Link.txt
    # 3043658717 bases of 3299210039 (92.254%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/525/GCA_018471525.1/GCA_018471525.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/471/525/GCA_018471525.1/GCA_018471525.1.chrom.sizes.txt" \
        hg38 GCA_018471525.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m18.828s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018471525.1.txt
    # 2834522281 bases of 3299210039 (85.915%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/525/GCA_018471525.1_HG02148.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018471525.1_HG02148.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471525.1.2023-04-06/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	129m20.070s

    sed -e 's/^/    # /;' fb.GCA_018471525.1.chainHg38Link.txt
    # 2867309757 bases of 3026089995 (94.753%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018471525.1.chainSynHg38Link.txt
    # 2861632279 bases of 3026089995 (94.565%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/525/GCA_018471525.1/GCA_018471525.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/525/GCA_018471525.1/GCA_018471525.1.chrom.sizes.txt" \
   GCA_018471525.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m44.824s

    sed -e 's/^/    # /;' fb.GCA_018471525.1.chainRBest.Hg38.txt
    # 2833122366 bases of 3026089995 (93.623%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018466845.1
#    (DONE - 2023-04-06 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018466845.1.2023-04-06
    cd /hive/data/genomes/hg38/bed/lastzGCA_018466845.1.2023-04-06

    printf '# human GCA_018466845.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018466845.1_HG02257.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/466/845/GCA_018466845.1/GCA_018466845.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/466/845/GCA_018466845.1/GCA_018466845.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018466845.1.2023-04-06
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018466845.1_HG02257.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	166m43.014s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018466845.1Link.txt
    # 3048520613 bases of 3299210039 (92.402%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018466845.1Link.txt
    # 3044355790 bases of 3299210039 (92.275%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/466/845/GCA_018466845.1/GCA_018466845.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/466/845/GCA_018466845.1/GCA_018466845.1.chrom.sizes.txt" \
        hg38 GCA_018466845.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m59.373s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018466845.1.txt
    # 2837807415 bases of 3299210039 (86.015%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/466/845/GCA_018466845.1_HG02257.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018466845.1_HG02257.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018466845.1.2023-04-06/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	131m42.117s

    sed -e 's/^/    # /;' fb.GCA_018466845.1.chainHg38Link.txt
    # 2868728444 bases of 3031071346 (94.644%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018466845.1.chainSynHg38Link.txt
    # 2862898817 bases of 3031071346 (94.452%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/466/845/GCA_018466845.1/GCA_018466845.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/466/845/GCA_018466845.1/GCA_018466845.1.chrom.sizes.txt" \
   GCA_018466845.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m25.977s

    sed -e 's/^/    # /;' fb.GCA_018466845.1.chainRBest.Hg38.txt
    # 2836714515 bases of 3031071346 (93.588%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018466835.1
#    (DONE - 2023-04-06 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018466835.1.2023-04-06
    cd /hive/data/genomes/hg38/bed/lastzGCA_018466835.1.2023-04-06

    printf '# human GCA_018466835.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018466835.1_HG02257.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/466/835/GCA_018466835.1/GCA_018466835.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/466/835/GCA_018466835.1/GCA_018466835.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018466835.1.2023-04-06
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018466835.1_HG02257.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	162m7.629s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018466835.1Link.txt
    # 3048799557 bases of 3299210039 (92.410%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018466835.1Link.txt
    # 3044037760 bases of 3299210039 (92.266%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/466/835/GCA_018466835.1/GCA_018466835.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/466/835/GCA_018466835.1/GCA_018466835.1.chrom.sizes.txt" \
        hg38 GCA_018466835.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m57.647s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018466835.1.txt
    # 2836005616 bases of 3299210039 (85.960%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/466/835/GCA_018466835.1_HG02257.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018466835.1_HG02257.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018466835.1.2023-04-06/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	128m0.411s

    sed -e 's/^/    # /;' fb.GCA_018466835.1.chainHg38Link.txt
    # 2868181746 bases of 3042496887 (94.271%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018466835.1.chainSynHg38Link.txt
    # 2862041590 bases of 3042496887 (94.069%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/466/835/GCA_018466835.1/GCA_018466835.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/466/835/GCA_018466835.1/GCA_018466835.1.chrom.sizes.txt" \
   GCA_018466835.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m5.888s

    sed -e 's/^/    # /;' fb.GCA_018466835.1.chainRBest.Hg38.txt
    # 2833276522 bases of 3042496887 (93.123%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018467015.1
#    (DONE - 2023-04-06 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018467015.1.2023-04-06
    cd /hive/data/genomes/hg38/bed/lastzGCA_018467015.1.2023-04-06

    printf '# human GCA_018467015.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018467015.1_HG02486.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/467/015/GCA_018467015.1/GCA_018467015.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/467/015/GCA_018467015.1/GCA_018467015.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018467015.1.2023-04-06
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018467015.1_HG02486.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	159m10.444s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018467015.1Link.txt
    # 3049099777 bases of 3299210039 (92.419%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018467015.1Link.txt
    # 3044686916 bases of 3299210039 (92.285%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/467/015/GCA_018467015.1/GCA_018467015.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/467/015/GCA_018467015.1/GCA_018467015.1.chrom.sizes.txt" \
        hg38 GCA_018467015.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	76m25.481s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018467015.1.txt
    # 2838256893 bases of 3299210039 (86.028%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/467/015/GCA_018467015.1_HG02486.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018467015.1_HG02486.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018467015.1.2023-04-06/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	128m37.068s

    sed -e 's/^/    # /;' fb.GCA_018467015.1.chainHg38Link.txt
    # 2866579968 bases of 3030662429 (94.586%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018467015.1.chainSynHg38Link.txt
    # 2860417977 bases of 3030662429 (94.383%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/467/015/GCA_018467015.1/GCA_018467015.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/467/015/GCA_018467015.1/GCA_018467015.1.chrom.sizes.txt" \
   GCA_018467015.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m58.358s

    sed -e 's/^/    # /;' fb.GCA_018467015.1.chainRBest.Hg38.txt
    # 2835053717 bases of 3030662429 (93.546%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018467005.1
#    (DONE - 2023-04-07 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018467005.1.2023-04-07
    cd /hive/data/genomes/hg38/bed/lastzGCA_018467005.1.2023-04-07

    printf '# human GCA_018467005.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018467005.1_HG02486.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/467/005/GCA_018467005.1/GCA_018467005.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/467/005/GCA_018467005.1/GCA_018467005.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018467005.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018467005.1_HG02486.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	154m54.566s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018467005.1Link.txt
    # 2919139205 bases of 3299210039 (88.480%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018467005.1Link.txt
    # 2913624178 bases of 3299210039 (88.313%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/467/005/GCA_018467005.1/GCA_018467005.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/467/005/GCA_018467005.1/GCA_018467005.1.chrom.sizes.txt" \
        hg38 GCA_018467005.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	73m26.599s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018467005.1.txt
    # 2709863131 bases of 3299210039 (82.137%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/467/005/GCA_018467005.1_HG02486.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018467005.1_HG02486.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018467005.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	119m40.935s

    sed -e 's/^/    # /;' fb.GCA_018467005.1.chainHg38Link.txt
    # 2746359980 bases of 2930935689 (93.702%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018467005.1.chainSynHg38Link.txt
    # 2740567458 bases of 2930935689 (93.505%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/467/005/GCA_018467005.1/GCA_018467005.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/467/005/GCA_018467005.1/GCA_018467005.1.chrom.sizes.txt" \
   GCA_018467005.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	75m13.437s

    sed -e 's/^/    # /;' fb.GCA_018467005.1.chainRBest.Hg38.txt
    # 2707309019 bases of 2930935689 (92.370%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018466985.1
#    (DONE - 2023-04-07 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018466985.1.2023-04-07
    cd /hive/data/genomes/hg38/bed/lastzGCA_018466985.1.2023-04-07

    printf '# human GCA_018466985.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018466985.1_HG02559.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/466/985/GCA_018466985.1/GCA_018466985.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/466/985/GCA_018466985.1/GCA_018466985.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018466985.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018466985.1_HG02559.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	168m39.764s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018466985.1Link.txt
    # 3048537861 bases of 3299210039 (92.402%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018466985.1Link.txt
    # 3043994251 bases of 3299210039 (92.264%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/466/985/GCA_018466985.1/GCA_018466985.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/466/985/GCA_018466985.1/GCA_018466985.1.chrom.sizes.txt" \
        hg38 GCA_018466985.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m0.574s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018466985.1.txt
    # 2838843387 bases of 3299210039 (86.046%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/466/985/GCA_018466985.1_HG02559.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018466985.1_HG02559.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018466985.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	125m16.825s

