##############################################################################
# LASTZ Peter's clawed frog GCA_038501915.1 vs. X. tropicalis XenTro10
#    (DONE - 2025-02-13 - hiram)

    mkdir /hive/data/genomes/asmHubs/allBuild/GCA/038/501/915/GCA_038501915.1_aXenPet1.maternal.cur/trackData/lastzXenTro10.2025-02-13
    cd /hive/data/genomes/asmHubs/allBuild/GCA/038/501/915/GCA_038501915.1_aXenPet1.maternal.cur/trackData/lastzXenTro10.2025-02-13

    printf '# X. tropicalis XenTro10 vs. Peter's clawed frog GCA_038501915.1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Peter's clawed frog 2024-04-29 GCA_038501915.1_aXenPet1.maternal.cur
SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/038/501/915/GCA_038501915.1/GCA_038501915.1.2bit
SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/038/501/915/GCA_038501915.1/GCA_038501915.1.chrom.sizes.txt
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

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

BASE=/hive/data/genomes/asmHubs/allBuild/GCA/038/501/915/GCA_038501915.1_aXenPet1.maternal.cur/trackData/lastzXenTro10.2025-02-13
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -tAsmId GCA_038501915.1_aXenPet1.maternal.cur  -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	1480m29.005s

    sed -e 's/^/    # /;' fb.GCA_038501915.1.chainXenTro10Link.txt
    # 1083830546 bases of 2613116200 (41.477%) in intersection
    sed -e 's/^/    # /;' fb.GCA_038501915.1.chainSynXenTro10Link.txt
    # 765321850 bases of 2613116200 (29.288%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
      -target2Bit="/hive/data/genomes/asmHubs/GCA/038/501/915/GCA_038501915.1/GCA_038501915.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/038/501/915/GCA_038501915.1/GCA_038501915.1.chrom.sizes.txt" \
       \
        GCA_038501915.1 xenTro10) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	1606m26.757s

    sed -e 's/^/    # /;' fb.GCA_038501915.1.chainRBest.XenTro10.txt
    # 576881473 bases of 2613116200 (22.076%) in intersection

    ### and for the swap

    cd /hive/data/genomes/xenTro10/bed/blastz.GCA_038501915.1.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
  -tAsmId GCA_038501915.1_aXenPet1.maternal.cur  /hive/data/genomes/asmHubs/allBuild/GCA/038/501/915/GCA_038501915.1_aXenPet1.maternal.cur/trackData/lastzXenTro10.2025-02-13/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
    -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	395m19.938s

    sed -e 's/^/    # /;' fb.xenTro10.chainGCA_038501915.1Link.txt
    # 764127358 bases of 1451301209 (52.651%) in intersection
    sed -e 's/^/    # /;' fb.xenTro10.chainSynGCA_038501915.1Link.txt
    # 440012956 bases of 1451301209 (30.319%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
   -query2bit="/hive/data/genomes/asmHubs/GCA/038/501/915/GCA_038501915.1/GCA_038501915.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/038/501/915/GCA_038501915.1/GCA_038501915.1.chrom.sizes.txt" \
    \
   xenTro10 GCA_038501915.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	1205m48.958s

    sed -e 's/^/    # /;' fb.xenTro10.chainRBest.GCA_038501915.1.txt
    # 560732929 bases of 1451301209 (38.637%) in intersection

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

real	4688m8.748s
user	0m4.677s
sys	0m1.347s
##############################################################################
# LASTZ Tungara frog GCA_040894015.1 vs. X. tropicalis XenTro10
#    (DONE - 2025-02-13 - hiram)

    mkdir /hive/data/genomes/asmHubs/allBuild/GCA/040/894/015/GCA_040894015.1_aEngPut4.paternal/trackData/lastzXenTro10.2025-02-13
    cd /hive/data/genomes/asmHubs/allBuild/GCA/040/894/015/GCA_040894015.1_aEngPut4.paternal/trackData/lastzXenTro10.2025-02-13

    printf '# X. tropicalis XenTro10 vs. Tungara frog GCA_040894015.1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Tungara frog 2024-07-30 GCA_040894015.1_aEngPut4.paternal
SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/040/894/015/GCA_040894015.1/GCA_040894015.1.2bit
SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/040/894/015/GCA_040894015.1/GCA_040894015.1.chrom.sizes.txt
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

