##############################################################################
# LASTZ sheep GCA_002844635.1 (DONE - 2021-04-20 - Hiram)
    mkdir /hive/data/genomes/susScr11/bed/lastzGCA_002844635.1.2021-04-20
    cd /hive/data/genomes/susScr11/bed/lastzGCA_002844635.1.2021-04-20

    printf '# GCA_002844635.1 vs hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# 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

# QUERY: sheep GCA_002844635.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/742/125/GCA_002844635.1/GCA_002844635.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/742/125/GCA_002844635.1/GCA_002844635.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_002844635.1.2021-04-20
TMPDIR=/dev/shm
' > DEF

export targetDb="hg38"
export asmId="GCA_002844635.1"
export gcPath="GCA/002/844/635"
cd /hive/data/genomes/$targetDb/bed/lastz${asmId}.2021-04-20
time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF \
   -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
     -syntenicNet -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
cat fb.${targetDb}.chain.${asmId}Link.txt
cat fb.${targetDb}.chainSyn.${asmId}Link.txt

grep -w real do.log | sed -e 's/^/    # /;'
    # real      318m24.582s

sed -e 's/^/    # /;' fb.$targetDb.chain.${asmId}Link.txt
    # 2431952924 bases of 2501912388 (97.204%) in intersection
sed -e 's/^/    # /;' fb.$targetDb.chainSyn.${asmId}Link.txt
    # 2409981908 bases of 2501912388 (96.326%) in intersection

time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
-query2Bit="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.2bit" \
-querySizes="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.chrom.sizes.txt" \
$targetDb ${asmId}) >> rbest.log 2>&1
grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      93m2.731s

sed -e 's/^/    # /;' fb.$targetDb.chainRBest.$asmId.txt
    # 2381230203 bases of 2501912388 (95.176%) in intersection

## Overall time for the above:
# real    411m27.346s

### the swap to the assembly hub
export target="susScr11"
export Target="SusScr11"
export query="GCA_002844635.1"
export asmId="GCA_002844635.1_USMARCv1.0"
export gcPath="GCA/002/844/635"

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

time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 -swapDir=`pwd` \
    /hive/data/genomes/${target}/bed/lastz.${query}/DEF -syntenicNet \
  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -swap -chainMinScore=3000 -chainLinearGap=medium) >> swap.log 2>&1
grep -w real swap.log | sed -e 's/^/    # /;'
    # real      90m38.556s

sed -e 's/^/    # /;' fb.${query}.chain.${Target}Link.txt
    # 2543057365 bases of 2755438182 (92.292%) in intersection
sed -e 's/^/    # /;' fb.${query}.chainSyn.${Target}Link.txt
    # 2514166037 bases of 2755438182 (91.244%) in intersection

time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
-target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \
$query $target) >> rbest.log 2>&1
grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      86m43.960s

sed -e 's/^/    # /;' fb.${query}.chainRBest.${Target}.txt
    # 2388751543 bases of 2755438182 (86.692%) in intersection

# Complete run time for all the swap operation:
    # real    285m1.340s

##############################################################################
# LASTZ Pig SusScr11 vs. Cow BosTau9
#    (DONE - 2024-08-09 - lrnassar)

    mkdir /hive/data/genomes/susScr11/bed/lastzBosTau9.2024-08-09
    cd /hive/data/genomes/susScr11/bed/lastzBosTau9.2024-08-09

    printf '# Cow BosTau9 vs. Pig SusScr11
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Pig  susScr11
SEQ1_DIR=/hive/data/genomes/susScr11/susScr11.2bit
SEQ1_LEN=/hive/data/genomes/susScr11/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

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

BASE=/hive/data/genomes/susScr11/bed/lastzBosTau9.2024-08-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -verbose=2 `pwd`/DEF -syntenicNet \
        -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real      844m2.282s

    sed -e 's/^/    # /;' fb.susScr11.chainBosTau9Link.txt
    # 1542224987 bases of 2472073034 (62.386%) in intersection
    sed -e 's/^/    # /;' fb.susScr11.chainSynBosTau9Link.txt
    # 1458188575 bases of 2472073034 (58.986%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
       \
       \
        susScr11 bosTau9) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      379m32.380s

    sed -e 's/^/    # /;' fb.susScr11.chainRBest.BosTau9.txt
    # 1451300013 bases of 2472073034 (58.708%) in intersection

    ### and for the swap

    cd /hive/data/genomes/bosTau9/bed/blastz.susScr11.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -swap -verbose=2 \
    /hive/data/genomes/susScr11/bed/lastzBosTau9.2024-08-09/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real      237m58.241s

    sed -e 's/^/    # /;' fb.bosTau9.chainSusScr11Link.txt
    # 1542795700 bases of 2715853792 (56.807%) in intersection
    sed -e 's/^/    # /;' fb.bosTau9.chainSynSusScr11Link.txt
    # 1464525591 bases of 2715853792 (53.925%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
    \
    \
   bosTau9 susScr11) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      418m4.992s

    sed -e 's/^/    # /;' fb.bosTau9.chainRBest.SusScr11.txt
    # 1452583914 bases of 2715853792 (53.485%) in intersection

##############################################################################
# LASTZ Pig SusScr11 vs. goat GCF_001704415.2
#    (DONE - 2024-08-12 - lrnassar)

    mkdir /hive/data/genomes/susScr11/bed/lastzGCF_001704415.2.2024-08-12
    cd /hive/data/genomes/susScr11/bed/lastzGCF_001704415.2.2024-08-12

    printf '# goat GCF_001704415.2 vs. Pig SusScr11
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Pig  susScr11
SEQ1_DIR=/hive/data/genomes/susScr11/susScr11.2bit
SEQ1_LEN=/hive/data/genomes/susScr11/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: goat 2016-08-24 GCF_001704415.2_ARS1.2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/susScr11/bed/lastzGCF_001704415.2.2024-08-12
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_001704415.2_ARS1.2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real      568m2.570s

    sed -e 's/^/    # /;' fb.susScr11.chainGCF_001704415.2Link.txt
    # 1532623567 bases of 2501912388 (61.258%) in intersection
    sed -e 's/^/    # /;' fb.susScr11.chainSynGCF_001704415.2Link.txt
    # 1448119731 bases of 2501912388 (57.881%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt" \
        susScr11 GCF_001704415.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      495m38.221s

    sed -e 's/^/    # /;' fb.susScr11.chainRBest.GCF_001704415.2.txt
    # 1444668348 bases of 2501912388 (57.743%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.susScr11.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/susScr11/bed/lastzGCF_001704415.2.2024-08-12/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real      413m9.780s

    sed -e 's/^/    # /;' fb.GCF_001704415.2.chainSusScr11Link.txt
    # 1557596633 bases of 2922617086 (53.295%) in intersection
    sed -e 's/^/    # /;' fb.GCF_001704415.2.chainSynSusScr11Link.txt
    # 1455695959 bases of 2922617086 (49.808%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt" \
   GCF_001704415.2 susScr11) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      578m18.029s

    sed -e 's/^/    # /;' fb.GCF_001704415.2.chainRBest.SusScr11.txt
    # 1446482758 bases of 2922617086 (49.493%) in intersection

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