    sed -e 's/^/    # /;' fb.GCA_018466985.1.chainHg38Link.txt
    # 2877195123 bases of 3040531780 (94.628%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018466985.1.chainSynHg38Link.txt
    # 2870421698 bases of 3040531780 (94.405%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/466/985/GCA_018466985.1/GCA_018466985.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/466/985/GCA_018466985.1/GCA_018466985.1.chrom.sizes.txt" \
   GCA_018466985.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	77m52.368s

    sed -e 's/^/    # /;' fb.GCA_018466985.1.chainRBest.Hg38.txt
    # 2836053795 bases of 3040531780 (93.275%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018466855.1
#    (DONE - 2023-04-07 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018466855.1.2023-04-07
    cd /hive/data/genomes/hg38/bed/lastzGCA_018466855.1.2023-04-07

    printf '# human GCA_018466855.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018466855.1_HG02559.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/466/855/GCA_018466855.1/GCA_018466855.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/466/855/GCA_018466855.1/GCA_018466855.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018466855.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018466855.1_HG02559.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	180m52.262s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018466855.1Link.txt
    # 3047647639 bases of 3299210039 (92.375%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018466855.1Link.txt
    # 3043300373 bases of 3299210039 (92.243%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/466/855/GCA_018466855.1/GCA_018466855.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/466/855/GCA_018466855.1/GCA_018466855.1.chrom.sizes.txt" \
        hg38 GCA_018466855.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	78m27.620s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018466855.1.txt
    # 2836585695 bases of 3299210039 (85.978%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/466/855/GCA_018466855.1_HG02559.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018466855.1_HG02559.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018466855.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	125m46.432s

    sed -e 's/^/    # /;' fb.GCA_018466855.1.chainHg38Link.txt
    # 2867238804 bases of 3024156283 (94.811%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018466855.1.chainSynHg38Link.txt
    # 2860664345 bases of 3024156283 (94.594%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/466/855/GCA_018466855.1/GCA_018466855.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/466/855/GCA_018466855.1/GCA_018466855.1.chrom.sizes.txt" \
   GCA_018466855.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m29.714s

    sed -e 's/^/    # /;' fb.GCA_018466855.1.chainRBest.Hg38.txt
    # 2834457188 bases of 3024156283 (93.727%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018470445.1
#    (DONE - 2023-04-07 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018470445.1.2023-04-07
    cd /hive/data/genomes/hg38/bed/lastzGCA_018470445.1.2023-04-07

    printf '# human GCA_018470445.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018470445.1_HG02572.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/470/445/GCA_018470445.1/GCA_018470445.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/470/445/GCA_018470445.1/GCA_018470445.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018470445.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018470445.1_HG02572.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	167m34.138s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018470445.1Link.txt
    # 3046703747 bases of 3299210039 (92.346%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018470445.1Link.txt
    # 3042415843 bases of 3299210039 (92.216%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/470/445/GCA_018470445.1/GCA_018470445.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/470/445/GCA_018470445.1/GCA_018470445.1.chrom.sizes.txt" \
        hg38 GCA_018470445.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m53.679s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018470445.1.txt
    # 2838092925 bases of 3299210039 (86.023%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/470/445/GCA_018470445.1_HG02572.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018470445.1_HG02572.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018470445.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	129m51.550s

    sed -e 's/^/    # /;' fb.GCA_018470445.1.chainHg38Link.txt
    # 2880139940 bases of 3055382050 (94.264%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018470445.1.chainSynHg38Link.txt
    # 2874364118 bases of 3055382050 (94.075%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/470/445/GCA_018470445.1/GCA_018470445.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/470/445/GCA_018470445.1/GCA_018470445.1.chrom.sizes.txt" \
   GCA_018470445.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	79m38.898s

    sed -e 's/^/    # /;' fb.GCA_018470445.1.chainRBest.Hg38.txt
    # 2834745077 bases of 3055382050 (92.779%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018470435.1
#    (DONE - 2023-04-07 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018470435.1.2023-04-07
    cd /hive/data/genomes/hg38/bed/lastzGCA_018470435.1.2023-04-07

    printf '# human GCA_018470435.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018470435.1_HG02572.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/470/435/GCA_018470435.1/GCA_018470435.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/470/435/GCA_018470435.1/GCA_018470435.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018470435.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018470435.1_HG02572.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	153m3.562s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018470435.1Link.txt
    # 2918269932 bases of 3299210039 (88.454%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018470435.1Link.txt
    # 2912992878 bases of 3299210039 (88.294%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/470/435/GCA_018470435.1/GCA_018470435.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/470/435/GCA_018470435.1/GCA_018470435.1.chrom.sizes.txt" \
        hg38 GCA_018470435.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	73m52.818s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018470435.1.txt
    # 2705925591 bases of 3299210039 (82.017%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/470/435/GCA_018470435.1_HG02572.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018470435.1_HG02572.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018470435.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	122m28.723s

    sed -e 's/^/    # /;' fb.GCA_018470435.1.chainHg38Link.txt
    # 2745415337 bases of 2943627449 (93.266%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018470435.1.chainSynHg38Link.txt
    # 2739934724 bases of 2943627449 (93.080%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/470/435/GCA_018470435.1/GCA_018470435.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/470/435/GCA_018470435.1/GCA_018470435.1.chrom.sizes.txt" \
   GCA_018470435.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	66m36.818s

    sed -e 's/^/    # /;' fb.GCA_018470435.1.chainRBest.Hg38.txt
    # 2704598255 bases of 2943627449 (91.880%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469875.1
#    (DONE - 2023-04-07 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469875.1.2023-04-07
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469875.1.2023-04-07

    printf '# human GCA_018469875.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469875.1_HG02622.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/875/GCA_018469875.1/GCA_018469875.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/875/GCA_018469875.1/GCA_018469875.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469875.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469875.1_HG02622.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	160m38.005s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469875.1Link.txt
    # 3046990416 bases of 3299210039 (92.355%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469875.1Link.txt
    # 3042466747 bases of 3299210039 (92.218%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/875/GCA_018469875.1/GCA_018469875.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/875/GCA_018469875.1/GCA_018469875.1.chrom.sizes.txt" \
        hg38 GCA_018469875.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	73m47.473s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469875.1.txt
    # 2836463596 bases of 3299210039 (85.974%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/875/GCA_018469875.1_HG02622.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469875.1_HG02622.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469875.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	114m55.509s

    sed -e 's/^/    # /;' fb.GCA_018469875.1.chainHg38Link.txt
    # 2879123954 bases of 3046105980 (94.518%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469875.1.chainSynHg38Link.txt
    # 2872440610 bases of 3046105980 (94.299%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/875/GCA_018469875.1/GCA_018469875.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/875/GCA_018469875.1/GCA_018469875.1.chrom.sizes.txt" \
   GCA_018469875.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m7.847s

    sed -e 's/^/    # /;' fb.GCA_018469875.1.chainRBest.Hg38.txt
    # 2832327993 bases of 3046105980 (92.982%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469925.1
#    (DONE - 2023-04-07 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469925.1.2023-04-07
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469925.1.2023-04-07

    printf '# human GCA_018469925.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469925.1_HG02622.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/925/GCA_018469925.1/GCA_018469925.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/925/GCA_018469925.1/GCA_018469925.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469925.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469925.1_HG02622.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	166m4.737s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469925.1Link.txt
    # 3048914025 bases of 3299210039 (92.413%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469925.1Link.txt
    # 3045147113 bases of 3299210039 (92.299%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/925/GCA_018469925.1/GCA_018469925.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/925/GCA_018469925.1/GCA_018469925.1.chrom.sizes.txt" \
        hg38 GCA_018469925.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m19.495s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469925.1.txt
    # 2840044567 bases of 3299210039 (86.083%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/925/GCA_018469925.1_HG02622.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469925.1_HG02622.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469925.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	112m33.104s

    sed -e 's/^/    # /;' fb.GCA_018469925.1.chainHg38Link.txt
    # 2874066434 bases of 3043426064 (94.435%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469925.1.chainSynHg38Link.txt
    # 2867454995 bases of 3043426064 (94.218%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/925/GCA_018469925.1/GCA_018469925.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/925/GCA_018469925.1/GCA_018469925.1.chrom.sizes.txt" \
   GCA_018469925.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	71m39.543s

    sed -e 's/^/    # /;' fb.GCA_018469925.1.chainRBest.Hg38.txt
    # 2836598476 bases of 3043426064 (93.204%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469955.1
#    (DONE - 2023-04-07 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469955.1.2023-04-07
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469955.1.2023-04-07