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

BASE=/hive/data/genomes/asmHubs/allBuild/GCA/040/894/015/GCA_040894015.1_aEngPut4.paternal/trackData/lastzXenTro10.2025-02-13
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -tAsmId GCA_040894015.1_aEngPut4.paternal  -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	999m15.041s

    sed -e 's/^/    # /;' fb.GCA_040894015.1.chainXenTro10Link.txt
    # 133488473 bases of 2081032022 (6.415%) in intersection
    sed -e 's/^/    # /;' fb.GCA_040894015.1.chainSynXenTro10Link.txt
    # 68568592 bases of 2081032022 (3.295%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
      -target2Bit="/hive/data/genomes/asmHubs/GCA/040/894/015/GCA_040894015.1/GCA_040894015.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/040/894/015/GCA_040894015.1/GCA_040894015.1.chrom.sizes.txt" \
       \
        GCA_040894015.1 xenTro10) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	160m38.277s

    sed -e 's/^/    # /;' fb.GCA_040894015.1.chainRBest.XenTro10.txt
    # 87644098 bases of 2081032022 (4.212%) in intersection

    ### and for the swap

    cd /hive/data/genomes/xenTro10/bed/blastz.GCA_040894015.1.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
  -tAsmId GCA_040894015.1_aEngPut4.paternal  /hive/data/genomes/asmHubs/allBuild/GCA/040/894/015/GCA_040894015.1_aEngPut4.paternal/trackData/lastzXenTro10.2025-02-13/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
    -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	11m31.922s

    sed -e 's/^/    # /;' fb.xenTro10.chainGCA_040894015.1Link.txt
    # 127498005 bases of 1451301209 (8.785%) in intersection
    sed -e 's/^/    # /;' fb.xenTro10.chainSynGCA_040894015.1Link.txt
    # 68364702 bases of 1451301209 (4.711%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
   -query2bit="/hive/data/genomes/asmHubs/GCA/040/894/015/GCA_040894015.1/GCA_040894015.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/040/894/015/GCA_040894015.1/GCA_040894015.1.chrom.sizes.txt" \
    \
   xenTro10 GCA_040894015.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	130m14.716s

    sed -e 's/^/    # /;' fb.xenTro10.chainRBest.GCA_040894015.1.txt
    # 86980009 bases of 1451301209 (5.993%) in intersection

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

real	1301m43.127s
user	0m4.023s
sys	0m1.174s
##############################################################################
# LASTZ X. tropicalis XenTro10 vs. zebrafish GCF_000002035.6
#    (DONE - 2025-02-13 - hiram)

    mkdir /hive/data/genomes/xenTro10/bed/lastzGCF_000002035.6.2025-02-13
    cd /hive/data/genomes/xenTro10/bed/lastzGCF_000002035.6.2025-02-13

    printf '# zebrafish GCF_000002035.6 vs. X. tropicalis XenTro10
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: X. tropicalis  xenTro10
SEQ1_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit
SEQ1_LEN=/hive/data/genomes/xenTro10/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: zebrafish 2017-05-09 GCF_000002035.6_GRCz11
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/002/035/GCF_000002035.6/GCF_000002035.6.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/002/035/GCF_000002035.6/GCF_000002035.6.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/xenTro10/bed/lastzGCF_000002035.6.2025-02-13
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_000002035.6_GRCz11 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	997m10.494s

    sed -e 's/^/    # /;' fb.xenTro10.chainGCF_000002035.6Link.txt
    # 49497650 bases of 1451301209 (3.411%) in intersection
    sed -e 's/^/    # /;' fb.xenTro10.chainSynGCF_000002035.6Link.txt
    # 6978571 bases of 1451301209 (0.481%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/000/002/035/GCF_000002035.6/GCF_000002035.6.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/000/002/035/GCF_000002035.6/GCF_000002035.6.chrom.sizes.txt" \
        xenTro10 GCF_000002035.6) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	63m43.386s

