#########################################################################
# LASTZ Cow BosTau9 vs. Cow BosTau5 (DONE - 2022-02-25 - Gerardo)

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

  time (~/kent/src/hg/utils/automation/pairLastz.sh \
        bosTau9 bosTau5 mammal mammal) \
           > bosTau9_bosTau5_20220225_secondTime.log 2>&1 &
  # check the total time
grep -w real  bosTau9_bosTau5_20220225_secondTime.log  | tail -1 | sed -e 's/^/    # /;'
    # real      675m26.699s
#########################################################################
# LASTZ Cow BosTau9 vs. Cow BosTau5
#    (DONE - 2022-02-25 - Gerardo)

    mkdir /hive/data/genomes/bosTau9/bed/lastzBosTau5.2022-02-18
    cd /hive/data/genomes/bosTau9/bed/lastzBosTau5.2022-02-18

    printf '# Cow BosTau5 vs. Cow BosTau9
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Cow BosTau9
SEQ1_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit
SEQ1_LEN=/hive/data/genomes/bosTau9/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: Cow BosTau5
SEQ2_DIR=/hive/data/genomes/bosTau5/bosTau5.2bit
SEQ2_LEN=/hive/data/genomes/bosTau5/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/bosTau9/bed/lastzBosTau5.2022-02-18
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	543m53.934s

    sed -e 's/^/    # /;' fb.bosTau9.chainBosTau5Link.txt
    # 2595387173 bases of 2715853792 (95.564%) in intersection
    sed -e 's/^/    # /;' fb.bosTau9.chainSynBosTau5Link.txt
    # 2560256591 bases of 2715853792 (94.271%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
       \
       \
        bosTau9 bosTau5) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	74m31.401s

    sed -e 's/^/    # /;' fb.bosTau9.chainRBest.BosTau5.txt
    # 2540513150 bases of 2715853792 (93.544%) in intersection

    ### and for the swap

    cd /hive/data/genomes/bosTau5/bed/blastz.bosTau9.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -swap -verbose=2 \
    /hive/data/genomes/bosTau9/bed/lastzBosTau5.2022-02-18/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	601m9.542s

    sed -e 's/^/    # /;' fb.bosTau5.chainBosTau9Link.txt
    # 2706702737 bases of 2732505379 (99.056%) in intersection
    sed -e 's/^/    # /;' fb.bosTau5.chainSynBosTau9Link.txt
    # 2673116410 bases of 2732505379 (97.827%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
    \
    \
   bosTau5 bosTau9) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	74m16.598s

    sed -e 's/^/    # /;' fb.bosTau5.chainRBest.BosTau9.txt
    # 2543778039 bases of 2732505379 (93.093%) in intersection


real	675m26.699s
user	0m0.945s
sys	0m1.486s

##############################################################################
##############################################################################
# LASTZ hybrid cattle GCF_003369695.1 vs. Cow BosTau9  redmine30648
#    (DONE - 2023-03-17 - hiram)

    mkdir /hive/data/genomes/asmHubs/allBuild/GCF/003/369/695/GCF_003369695.1_UOA_Brahman_1/trackData/lastzBosTau9.2023-02-24
    cd /hive/data/genomes/asmHubs/allBuild/GCF/003/369/695/GCF_003369695.1_UOA_Brahman_1/trackData/lastzBosTau9.2023-02-24

    printf '# Cow BosTau9 vs. hybrid cattle GCF_003369695.1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: hybrid cattle 2018-11-30 GCF_003369695.1_UOA_Brahman_1
SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/003/369/695/GCF_003369695.1/GCF_003369695.1.2bit
SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/003/369/695/GCF_003369695.1/GCF_003369695.1.chrom.sizes.txt
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/asmHubs/allBuild/GCF/003/369/695/GCF_003369695.1_UOA_Brahman_1/trackData/lastzBosTau9.2023-02-24
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -tAsmId GCF_003369695.1_UOA_Brahman_1  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	469m2.411s

    sed -e 's/^/    # /;' fb.GCF_003369695.1.chainBosTau9Link.txt
    # 2657463787 bases of 2680953056 (99.124%) in intersection
    sed -e 's/^/    # /;' fb.GCF_003369695.1.chainSynBosTau9Link.txt
    # 2644164750 bases of 2680953056 (98.628%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
      -target2Bit="/hive/data/genomes/asmHubs/GCF/003/369/695/GCF_003369695.1/GCF_003369695.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/003/369/695/GCF_003369695.1/GCF_003369695.1.chrom.sizes.txt" \
       \
        GCF_003369695.1 bosTau9) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	65m55.031s

    sed -e 's/^/    # /;' fb.GCF_003369695.1.chainRBest.BosTau9.txt
    # 2603287922 bases of 2680953056 (97.103%) in intersection