    printf '# human GCA_018469955.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469955.1_HG02630.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/955/GCA_018469955.1/GCA_018469955.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/955/GCA_018469955.1/GCA_018469955.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469955.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469955.1_HG02630.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	166m19.362s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469955.1Link.txt
    # 3047967357 bases of 3299210039 (92.385%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469955.1Link.txt
    # 3043427471 bases of 3299210039 (92.247%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/955/GCA_018469955.1/GCA_018469955.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/955/GCA_018469955.1/GCA_018469955.1.chrom.sizes.txt" \
        hg38 GCA_018469955.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	71m13.384s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469955.1.txt
    # 2838760330 bases of 3299210039 (86.044%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/955/GCA_018469955.1_HG02630.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469955.1_HG02630.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469955.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	115m3.149s

    sed -e 's/^/    # /;' fb.GCA_018469955.1.chainHg38Link.txt
    # 2878441093 bases of 3041877443 (94.627%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469955.1.chainSynHg38Link.txt
    # 2871787466 bases of 3041877443 (94.408%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/955/GCA_018469955.1/GCA_018469955.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/955/GCA_018469955.1/GCA_018469955.1.chrom.sizes.txt" \
   GCA_018469955.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m51.137s

    sed -e 's/^/    # /;' fb.GCA_018469955.1.chainRBest.Hg38.txt
    # 2835585092 bases of 3041877443 (93.218%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469945.1
#    (DONE - 2023-04-07 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469945.1.2023-04-07
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469945.1.2023-04-07

    printf '# human GCA_018469945.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469945.1_HG02630.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/945/GCA_018469945.1/GCA_018469945.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/945/GCA_018469945.1/GCA_018469945.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469945.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469945.1_HG02630.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	186m36.875s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469945.1Link.txt
    # 3047798340 bases of 3299210039 (92.380%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469945.1Link.txt
    # 3043116786 bases of 3299210039 (92.238%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/945/GCA_018469945.1/GCA_018469945.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/945/GCA_018469945.1/GCA_018469945.1.chrom.sizes.txt" \
        hg38 GCA_018469945.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m35.488s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469945.1.txt
    # 2837773116 bases of 3299210039 (86.014%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/945/GCA_018469945.1_HG02630.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469945.1_HG02630.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469945.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	113m46.740s

    sed -e 's/^/    # /;' fb.GCA_018469945.1.chainHg38Link.txt
    # 2875273230 bases of 3053402297 (94.166%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469945.1.chainSynHg38Link.txt
    # 2869163332 bases of 3053402297 (93.966%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/945/GCA_018469945.1/GCA_018469945.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/945/GCA_018469945.1/GCA_018469945.1.chrom.sizes.txt" \
   GCA_018469945.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m22.304s

    sed -e 's/^/    # /;' fb.GCA_018469945.1.chainRBest.Hg38.txt
    # 2834968677 bases of 3053402297 (92.846%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469935.1
#    (DONE - 2023-04-07 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469935.1.2023-04-07
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469935.1.2023-04-07

    printf '# human GCA_018469935.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469935.1_HG02717.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/935/GCA_018469935.1/GCA_018469935.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/935/GCA_018469935.1/GCA_018469935.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469935.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469935.1_HG02717.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	143m5.500s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469935.1Link.txt
    # 3048207075 bases of 3299210039 (92.392%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469935.1Link.txt
    # 3043933887 bases of 3299210039 (92.263%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/935/GCA_018469935.1/GCA_018469935.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/935/GCA_018469935.1/GCA_018469935.1.chrom.sizes.txt" \
        hg38 GCA_018469935.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m42.444s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469935.1.txt
    # 2834250707 bases of 3299210039 (85.907%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/935/GCA_018469935.1_HG02717.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469935.1_HG02717.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469935.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	115m25.318s

    sed -e 's/^/    # /;' fb.GCA_018469935.1.chainHg38Link.txt
    # 2867343454 bases of 3038320685 (94.373%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469935.1.chainSynHg38Link.txt
    # 2861652771 bases of 3038320685 (94.185%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/935/GCA_018469935.1/GCA_018469935.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/935/GCA_018469935.1/GCA_018469935.1.chrom.sizes.txt" \
   GCA_018469935.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m23.032s

    sed -e 's/^/    # /;' fb.GCA_018469935.1.chainRBest.Hg38.txt
    # 2831881683 bases of 3038320685 (93.205%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018470425.1
#    (DONE - 2023-04-07 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018470425.1.2023-04-07
    cd /hive/data/genomes/hg38/bed/lastzGCA_018470425.1.2023-04-07

    printf '# human GCA_018470425.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018470425.1_HG02717.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/470/425/GCA_018470425.1/GCA_018470425.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/470/425/GCA_018470425.1/GCA_018470425.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018470425.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018470425.1_HG02717.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	146m21.535s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018470425.1Link.txt
    # 2920132976 bases of 3299210039 (88.510%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018470425.1Link.txt
    # 2915013032 bases of 3299210039 (88.355%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/470/425/GCA_018470425.1/GCA_018470425.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/470/425/GCA_018470425.1/GCA_018470425.1.chrom.sizes.txt" \
        hg38 GCA_018470425.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	64m50.255s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018470425.1.txt
    # 2710904838 bases of 3299210039 (82.168%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/470/425/GCA_018470425.1_HG02717.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018470425.1_HG02717.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018470425.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	113m41.159s

    sed -e 's/^/    # /;' fb.GCA_018470425.1.chainHg38Link.txt
    # 2747654607 bases of 2946102667 (93.264%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018470425.1.chainSynHg38Link.txt
    # 2741571691 bases of 2946102667 (93.058%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/470/425/GCA_018470425.1/GCA_018470425.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/470/425/GCA_018470425.1/GCA_018470425.1.chrom.sizes.txt" \
   GCA_018470425.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	66m41.342s

    sed -e 's/^/    # /;' fb.GCA_018470425.1.chainRBest.Hg38.txt
    # 2707861909 bases of 2946102667 (91.913%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018504065.1
#    (DONE - 2023-04-07 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018504065.1.2023-04-07
    cd /hive/data/genomes/hg38/bed/lastzGCA_018504065.1.2023-04-07

    printf '# human GCA_018504065.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018504065.1_HG02723.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/504/065/GCA_018504065.1/GCA_018504065.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/504/065/GCA_018504065.1/GCA_018504065.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018504065.1.2023-04-07
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018504065.1_HG02723.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	145m1.623s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018504065.1Link.txt
    # 3047036500 bases of 3299210039 (92.357%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018504065.1Link.txt
    # 3042718110 bases of 3299210039 (92.226%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/504/065/GCA_018504065.1/GCA_018504065.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/504/065/GCA_018504065.1/GCA_018504065.1.chrom.sizes.txt" \
        hg38 GCA_018504065.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m21.991s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018504065.1.txt
    # 2835281526 bases of 3299210039 (85.938%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/504/065/GCA_018504065.1_HG02723.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018504065.1_HG02723.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018504065.1.2023-04-07/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	115m22.752s

    sed -e 's/^/    # /;' fb.GCA_018504065.1.chainHg38Link.txt
    # 2866553698 bases of 3027203092 (94.693%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018504065.1.chainSynHg38Link.txt
    # 2860487402 bases of 3027203092 (94.493%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/504/065/GCA_018504065.1/GCA_018504065.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/504/065/GCA_018504065.1/GCA_018504065.1.chrom.sizes.txt" \
   GCA_018504065.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m48.932s

    sed -e 's/^/    # /;' fb.GCA_018504065.1.chainRBest.Hg38.txt
    # 2833296233 bases of 3027203092 (93.595%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018504075.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018504075.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018504075.1.2023-04-08

    printf '# human GCA_018504075.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018504075.1_HG02723.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/504/075/GCA_018504075.1/GCA_018504075.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/504/075/GCA_018504075.1/GCA_018504075.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018504075.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018504075.1_HG02723.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	157m5.437s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018504075.1Link.txt
    # 3048778510 bases of 3299210039 (92.409%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018504075.1Link.txt
    # 3044794623 bases of 3299210039 (92.289%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/504/075/GCA_018504075.1/GCA_018504075.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/504/075/GCA_018504075.1/GCA_018504075.1.chrom.sizes.txt" \
        hg38 GCA_018504075.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m21.382s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018504075.1.txt
    # 2838953498 bases of 3299210039 (86.049%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/504/075/GCA_018504075.1_HG02723.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018504075.1_HG02723.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018504075.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	113m28.888s

    sed -e 's/^/    # /;' fb.GCA_018504075.1.chainHg38Link.txt
    # 2874220378 bases of 3049492048 (94.252%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018504075.1.chainSynHg38Link.txt
    # 2868644210 bases of 3049492048 (94.070%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/504/075/GCA_018504075.1/GCA_018504075.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/504/075/GCA_018504075.1/GCA_018504075.1.chrom.sizes.txt" \
   GCA_018504075.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m55.468s