    sed -e 's/^/    # /;' fb.xenTro10.chainRBest.GCF_000002035.6.txt
    # 28398632 bases of 1451301209 (1.957%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/000/002/035/GCF_000002035.6_GRCz11/trackData/blastz.xenTro10.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_000002035.6_GRCz11 /hive/data/genomes/xenTro10/bed/lastzGCF_000002035.6.2025-02-13/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
    -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	4m7.885s

    sed -e 's/^/    # /;' fb.GCF_000002035.6.chainXenTro10Link.txt
    # 49866746 bases of 1679203469 (2.970%) in intersection
    sed -e 's/^/    # /;' fb.GCF_000002035.6.chainSynXenTro10Link.txt
    # 8305312 bases of 1679203469 (0.495%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/000/002/035/GCF_000002035.6/GCF_000002035.6.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/000/002/035/GCF_000002035.6/GCF_000002035.6.chrom.sizes.txt" \
   GCF_000002035.6 xenTro10) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	68m54.720s

    sed -e 's/^/    # /;' fb.GCF_000002035.6.chainRBest.XenTro10.txt
    # 28571626 bases of 1679203469 (1.701%) in intersection

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

real	1133m59.601s
user	0m3.890s
sys	0m1.493s
##############################################################################
# LASTZ X. tropicalis XenTro10 vs. African clawed frog GCF_017654675.1
#    (DONE - 2025-02-26 - hiram)

    mkdir /hive/data/genomes/xenTro10/bed/lastzGCF_017654675.1.2025-02-13
    cd /hive/data/genomes/xenTro10/bed/lastzGCF_017654675.1.2025-02-13

    printf '# African clawed frog GCF_017654675.1 vs. X. tropicalis XenTro10
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: X. tropicalis  xenTro10
SEQ1_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit
SEQ1_LEN=/hive/data/genomes/xenTro10/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: African clawed frog 2021-04-12 GCF_017654675.1_Xenopus_laevis_v10.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/017/654/675/GCF_017654675.1/GCF_017654675.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/017/654/675/GCF_017654675.1/GCF_017654675.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/xenTro10/bed/lastzGCF_017654675.1.2025-02-13
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_017654675.1_Xenopus_laevis_v10.1 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	1107m12.745s

    sed -e 's/^/    # /;' fb.xenTro10.chainGCF_017654675.1Link.txt
    # 787548572 bases of 1451301209 (54.265%) in intersection
    sed -e 's/^/    # /;' fb.xenTro10.chainSynGCF_017654675.1Link.txt
    # 453079461 bases of 1451301209 (31.219%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/017/654/675/GCF_017654675.1/GCF_017654675.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/017/654/675/GCF_017654675.1/GCF_017654675.1.chrom.sizes.txt" \
        xenTro10 GCF_017654675.1) > rbest.log 2>&1

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

    sed -e 's/^/    # /;' fb.xenTro10.chainRBest.GCF_017654675.1.txt

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/017/654/675/GCF_017654675.1_Xenopus_laevis_v10.1/trackData/blastz.xenTro10.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_017654675.1_Xenopus_laevis_v10.1 /hive/data/genomes/xenTro10/bed/lastzGCF_017654675.1.2025-02-13/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
    -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	627m20.150s

    sed -e 's/^/    # /;' fb.GCF_017654675.1.chainXenTro10Link.txt
    # 1159922816 bases of 2742469346 (42.295%) in intersection
    sed -e 's/^/    # /;' fb.GCF_017654675.1.chainSynXenTro10Link.txt
    # 831958092 bases of 2742469346 (30.336%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/017/654/675/GCF_017654675.1/GCF_017654675.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/017/654/675/GCF_017654675.1/GCF_017654675.1.chrom.sizes.txt" \
   GCF_017654675.1 xenTro10) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	2253m11.082s

    sed -e 's/^/    # /;' fb.GCF_017654675.1.chainRBest.XenTro10.txt
    # 604418262 bases of 2742469346 (22.039%) in intersection