    ### and for the swap

    cd /hive/data/genomes/bosTau9/bed/blastz.GCF_003369695.1.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
  -tAsmId GCF_003369695.1_UOA_Brahman_1  /hive/data/genomes/asmHubs/allBuild/GCF/003/369/695/GCF_003369695.1_UOA_Brahman_1/trackData/lastzBosTau9.2023-02-24/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	558m50.584s

    sed -e 's/^/    # /;' fb.bosTau9.chainGCF_003369695.1Link.txt
    # 2642343563 bases of 2715853792 (97.293%) in intersection
    sed -e 's/^/    # /;' fb.bosTau9.chainSynGCF_003369695.1Link.txt
    # 2630064290 bases of 2715853792 (96.841%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
   -query2bit="/hive/data/genomes/asmHubs/GCF/003/369/695/GCF_003369695.1/GCF_003369695.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/003/369/695/GCF_003369695.1/GCF_003369695.1.chrom.sizes.txt" \
    \
   bosTau9 GCF_003369695.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	72m1.651s

    sed -e 's/^/    # /;' fb.bosTau9.chainRBest.GCF_003369695.1.txt
    # 2603923510 bases of 2715853792 (95.879%) in intersection


real	630m53.197s
user	0m0.615s
sys	0m0.648s

##############################################################################
# LASTZ water buffalo GCF_019923935.1 vs. Cow BosTau9
#    (DONE - 2024-01-05 - mspeir)

    mkdir /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05
    cd /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05

    printf '# Cow BosTau9 vs. water buffalo GCF_019923935.1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1
SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit
SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt
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/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -tAsmId GCF_019923935.1_NDDB_SH_1  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	2623m44.119s

    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainBosTau9Link.txt
    # 2522886084 bases of 2622460639 (96.203%) in intersection
    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainSynBosTau9Link.txt
    # 2484746893 bases of 2622460639 (94.749%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
      -target2Bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \
       \
        GCF_019923935.1 bosTau9) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	146m41.533s

    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainRBest.BosTau9.txt
    # 2476483890 bases of 2622460639 (94.434%) in intersection

    ### and for the swap
# swap into: /hive/data/genomes/bosTau9/bed/blastz.GCF_019923935.1.swap
# running /hive/data/genomes/bosTau9/bed/blastz.GCF_019923935.1.swap/runSwap.sh
# do not find qTdb 'xxx'
##############################################################################
# LASTZ water buffalo GCF_019923935.1 vs. Cow BosTau9
#    (DONE - 2024-01-05 - mspeir)

    mkdir /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05
    cd /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05

    printf '# Cow BosTau9 vs. water buffalo GCF_019923935.1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1
SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit
SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt
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/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -tAsmId GCF_019923935.1_NDDB_SH_1  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	2623m44.119s

    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainBosTau9Link.txt
    # 2522886084 bases of 2622460639 (96.203%) in intersection
    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainSynBosTau9Link.txt
    # 2484746893 bases of 2622460639 (94.749%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
      -target2Bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \
       \
        GCF_019923935.1 bosTau9) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	146m41.533s

    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainRBest.BosTau9.txt
    # 2476483890 bases of 2622460639 (94.434%) in intersection