    sed -e 's/^/    # /;' fb.GCA_018504075.1.chainRBest.Hg38.txt
    # 2835433833 bases of 3049492048 (92.981%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018503585.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018503585.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018503585.1.2023-04-08

    printf '# human GCA_018503585.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018503585.1_HG02818.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/503/585/GCA_018503585.1/GCA_018503585.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/503/585/GCA_018503585.1/GCA_018503585.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018503585.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018503585.1_HG02818.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	145m50.514s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018503585.1Link.txt
    # 3047050654 bases of 3299210039 (92.357%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018503585.1Link.txt
    # 3042350336 bases of 3299210039 (92.215%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/503/585/GCA_018503585.1/GCA_018503585.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/503/585/GCA_018503585.1/GCA_018503585.1.chrom.sizes.txt" \
        hg38 GCA_018503585.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m19.274s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018503585.1.txt
    # 2835297060 bases of 3299210039 (85.939%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/503/585/GCA_018503585.1_HG02818.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018503585.1_HG02818.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018503585.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	111m38.835s

    sed -e 's/^/    # /;' fb.GCA_018503585.1.chainHg38Link.txt
    # 2868996933 bases of 3037441458 (94.454%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018503585.1.chainSynHg38Link.txt
    # 2862957568 bases of 3037441458 (94.256%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/503/585/GCA_018503585.1/GCA_018503585.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/503/585/GCA_018503585.1/GCA_018503585.1.chrom.sizes.txt" \
   GCA_018503585.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m23.560s

    sed -e 's/^/    # /;' fb.GCA_018503585.1.chainRBest.Hg38.txt
    # 2832610253 bases of 3037441458 (93.256%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018503575.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018503575.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018503575.1.2023-04-08

    printf '# human GCA_018503575.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018503575.1_HG02818.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/503/575/GCA_018503575.1/GCA_018503575.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/503/575/GCA_018503575.1/GCA_018503575.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018503575.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018503575.1_HG02818.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	154m0.530s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018503575.1Link.txt
    # 3047716949 bases of 3299210039 (92.377%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018503575.1Link.txt
    # 3043231493 bases of 3299210039 (92.241%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/503/575/GCA_018503575.1/GCA_018503575.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/503/575/GCA_018503575.1/GCA_018503575.1.chrom.sizes.txt" \
        hg38 GCA_018503575.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m6.915s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018503575.1.txt
    # 2835427201 bases of 3299210039 (85.943%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/503/575/GCA_018503575.1_HG02818.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018503575.1_HG02818.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018503575.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	113m45.516s

    sed -e 's/^/    # /;' fb.GCA_018503575.1.chainHg38Link.txt
    # 2870529037 bases of 3019578985 (95.064%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018503575.1.chainSynHg38Link.txt
    # 2865077367 bases of 3019578985 (94.883%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/503/575/GCA_018503575.1/GCA_018503575.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/503/575/GCA_018503575.1/GCA_018503575.1.chrom.sizes.txt" \
   GCA_018503575.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m43.058s

    sed -e 's/^/    # /;' fb.GCA_018503575.1.chainRBest.Hg38.txt
    # 2831990323 bases of 3019578985 (93.788%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018470455.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018470455.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018470455.1.2023-04-08

    printf '# human GCA_018470455.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018470455.1_HG02886.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/470/455/GCA_018470455.1/GCA_018470455.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/470/455/GCA_018470455.1/GCA_018470455.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018470455.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018470455.1_HG02886.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	151m13.972s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018470455.1Link.txt
    # 3049039851 bases of 3299210039 (92.417%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018470455.1Link.txt
    # 3045041224 bases of 3299210039 (92.296%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/470/455/GCA_018470455.1/GCA_018470455.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/470/455/GCA_018470455.1/GCA_018470455.1.chrom.sizes.txt" \
        hg38 GCA_018470455.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m5.963s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018470455.1.txt
    # 2842175366 bases of 3299210039 (86.147%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/470/455/GCA_018470455.1_HG02886.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018470455.1_HG02886.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018470455.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	115m43.481s

    sed -e 's/^/    # /;' fb.GCA_018470455.1.chainHg38Link.txt
    # 2889717747 bases of 3049134634 (94.772%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018470455.1.chainSynHg38Link.txt
    # 2882827497 bases of 3049134634 (94.546%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/470/455/GCA_018470455.1/GCA_018470455.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/470/455/GCA_018470455.1/GCA_018470455.1.chrom.sizes.txt" \
   GCA_018470455.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	70m3.504s

    sed -e 's/^/    # /;' fb.GCA_018470455.1.chainRBest.Hg38.txt
    # 2837125612 bases of 3049134634 (93.047%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018470465.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018470465.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018470465.1.2023-04-08

    printf '# human GCA_018470465.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018470465.1_HG02886.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/470/465/GCA_018470465.1/GCA_018470465.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/470/465/GCA_018470465.1/GCA_018470465.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018470465.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018470465.1_HG02886.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	140m46.432s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018470465.1Link.txt
    # 3048859482 bases of 3299210039 (92.412%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018470465.1Link.txt
    # 3044531947 bases of 3299210039 (92.281%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/470/465/GCA_018470465.1/GCA_018470465.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/470/465/GCA_018470465.1/GCA_018470465.1.chrom.sizes.txt" \
        hg38 GCA_018470465.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m15.743s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018470465.1.txt
    # 2839333672 bases of 3299210039 (86.061%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/470/465/GCA_018470465.1_HG02886.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018470465.1_HG02886.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018470465.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	113m8.159s

    sed -e 's/^/    # /;' fb.GCA_018470465.1.chainHg38Link.txt
    # 2882182561 bases of 3047149239 (94.586%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018470465.1.chainSynHg38Link.txt
    # 2876088782 bases of 3047149239 (94.386%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/470/465/GCA_018470465.1/GCA_018470465.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/470/465/GCA_018470465.1/GCA_018470465.1.chrom.sizes.txt" \
   GCA_018470465.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m29.256s

    sed -e 's/^/    # /;' fb.GCA_018470465.1.chainRBest.Hg38.txt
    # 2836585833 bases of 3047149239 (93.090%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018506155.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018506155.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018506155.1.2023-04-08

    printf '# human GCA_018506155.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018506155.1_HG03098.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/506/155/GCA_018506155.1/GCA_018506155.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/506/155/GCA_018506155.1/GCA_018506155.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018506155.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018506155.1_HG03098.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	138m53.730s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018506155.1Link.txt
    # 2917779887 bases of 3299210039 (88.439%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018506155.1Link.txt
    # 2912371470 bases of 3299210039 (88.275%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/506/155/GCA_018506155.1/GCA_018506155.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/506/155/GCA_018506155.1/GCA_018506155.1.chrom.sizes.txt" \
        hg38 GCA_018506155.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	65m23.238s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018506155.1.txt
    # 2707564429 bases of 3299210039 (82.067%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/506/155/GCA_018506155.1_HG03098.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018506155.1_HG03098.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018506155.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	107m45.201s

    sed -e 's/^/    # /;' fb.GCA_018506155.1.chainHg38Link.txt
    # 2742295591 bases of 2935645968 (93.414%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018506155.1.chainSynHg38Link.txt
    # 2735790014 bases of 2935645968 (93.192%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/506/155/GCA_018506155.1/GCA_018506155.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/506/155/GCA_018506155.1/GCA_018506155.1.chrom.sizes.txt" \
   GCA_018506155.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	65m27.147s

    sed -e 's/^/    # /;' fb.GCA_018506155.1.chainRBest.Hg38.txt
    # 2705334349 bases of 2935645968 (92.155%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018506165.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018506165.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018506165.1.2023-04-08

    printf '# human GCA_018506165.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018506165.1_HG03098.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/506/165/GCA_018506165.1/GCA_018506165.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/506/165/GCA_018506165.1/GCA_018506165.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018506165.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018506165.1_HG03098.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	158m44.329s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018506165.1Link.txt
    # 3050957180 bases of 3299210039 (92.475%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018506165.1Link.txt
    # 3046730633 bases of 3299210039 (92.347%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/506/165/GCA_018506165.1/GCA_018506165.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/506/165/GCA_018506165.1/GCA_018506165.1.chrom.sizes.txt" \
        hg38 GCA_018506165.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m12.118s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018506165.1.txt
    # 2838797889 bases of 3299210039 (86.045%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/506/165/GCA_018506165.1_HG03098.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018506165.1_HG03098.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018506165.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	112m37.775s

    sed -e 's/^/    # /;' fb.GCA_018506165.1.chainHg38Link.txt
    # 2872418109 bases of 3059522785 (93.885%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018506165.1.chainSynHg38Link.txt
    # 2866192181 bases of 3059522785 (93.681%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/506/165/GCA_018506165.1/GCA_018506165.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/506/165/GCA_018506165.1/GCA_018506165.1.chrom.sizes.txt" \
   GCA_018506165.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m56.166s