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

real	2880m34.676s
user	0m2.816s
sys	0m0.974s
##############################################################################
# LASTZ X. tropicalis XenTro10 vs. Lizard AnoCar2
#    (DONE - 2025-02-13 - hiram)

    mkdir /hive/data/genomes/xenTro10/bed/lastzAnoCar2.2025-02-13
    cd /hive/data/genomes/xenTro10/bed/lastzAnoCar2.2025-02-13

    printf '# Lizard AnoCar2 vs. X. tropicalis XenTro10
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: X. tropicalis  xenTro10
SEQ1_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit
SEQ1_LEN=/hive/data/genomes/xenTro10/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: Lizard  anoCar2
SEQ2_DIR=/hive/data/genomes/anoCar2/anoCar2.2bit
SEQ2_LEN=/hive/data/genomes/anoCar2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/xenTro10/bed/lastzAnoCar2.2025-02-13
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -verbose=2 `pwd`/DEF -syntenicNet \
        -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	1001m2.254s

    sed -e 's/^/    # /;' fb.xenTro10.chainAnoCar2Link.txt
    # 46493232 bases of 1448461978 (3.210%) in intersection
    sed -e 's/^/    # /;' fb.xenTro10.chainSynAnoCar2Link.txt
    # 23478176 bases of 1448461978 (1.621%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
       \
       \
        xenTro10 anoCar2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	54m20.733s

    sed -e 's/^/    # /;' fb.xenTro10.chainRBest.AnoCar2.txt
    # 34957007 bases of 1448461978 (2.413%) in intersection

    ### and for the swap

    cd /hive/data/genomes/anoCar2/bed/blastz.xenTro10.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -swap -verbose=2 \
    /hive/data/genomes/xenTro10/bed/lastzAnoCar2.2025-02-13/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
    -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	4m41.713s

    sed -e 's/^/    # /;' fb.anoCar2.chainXenTro10Link.txt
    # 40831822 bases of 1701353770 (2.400%) in intersection
    sed -e 's/^/    # /;' fb.anoCar2.chainSynXenTro10Link.txt
    # 22681746 bases of 1701353770 (1.333%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
    \
    \
   anoCar2 xenTro10) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	51m45.564s

    sed -e 's/^/    # /;' fb.anoCar2.chainRBest.XenTro10.txt
    # 34961125 bases of 1701353770 (2.055%) in intersection

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

real	1111m50.936s
user	0m3.159s
sys	0m0.749s
##############################################################################
# LASTZ X. tropicalis XenTro10 vs. Chicken GalGal6
#    (DONE - 2025-02-13 - hiram)

    mkdir /hive/data/genomes/xenTro10/bed/lastzGalGal6.2025-02-13
    cd /hive/data/genomes/xenTro10/bed/lastzGalGal6.2025-02-13

    printf '# Chicken GalGal6 vs. X. tropicalis XenTro10
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: X. tropicalis  xenTro10
SEQ1_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit
SEQ1_LEN=/hive/data/genomes/xenTro10/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

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

BASE=/hive/data/genomes/xenTro10/bed/lastzGalGal6.2025-02-13
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -verbose=2 `pwd`/DEF -syntenicNet \
        -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	1000m18.466s

    sed -e 's/^/    # /;' fb.xenTro10.chainGalGal6Link.txt
    # 50287701 bases of 1448461978 (3.472%) in intersection
    sed -e 's/^/    # /;' fb.xenTro10.chainSynGalGal6Link.txt
    # 31107843 bases of 1448461978 (2.148%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
       \
       \
        xenTro10 galGal6) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	40m0.991s

    sed -e 's/^/    # /;' fb.xenTro10.chainRBest.GalGal6.txt
    # 37686782 bases of 1448461978 (2.602%) in intersection

    ### and for the swap

    cd /hive/data/genomes/galGal6/bed/blastz.xenTro10.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -swap -verbose=2 \
    /hive/data/genomes/xenTro10/bed/lastzGalGal6.2025-02-13/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
    -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	3m47.069s

    sed -e 's/^/    # /;' fb.galGal6.chainXenTro10Link.txt
    # 40888835 bases of 1055588482 (3.874%) in intersection
    sed -e 's/^/    # /;' fb.galGal6.chainSynXenTro10Link.txt
    # 30606958 bases of 1055588482 (2.900%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
    \
    \
   galGal6 xenTro10) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	29m33.510s

    sed -e 's/^/    # /;' fb.galGal6.chainRBest.XenTro10.txt
    # 37557937 bases of 1055588482 (3.558%) in intersection

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

real	1073m40.468s
user	0m3.180s
sys	0m0.639s