    ### and for the swap

    cd /hive/data/genomes/bosTau9/bed/blastz.GCF_019923935.1.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
  -tAsmId GCF_019923935.1_NDDB_SH_1  /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05/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	1392m58.161s

    sed -e 's/^/    # /;' fb.bosTau9.chainGCF_019923935.1Link.txt
    # 2549407306 bases of 2715853792 (93.871%) in intersection
    sed -e 's/^/    # /;' fb.bosTau9.chainSynGCF_019923935.1Link.txt
    # 2510417468 bases of 2715853792 (92.436%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
   -query2bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \
    \
   bosTau9 GCF_019923935.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	124m20.231s

    sed -e 's/^/    # /;' fb.bosTau9.chainRBest.GCF_019923935.1.txt
    # 2476775898 bases of 2715853792 (91.197%) in intersection

real	4287m53.907s
user	0m2.895s
sys	0m2.314s

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

##############################################################################
# LASTZ Cow BosTau9 vs. Horse EquCab3
#    (DONE - 2024-08-09 - lrnassar)

    mkdir /hive/data/genomes/bosTau9/bed/lastzEquCab3.2024-08-09
    cd /hive/data/genomes/bosTau9/bed/lastzEquCab3.2024-08-09

    printf '# Horse EquCab3 vs. Cow BosTau9
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Cow  bosTau9
SEQ1_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit
SEQ1_LEN=/hive/data/genomes/bosTau9/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

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

BASE=/hive/data/genomes/bosTau9/bed/lastzEquCab3.2024-08-09
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      846m27.399s

    sed -e 's/^/    # /;' fb.bosTau9.chainEquCab3Link.txt
    # 1554179648 bases of 2715853792 (57.226%) in intersection
    sed -e 's/^/    # /;' fb.bosTau9.chainSynEquCab3Link.txt
    # 1502506284 bases of 2715853792 (55.324%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
       \
       \
        bosTau9 equCab3) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      244m38.025s

    sed -e 's/^/    # /;' fb.bosTau9.chainRBest.EquCab3.txt
    # 1481921961 bases of 2715853792 (54.566%) in intersection

    ### and for the swap

    cd /hive/data/genomes/equCab3/bed/blastz.bosTau9.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -swap -verbose=2 \
    /hive/data/genomes/bosTau9/bed/lastzEquCab3.2024-08-09/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      151m32.417s

    sed -e 's/^/    # /;' fb.equCab3.chainBosTau9Link.txt
    # 1588535515 bases of 2497530654 (63.604%) in intersection
    sed -e 's/^/    # /;' fb.equCab3.chainSynBosTau9Link.txt
    # 1536072990 bases of 2497530654 (61.504%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
    \
    \
   equCab3 bosTau9) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      198m27.720s

    sed -e 's/^/    # /;' fb.equCab3.chainRBest.BosTau9.txt
    # 1481165695 bases of 2497530654 (59.305%) in intersection

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

# LASTZ sheep GCF_016772045.2 vs. Cow BosTau9
#    (DONE - 2024-08-09 - lrnassar)

    mkdir /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzBosTau9.2024-08-09
    cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzBosTau9.2024-08-09

    printf '# Cow BosTau9 vs. sheep GCF_016772045.2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: sheep 2023-07-20 GCF_016772045.2_ARS-UI_Ramb_v3.0
SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit
SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt
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/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzBosTau9.2024-08-09
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -tAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real      1131m30.899s

    sed -e 's/^/    # /;' fb.GCF_016772045.2.chainBosTau9Link.txt
    # 2345286242 bases of 2654063983 (88.366%) in intersection
    sed -e 's/^/    # /;' fb.GCF_016772045.2.chainSynBosTau9Link.txt
    # 2290967435 bases of 2654063983 (86.319%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
      -target2Bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \
       \
        GCF_016772045.2 bosTau9) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      225m50.587s

    sed -e 's/^/    # /;' fb.GCF_016772045.2.chainRBest.BosTau9.txt
    # 2278884591 bases of 2654063983 (85.864%) in intersection

    ### and for the swap

    cd /hive/data/genomes/bosTau9/bed/blastz.GCF_016772045.2.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
  -tAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0  /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/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      447m1.738s

    sed -e 's/^/    # /;' fb.bosTau9.chainGCF_016772045.2Link.txt
    # 2366545255 bases of 2715853792 (87.138%) in intersection
    sed -e 's/^/    # /;' fb.bosTau9.chainSynGCF_016772045.2Link.txt
    # 2307155872 bases of 2715853792 (84.951%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
   -query2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \
    \
   bosTau9 GCF_016772045.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      221m53.772s

    sed -e 's/^/    # /;' fb.bosTau9.chainRBest.GCF_016772045.2.txt
    # 2279192983 bases of 2715853792 (83.922%) in intersection

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