    sed -e 's/^/    # /;' fb.GCA_018506165.1.chainRBest.Hg38.txt
    # 2836654978 bases of 3059522785 (92.716%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472855.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472855.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472855.1.2023-04-08

    printf '# human GCA_018472855.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472855.1_HG03453.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/855/GCA_018472855.1/GCA_018472855.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/855/GCA_018472855.1/GCA_018472855.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472855.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472855.1_HG03453.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	146m16.782s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472855.1Link.txt
    # 3048660103 bases of 3299210039 (92.406%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472855.1Link.txt
    # 3044359486 bases of 3299210039 (92.275%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/855/GCA_018472855.1/GCA_018472855.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/855/GCA_018472855.1/GCA_018472855.1.chrom.sizes.txt" \
        hg38 GCA_018472855.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m24.846s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472855.1.txt
    # 2839579588 bases of 3299210039 (86.068%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/855/GCA_018472855.1_HG03453.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472855.1_HG03453.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472855.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	113m18.244s

    sed -e 's/^/    # /;' fb.GCA_018472855.1.chainHg38Link.txt
    # 2878398642 bases of 3047998942 (94.436%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472855.1.chainSynHg38Link.txt
    # 2871613262 bases of 3047998942 (94.213%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/855/GCA_018472855.1/GCA_018472855.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/855/GCA_018472855.1/GCA_018472855.1.chrom.sizes.txt" \
   GCA_018472855.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m31.060s

    sed -e 's/^/    # /;' fb.GCA_018472855.1.chainRBest.Hg38.txt
    # 2837523726 bases of 3047998942 (93.095%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018473305.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018473305.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018473305.1.2023-04-08

    printf '# human GCA_018473305.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018473305.1_HG03453.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/473/305/GCA_018473305.1/GCA_018473305.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/473/305/GCA_018473305.1/GCA_018473305.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018473305.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018473305.1_HG03453.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	143m32.101s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018473305.1Link.txt
    # 3048688244 bases of 3299210039 (92.407%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018473305.1Link.txt
    # 3044482066 bases of 3299210039 (92.279%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/473/305/GCA_018473305.1/GCA_018473305.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/473/305/GCA_018473305.1/GCA_018473305.1.chrom.sizes.txt" \
        hg38 GCA_018473305.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m23.006s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018473305.1.txt
    # 2840276774 bases of 3299210039 (86.090%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/473/305/GCA_018473305.1_HG03453.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018473305.1_HG03453.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018473305.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	115m17.339s

    sed -e 's/^/    # /;' fb.GCA_018473305.1.chainHg38Link.txt
    # 2875705614 bases of 3050441176 (94.272%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018473305.1.chainSynHg38Link.txt
    # 2869424984 bases of 3050441176 (94.066%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/473/305/GCA_018473305.1/GCA_018473305.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/473/305/GCA_018473305.1/GCA_018473305.1.chrom.sizes.txt" \
   GCA_018473305.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m52.797s

    sed -e 's/^/    # /;' fb.GCA_018473305.1.chainRBest.Hg38.txt
    # 2836364483 bases of 3050441176 (92.982%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018503525.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018503525.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018503525.1.2023-04-08

    printf '# human GCA_018503525.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018503525.1_HG03486.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/503/525/GCA_018503525.1/GCA_018503525.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/503/525/GCA_018503525.1/GCA_018503525.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018503525.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018503525.1_HG03486.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	153m44.779s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018503525.1Link.txt
    # 3047358388 bases of 3299210039 (92.366%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018503525.1Link.txt
    # 3042740480 bases of 3299210039 (92.226%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/503/525/GCA_018503525.1/GCA_018503525.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/503/525/GCA_018503525.1/GCA_018503525.1.chrom.sizes.txt" \
        hg38 GCA_018503525.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m14.082s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018503525.1.txt
    # 2837580736 bases of 3299210039 (86.008%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/503/525/GCA_018503525.1_HG03486.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018503525.1_HG03486.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018503525.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	112m29.636s

    sed -e 's/^/    # /;' fb.GCA_018503525.1.chainHg38Link.txt
    # 2875977483 bases of 3034915351 (94.763%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018503525.1.chainSynHg38Link.txt
    # 2869607621 bases of 3034915351 (94.553%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/503/525/GCA_018503525.1/GCA_018503525.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/503/525/GCA_018503525.1/GCA_018503525.1.chrom.sizes.txt" \
   GCA_018503525.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m21.588s

    sed -e 's/^/    # /;' fb.GCA_018503525.1.chainRBest.Hg38.txt
    # 2835604766 bases of 3034915351 (93.433%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018503245.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018503245.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018503245.1.2023-04-08

    printf '# human GCA_018503245.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018503245.1_HG03486.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/503/245/GCA_018503245.1/GCA_018503245.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/503/245/GCA_018503245.1/GCA_018503245.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018503245.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018503245.1_HG03486.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	154m9.968s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018503245.1Link.txt
    # 3048000864 bases of 3299210039 (92.386%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018503245.1Link.txt
    # 3043742671 bases of 3299210039 (92.257%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/503/245/GCA_018503245.1/GCA_018503245.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/503/245/GCA_018503245.1/GCA_018503245.1.chrom.sizes.txt" \
        hg38 GCA_018503245.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m57.790s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018503245.1.txt
    # 2838510414 bases of 3299210039 (86.036%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/503/245/GCA_018503245.1_HG03486.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018503245.1_HG03486.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018503245.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	112m19.435s

    sed -e 's/^/    # /;' fb.GCA_018503245.1.chainHg38Link.txt
    # 2876094457 bases of 3049588884 (94.311%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018503245.1.chainSynHg38Link.txt
    # 2870019643 bases of 3049588884 (94.112%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/503/245/GCA_018503245.1/GCA_018503245.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/503/245/GCA_018503245.1/GCA_018503245.1.chrom.sizes.txt" \
   GCA_018503245.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m57.111s

    sed -e 's/^/    # /;' fb.GCA_018503245.1.chainRBest.Hg38.txt
    # 2836104858 bases of 3049588884 (93.000%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018505845.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018505845.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018505845.1.2023-04-08

    printf '# human GCA_018505845.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018505845.1_HG03492.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/505/845/GCA_018505845.1/GCA_018505845.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/505/845/GCA_018505845.1/GCA_018505845.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018505845.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018505845.1_HG03492.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	142m13.580s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018505845.1Link.txt
    # 3048116679 bases of 3299210039 (92.389%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018505845.1Link.txt
    # 3043503532 bases of 3299210039 (92.249%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/505/845/GCA_018505845.1/GCA_018505845.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/505/845/GCA_018505845.1/GCA_018505845.1.chrom.sizes.txt" \
        hg38 GCA_018505845.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m42.445s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018505845.1.txt
    # 2837666242 bases of 3299210039 (86.010%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/505/845/GCA_018505845.1_HG03492.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018505845.1_HG03492.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018505845.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	112m57.189s

    sed -e 's/^/    # /;' fb.GCA_018505845.1.chainHg38Link.txt
    # 2869769190 bases of 3023922307 (94.902%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018505845.1.chainSynHg38Link.txt
    # 2864230968 bases of 3023922307 (94.719%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/505/845/GCA_018505845.1/GCA_018505845.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/505/845/GCA_018505845.1/GCA_018505845.1.chrom.sizes.txt" \
   GCA_018505845.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m31.847s

    sed -e 's/^/    # /;' fb.GCA_018505845.1.chainRBest.Hg38.txt
    # 2834955640 bases of 3023922307 (93.751%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018505835.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018505835.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018505835.1.2023-04-08

    printf '# human GCA_018505835.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018505835.1_HG03492.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/505/835/GCA_018505835.1/GCA_018505835.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/505/835/GCA_018505835.1/GCA_018505835.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018505835.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018505835.1_HG03492.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	137m56.656s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018505835.1Link.txt
    # 2919889327 bases of 3299210039 (88.503%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018505835.1Link.txt
    # 2914856422 bases of 3299210039 (88.350%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/505/835/GCA_018505835.1/GCA_018505835.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/505/835/GCA_018505835.1/GCA_018505835.1.chrom.sizes.txt" \
        hg38 GCA_018505835.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	65m43.747s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018505835.1.txt
    # 2711846980 bases of 3299210039 (82.197%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/505/835/GCA_018505835.1_HG03492.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018505835.1_HG03492.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018505835.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	113m28.531s

    sed -e 's/^/    # /;' fb.GCA_018505835.1.chainHg38Link.txt
    # 2744883930 bases of 2923665925 (93.885%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018505835.1.chainSynHg38Link.txt
    # 2739558916 bases of 2923665925 (93.703%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/505/835/GCA_018505835.1/GCA_018505835.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/505/835/GCA_018505835.1/GCA_018505835.1.chrom.sizes.txt" \
   GCA_018505835.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	66m16.004s

    sed -e 's/^/    # /;' fb.GCA_018505835.1.chainRBest.Hg38.txt
    # 2710514656 bases of 2923665925 (92.709%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469425.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469425.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469425.1.2023-04-08

    printf '# human GCA_018469425.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469425.1_HG03516.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/425/GCA_018469425.1/GCA_018469425.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/425/GCA_018469425.1/GCA_018469425.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469425.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469425.1_HG03516.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	168m28.923s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469425.1Link.txt
    # 3049068814 bases of 3299210039 (92.418%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469425.1Link.txt
    # 3044879505 bases of 3299210039 (92.291%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/425/GCA_018469425.1/GCA_018469425.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/425/GCA_018469425.1/GCA_018469425.1.chrom.sizes.txt" \
        hg38 GCA_018469425.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	71m18.533s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469425.1.txt
    # 2840250282 bases of 3299210039 (86.089%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/425/GCA_018469425.1_HG03516.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469425.1_HG03516.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469425.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	116m34.181s

    sed -e 's/^/    # /;' fb.GCA_018469425.1.chainHg38Link.txt
    # 2878183079 bases of 3033479640 (94.881%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469425.1.chainSynHg38Link.txt
    # 2871903638 bases of 3033479640 (94.674%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/425/GCA_018469425.1/GCA_018469425.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/425/GCA_018469425.1/GCA_018469425.1.chrom.sizes.txt" \
   GCA_018469425.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m43.890s

    sed -e 's/^/    # /;' fb.GCA_018469425.1.chainRBest.Hg38.txt
    # 2837661089 bases of 3033479640 (93.545%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018469415.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469415.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018469415.1.2023-04-08

    printf '# human GCA_018469415.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018469415.1_HG03516.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/415/GCA_018469415.1/GCA_018469415.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/415/GCA_018469415.1/GCA_018469415.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469415.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018469415.1_HG03516.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	169m22.631s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018469415.1Link.txt
    # 3049005577 bases of 3299210039 (92.416%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018469415.1Link.txt
    # 3044508472 bases of 3299210039 (92.280%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/415/GCA_018469415.1/GCA_018469415.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/415/GCA_018469415.1/GCA_018469415.1.chrom.sizes.txt" \
        hg38 GCA_018469415.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	70m20.952s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018469415.1.txt
    # 2839746925 bases of 3299210039 (86.074%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/415/GCA_018469415.1_HG03516.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018469415.1_HG03516.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469415.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	115m50.538s

    sed -e 's/^/    # /;' fb.GCA_018469415.1.chainHg38Link.txt
    # 2880879883 bases of 3067004974 (93.931%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018469415.1.chainSynHg38Link.txt
    # 2874906249 bases of 3067004974 (93.737%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/415/GCA_018469415.1/GCA_018469415.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/415/GCA_018469415.1/GCA_018469415.1.chrom.sizes.txt" \
   GCA_018469415.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m0.567s

    sed -e 's/^/    # /;' fb.GCA_018469415.1.chainRBest.Hg38.txt
    # 2838184512 bases of 3067004974 (92.539%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018473295.1
#    (DONE - 2023-04-08 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018473295.1.2023-04-08
    cd /hive/data/genomes/hg38/bed/lastzGCA_018473295.1.2023-04-08

    printf '# human GCA_018473295.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018473295.1_HG03540.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/473/295/GCA_018473295.1/GCA_018473295.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/473/295/GCA_018473295.1/GCA_018473295.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018473295.1.2023-04-08
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018473295.1_HG03540.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	157m58.530s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018473295.1Link.txt
    # 3047425880 bases of 3299210039 (92.368%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018473295.1Link.txt
    # 3043069344 bases of 3299210039 (92.236%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/473/295/GCA_018473295.1/GCA_018473295.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/473/295/GCA_018473295.1/GCA_018473295.1.chrom.sizes.txt" \
        hg38 GCA_018473295.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m52.193s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018473295.1.txt
    # 2836265482 bases of 3299210039 (85.968%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/473/295/GCA_018473295.1_HG03540.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018473295.1_HG03540.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018473295.1.2023-04-08/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	115m2.664s

    sed -e 's/^/    # /;' fb.GCA_018473295.1.chainHg38Link.txt
    # 2871124182 bases of 3048418776 (94.184%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018473295.1.chainSynHg38Link.txt
    # 2864919696 bases of 3048418776 (93.981%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/473/295/GCA_018473295.1/GCA_018473295.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/473/295/GCA_018473295.1/GCA_018473295.1.chrom.sizes.txt" \
   GCA_018473295.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m42.096s

    sed -e 's/^/    # /;' fb.GCA_018473295.1.chainRBest.Hg38.txt
    # 2834715361 bases of 3048418776 (92.990%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018473315.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018473315.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018473315.1.2023-04-09

    printf '# human GCA_018473315.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018473315.1_HG03540.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/473/315/GCA_018473315.1/GCA_018473315.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/473/315/GCA_018473315.1/GCA_018473315.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018473315.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018473315.1_HG03540.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	152m1.388s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018473315.1Link.txt
    # 3046844231 bases of 3299210039 (92.351%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018473315.1Link.txt
    # 3041789375 bases of 3299210039 (92.198%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/473/315/GCA_018473315.1/GCA_018473315.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/473/315/GCA_018473315.1/GCA_018473315.1.chrom.sizes.txt" \
        hg38 GCA_018473315.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m11.878s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018473315.1.txt
    # 2835767695 bases of 3299210039 (85.953%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/473/315/GCA_018473315.1_HG03540.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018473315.1_HG03540.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018473315.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	113m16.324s

    sed -e 's/^/    # /;' fb.GCA_018473315.1.chainHg38Link.txt
    # 2884301680 bases of 3065276644 (94.096%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018473315.1.chainSynHg38Link.txt
    # 2877994776 bases of 3065276644 (93.890%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/473/315/GCA_018473315.1/GCA_018473315.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/473/315/GCA_018473315.1/GCA_018473315.1.chrom.sizes.txt" \
   GCA_018473315.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	71m23.112s

    sed -e 's/^/    # /;' fb.GCA_018473315.1.chainRBest.Hg38.txt
    # 2833683404 bases of 3065276644 (92.445%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472825.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472825.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472825.1.2023-04-09

    printf '# human GCA_018472825.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472825.1_HG03579.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/825/GCA_018472825.1/GCA_018472825.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/825/GCA_018472825.1/GCA_018472825.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472825.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472825.1_HG03579.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	157m56.205s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472825.1Link.txt
    # 3047603071 bases of 3299210039 (92.374%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472825.1Link.txt
    # 3043484395 bases of 3299210039 (92.249%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/825/GCA_018472825.1/GCA_018472825.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/825/GCA_018472825.1/GCA_018472825.1.chrom.sizes.txt" \
        hg38 GCA_018472825.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m4.850s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472825.1.txt
    # 2838432883 bases of 3299210039 (86.034%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/825/GCA_018472825.1_HG03579.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472825.1_HG03579.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472825.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	113m53.440s

    sed -e 's/^/    # /;' fb.GCA_018472825.1.chainHg38Link.txt
    # 2873930846 bases of 3035143227 (94.688%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472825.1.chainSynHg38Link.txt
    # 2867787684 bases of 3035143227 (94.486%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/825/GCA_018472825.1/GCA_018472825.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/825/GCA_018472825.1/GCA_018472825.1.chrom.sizes.txt" \
   GCA_018472825.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m54.784s

    sed -e 's/^/    # /;' fb.GCA_018472825.1.chainRBest.Hg38.txt
    # 2835122275 bases of 3035143227 (93.410%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018503285.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018503285.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018503285.1.2023-04-09

    printf '# human GCA_018503285.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018503285.1_NA18906.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/503/285/GCA_018503285.1/GCA_018503285.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/503/285/GCA_018503285.1/GCA_018503285.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018503285.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018503285.1_NA18906.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	165m35.313s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018503285.1Link.txt
    # 3048547962 bases of 3299210039 (92.402%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018503285.1Link.txt
    # 3044067611 bases of 3299210039 (92.267%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/503/285/GCA_018503285.1/GCA_018503285.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/503/285/GCA_018503285.1/GCA_018503285.1.chrom.sizes.txt" \
        hg38 GCA_018503285.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m52.504s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018503285.1.txt
    # 2839885987 bases of 3299210039 (86.078%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/503/285/GCA_018503285.1_NA18906.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018503285.1_NA18906.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018503285.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	113m9.076s

    sed -e 's/^/    # /;' fb.GCA_018503285.1.chainHg38Link.txt
    # 2886269334 bases of 3046330261 (94.746%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018503285.1.chainSynHg38Link.txt
    # 2880405199 bases of 3046330261 (94.553%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/503/285/GCA_018503285.1/GCA_018503285.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/503/285/GCA_018503285.1/GCA_018503285.1.chrom.sizes.txt" \
   GCA_018503285.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m55.375s

    sed -e 's/^/    # /;' fb.GCA_018503285.1.chainRBest.Hg38.txt
    # 2837715598 bases of 3046330261 (93.152%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018472835.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472835.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018472835.1.2023-04-09

    printf '# human GCA_018472835.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-24 GCA_018472835.1_HG03579.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/835/GCA_018472835.1/GCA_018472835.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/835/GCA_018472835.1/GCA_018472835.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472835.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018472835.1_HG03579.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	205m46.146s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018472835.1Link.txt
    # 2919091631 bases of 3299210039 (88.479%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018472835.1Link.txt
    # 2914194294 bases of 3299210039 (88.330%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/835/GCA_018472835.1/GCA_018472835.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/835/GCA_018472835.1/GCA_018472835.1.chrom.sizes.txt" \
        hg38 GCA_018472835.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	66m3.647s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018472835.1.txt
    # 2712867894 bases of 3299210039 (82.228%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/835/GCA_018472835.1_HG03579.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018472835.1_HG03579.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472835.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	107m55.939s

    sed -e 's/^/    # /;' fb.GCA_018472835.1.chainHg38Link.txt
    # 2750949104 bases of 2947164001 (93.342%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018472835.1.chainSynHg38Link.txt
    # 2744987096 bases of 2947164001 (93.140%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/835/GCA_018472835.1/GCA_018472835.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/835/GCA_018472835.1/GCA_018472835.1.chrom.sizes.txt" \
   GCA_018472835.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	65m10.419s

    sed -e 's/^/    # /;' fb.GCA_018472835.1.chainRBest.Hg38.txt
    # 2708338869 bases of 2947164001 (91.896%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018503275.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018503275.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018503275.1.2023-04-09

    printf '# human GCA_018503275.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018503275.1_NA19240.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/503/275/GCA_018503275.1/GCA_018503275.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/503/275/GCA_018503275.1/GCA_018503275.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018503275.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018503275.1_NA19240.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	141m41.376s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018503275.1Link.txt
    # 3047059503 bases of 3299210039 (92.357%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018503275.1Link.txt
    # 3042840690 bases of 3299210039 (92.229%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/503/275/GCA_018503275.1/GCA_018503275.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/503/275/GCA_018503275.1/GCA_018503275.1.chrom.sizes.txt" \
        hg38 GCA_018503275.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m21.376s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018503275.1.txt
    # 2837607573 bases of 3299210039 (86.009%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/503/275/GCA_018503275.1_NA19240.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018503275.1_NA19240.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018503275.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	111m33.408s

    sed -e 's/^/    # /;' fb.GCA_018503275.1.chainHg38Link.txt
    # 2878343413 bases of 3032066086 (94.930%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018503275.1.chainSynHg38Link.txt
    # 2872472422 bases of 3032066086 (94.736%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/503/275/GCA_018503275.1/GCA_018503275.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/503/275/GCA_018503275.1/GCA_018503275.1.chrom.sizes.txt" \
   GCA_018503275.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m28.765s

    sed -e 's/^/    # /;' fb.GCA_018503275.1.chainRBest.Hg38.txt
    # 2836420733 bases of 3032066086 (93.547%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018503265.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018503265.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018503265.1.2023-04-09

    printf '# human GCA_018503265.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018503265.1_NA19240.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/503/265/GCA_018503265.1/GCA_018503265.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/503/265/GCA_018503265.1/GCA_018503265.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018503265.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018503265.1_NA19240.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	149m40.461s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018503265.1Link.txt
    # 3048141242 bases of 3299210039 (92.390%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018503265.1Link.txt
    # 3043919815 bases of 3299210039 (92.262%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/503/265/GCA_018503265.1/GCA_018503265.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/503/265/GCA_018503265.1/GCA_018503265.1.chrom.sizes.txt" \
        hg38 GCA_018503265.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m43.855s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018503265.1.txt
    # 2837658200 bases of 3299210039 (86.010%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/503/265/GCA_018503265.1_NA19240.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018503265.1_NA19240.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018503265.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	110m51.162s

    sed -e 's/^/    # /;' fb.GCA_018503265.1.chainHg38Link.txt
    # 2877667479 bases of 3038325696 (94.712%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018503265.1.chainSynHg38Link.txt
    # 2872021157 bases of 3038325696 (94.526%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/503/265/GCA_018503265.1/GCA_018503265.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/503/265/GCA_018503265.1/GCA_018503265.1.chrom.sizes.txt" \
   GCA_018503265.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m49.916s

    sed -e 's/^/    # /;' fb.GCA_018503265.1.chainRBest.Hg38.txt
    # 2835593517 bases of 3038325696 (93.328%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018504635.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018504635.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018504635.1.2023-04-09

    printf '# human GCA_018504635.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018504635.1_NA20129.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/504/635/GCA_018504635.1/GCA_018504635.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/504/635/GCA_018504635.1/GCA_018504635.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018504635.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018504635.1_NA20129.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	146m30.643s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018504635.1Link.txt
    # 3047734796 bases of 3299210039 (92.378%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018504635.1Link.txt
    # 3043332464 bases of 3299210039 (92.244%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/504/635/GCA_018504635.1/GCA_018504635.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/504/635/GCA_018504635.1/GCA_018504635.1.chrom.sizes.txt" \
        hg38 GCA_018504635.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m15.026s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018504635.1.txt
    # 2838621352 bases of 3299210039 (86.039%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/504/635/GCA_018504635.1_NA20129.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018504635.1_NA20129.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018504635.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	112m46.693s

    sed -e 's/^/    # /;' fb.GCA_018504635.1.chainHg38Link.txt
    # 2873032239 bases of 3045049146 (94.351%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018504635.1.chainSynHg38Link.txt
    # 2866312725 bases of 3045049146 (94.130%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/504/635/GCA_018504635.1/GCA_018504635.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/504/635/GCA_018504635.1/GCA_018504635.1.chrom.sizes.txt" \
   GCA_018504635.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m46.830s

    sed -e 's/^/    # /;' fb.GCA_018504635.1.chainRBest.Hg38.txt
    # 2834630660 bases of 3045049146 (93.090%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018504625.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018504625.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018504625.1.2023-04-09

    printf '# human GCA_018504625.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018504625.1_NA20129.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/504/625/GCA_018504625.1/GCA_018504625.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/504/625/GCA_018504625.1/GCA_018504625.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018504625.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018504625.1_NA20129.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	150m9.736s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018504625.1Link.txt
    # 3048451287 bases of 3299210039 (92.399%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018504625.1Link.txt
    # 3044043138 bases of 3299210039 (92.266%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/504/625/GCA_018504625.1/GCA_018504625.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/504/625/GCA_018504625.1/GCA_018504625.1.chrom.sizes.txt" \
        hg38 GCA_018504625.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m51.076s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018504625.1.txt
    # 2838491380 bases of 3299210039 (86.035%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/504/625/GCA_018504625.1_NA20129.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018504625.1_NA20129.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018504625.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	112m35.291s

    sed -e 's/^/    # /;' fb.GCA_018504625.1.chainHg38Link.txt
    # 2870908903 bases of 3029071557 (94.779%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018504625.1.chainSynHg38Link.txt
    # 2864758653 bases of 3029071557 (94.575%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/504/625/GCA_018504625.1/GCA_018504625.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/504/625/GCA_018504625.1/GCA_018504625.1.chrom.sizes.txt" \
   GCA_018504625.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m23.662s

    sed -e 's/^/    # /;' fb.GCA_018504625.1.chainRBest.Hg38.txt
    # 2835742950 bases of 3029071557 (93.618%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018504655.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018504655.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018504655.1.2023-04-09

    printf '# human GCA_018504655.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018504655.1_NA21309.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/504/655/GCA_018504655.1/GCA_018504655.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/504/655/GCA_018504655.1/GCA_018504655.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018504655.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018504655.1_NA21309.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	144m18.408s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018504655.1Link.txt
    # 3047599808 bases of 3299210039 (92.374%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018504655.1Link.txt
    # 3042625085 bases of 3299210039 (92.223%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/504/655/GCA_018504655.1/GCA_018504655.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/504/655/GCA_018504655.1/GCA_018504655.1.chrom.sizes.txt" \
        hg38 GCA_018504655.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	66m56.699s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018504655.1.txt
    # 2836944995 bases of 3299210039 (85.989%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/504/655/GCA_018504655.1_NA21309.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018504655.1_NA21309.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018504655.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	112m31.764s

    sed -e 's/^/    # /;' fb.GCA_018504655.1.chainHg38Link.txt
    # 2867028873 bases of 3036775048 (94.410%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018504655.1.chainSynHg38Link.txt
    # 2861473710 bases of 3036775048 (94.227%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/504/655/GCA_018504655.1/GCA_018504655.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/504/655/GCA_018504655.1/GCA_018504655.1.chrom.sizes.txt" \
   GCA_018504655.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m56.060s

    sed -e 's/^/    # /;' fb.GCA_018504655.1.chainRBest.Hg38.txt
    # 2833196674 bases of 3036775048 (93.296%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018504665.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018504665.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018504665.1.2023-04-09

    printf '# human GCA_018504665.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018504665.1_NA21309.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/504/665/GCA_018504665.1/GCA_018504665.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/504/665/GCA_018504665.1/GCA_018504665.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018504665.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018504665.1_NA21309.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	147m16.672s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018504665.1Link.txt
    # 3047724188 bases of 3299210039 (92.377%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018504665.1Link.txt
    # 3043575114 bases of 3299210039 (92.252%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/504/665/GCA_018504665.1/GCA_018504665.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/504/665/GCA_018504665.1/GCA_018504665.1.chrom.sizes.txt" \
        hg38 GCA_018504665.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m14.393s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018504665.1.txt
    # 2837466225 bases of 3299210039 (86.004%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/504/665/GCA_018504665.1_NA21309.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018504665.1_NA21309.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018504665.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	112m46.893s

    sed -e 's/^/    # /;' fb.GCA_018504665.1.chainHg38Link.txt
    # 2868057941 bases of 3029616838 (94.667%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018504665.1.chainSynHg38Link.txt
    # 2862865509 bases of 3029616838 (94.496%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/504/665/GCA_018504665.1/GCA_018504665.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/504/665/GCA_018504665.1/GCA_018504665.1.chrom.sizes.txt" \
   GCA_018504665.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	70m54.045s

    sed -e 's/^/    # /;' fb.GCA_018504665.1.chainRBest.Hg38.txt
    # 2834925139 bases of 3029616838 (93.574%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018852615.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018852615.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018852615.1.2023-04-09

    printf '# human GCA_018852615.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-06-11 GCA_018852615.1_HG002.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/852/615/GCA_018852615.1/GCA_018852615.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/852/615/GCA_018852615.1/GCA_018852615.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018852615.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018852615.1_HG002.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	151m1.654s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018852615.1Link.txt
    # 3048312331 bases of 3299210039 (92.395%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018852615.1Link.txt
    # 3044059808 bases of 3299210039 (92.266%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/852/615/GCA_018852615.1/GCA_018852615.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/852/615/GCA_018852615.1/GCA_018852615.1.chrom.sizes.txt" \
        hg38 GCA_018852615.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	67m28.117s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018852615.1.txt
    # 2837642280 bases of 3299210039 (86.010%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/852/615/GCA_018852615.1_HG002.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018852615.1_HG002.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018852615.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	112m32.739s

    sed -e 's/^/    # /;' fb.GCA_018852615.1.chainHg38Link.txt
    # 2877447787 bases of 3060609068 (94.016%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018852615.1.chainSynHg38Link.txt
    # 2871626305 bases of 3060609068 (93.825%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/852/615/GCA_018852615.1/GCA_018852615.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/852/615/GCA_018852615.1/GCA_018852615.1.chrom.sizes.txt" \
   GCA_018852615.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	70m7.951s

    sed -e 's/^/    # /;' fb.GCA_018852615.1.chainRBest.Hg38.txt
    # 2834490541 bases of 3060609068 (92.612%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018852605.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018852605.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018852605.1.2023-04-09

    printf '# human GCA_018852605.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-06-11 GCA_018852605.1_HG002.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/852/605/GCA_018852605.1/GCA_018852605.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/852/605/GCA_018852605.1/GCA_018852605.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018852605.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018852605.1_HG002.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	150m13.088s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018852605.1Link.txt
    # 2920061632 bases of 3299210039 (88.508%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018852605.1Link.txt
    # 2915152917 bases of 3299210039 (88.359%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/852/605/GCA_018852605.1/GCA_018852605.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/852/605/GCA_018852605.1/GCA_018852605.1.chrom.sizes.txt" \
        hg38 GCA_018852605.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	64m27.233s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018852605.1.txt
    # 2707278829 bases of 3299210039 (82.058%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/852/605/GCA_018852605.1_HG002.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018852605.1_HG002.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018852605.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	108m29.282s

    sed -e 's/^/    # /;' fb.GCA_018852605.1.chainHg38Link.txt
    # 2747160113 bases of 2958633312 (92.852%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018852605.1.chainSynHg38Link.txt
    # 2741663610 bases of 2958633312 (92.667%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/852/605/GCA_018852605.1/GCA_018852605.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/852/605/GCA_018852605.1/GCA_018852605.1.chrom.sizes.txt" \
   GCA_018852605.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	66m47.541s

    sed -e 's/^/    # /;' fb.GCA_018852605.1.chainRBest.Hg38.txt
    # 2708589884 bases of 2958633312 (91.549%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018506965.1
#    (DONE - 2023-04-09 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018506965.1.2023-04-09
    cd /hive/data/genomes/hg38/bed/lastzGCA_018506965.1.2023-04-09

    printf '# human GCA_018506965.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018506965.1_HG005.pri.mat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/506/965/GCA_018506965.1/GCA_018506965.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/506/965/GCA_018506965.1/GCA_018506965.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018506965.1.2023-04-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018506965.1_HG005.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	148m42.540s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018506965.1Link.txt
    # 3049250178 bases of 3299210039 (92.424%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018506965.1Link.txt
    # 3044850522 bases of 3299210039 (92.290%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/506/965/GCA_018506965.1/GCA_018506965.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/506/965/GCA_018506965.1/GCA_018506965.1.chrom.sizes.txt" \
        hg38 GCA_018506965.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m41.216s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018506965.1.txt
    # 2837341922 bases of 3299210039 (86.001%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/506/965/GCA_018506965.1_HG005.pri.mat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018506965.1_HG005.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018506965.1.2023-04-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	113m19.877s

    sed -e 's/^/    # /;' fb.GCA_018506965.1.chainHg38Link.txt
    # 2874326020 bases of 3029694013 (94.872%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018506965.1.chainSynHg38Link.txt
    # 2868394773 bases of 3029694013 (94.676%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/506/965/GCA_018506965.1/GCA_018506965.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/506/965/GCA_018506965.1/GCA_018506965.1.chrom.sizes.txt" \
   GCA_018506965.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	73m28.912s

    sed -e 's/^/    # /;' fb.GCA_018506965.1.chainRBest.Hg38.txt
    # 2836696337 bases of 3029694013 (93.630%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_018506945.1
#    (DONE - 2023-04-10 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_018506945.1.2023-04-10
    cd /hive/data/genomes/hg38/bed/lastzGCA_018506945.1.2023-04-10

    printf '# human GCA_018506945.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human  hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human 2021-05-26 GCA_018506945.1_HG005.alt.pat.f1_v2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/506/945/GCA_018506945.1/GCA_018506945.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/506/945/GCA_018506945.1/GCA_018506945.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_018506945.1.2023-04-10
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_018506945.1_HG005.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	145m58.290s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_018506945.1Link.txt
    # 2920733867 bases of 3299210039 (88.528%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_018506945.1Link.txt
    # 2915764385 bases of 3299210039 (88.378%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/018/506/945/GCA_018506945.1/GCA_018506945.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/018/506/945/GCA_018506945.1/GCA_018506945.1.chrom.sizes.txt" \
        hg38 GCA_018506945.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	69m36.569s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_018506945.1.txt
    # 2711031495 bases of 3299210039 (82.172%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/018/506/945/GCA_018506945.1_HG005.alt.pat.f1_v2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_018506945.1_HG005.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018506945.1.2023-04-10/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	108m28.293s

    sed -e 's/^/    # /;' fb.GCA_018506945.1.chainHg38Link.txt
    # 2752380759 bases of 2937775295 (93.689%) in intersection
    sed -e 's/^/    # /;' fb.GCA_018506945.1.chainSynHg38Link.txt
    # 2746722452 bases of 2937775295 (93.497%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/018/506/945/GCA_018506945.1/GCA_018506945.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/018/506/945/GCA_018506945.1/GCA_018506945.1.chrom.sizes.txt" \
   GCA_018506945.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	66m38.476s

    sed -e 's/^/    # /;' fb.GCA_018506945.1.chainRBest.Hg38.txt
    # 2709508288 bases of 2937775295 (92.230%) in intersection

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